pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Darya and Carsten,

The "regular display mode" (real-time OpenGL graphics) does take lights into account, and their position can be updated in real-time. A neat way to play around with lights is in lights mouse mode (new in PyMOL 1.5).

From the menu, select "Mouse > 3 Button Lights"

Now hold down the SHIFT key on the keyboard, press the left mouse button and drag (just like rotating the molecule, but now it rotates the light position). The "edit_light" setting controls which light get updated.

The effect is most obvious with spheres representation.

Note that "light_count=2" corresponds to one specular light, the first light is ambient only.

Cheers,
  Thomas

On 30 Nov 2015, at 13:56, Schubert, Carsten [JRDUS] <CSC...@it...> wrote:

> Darya,
>  
> I have never used that feature, but do you see a difference when raytracing or drawing the scene? Could be that the regular display mode does not take these feature into account (this is a wild guess though)
>  
> Cheers,
>  
>                 Carsten
>  
> From: Дарья Николаева [mailto:dar...@gm...] 
> Sent: Monday, November 30, 2015 9:58 AM
> To: pym...@li...
> Subject: [PyMOL] light reposition
>  
> Hello,
>  
> I want to change the position of my light sources.
>  
> First I set the number of light sources:
> >set light_count, 3
>  
> Then I attempt to reposition the light source, e.g., #2:
> >set light2, [x, y, z]
>  
> The problem is - I see no changes to the scene.
>  
> The question: How to use the "set light(2-8)" command or is there any
> other way to reposition light sources?
>  
> Thank you,
> Darya

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Darya,

I have never used that feature, but do you see a difference when raytracing or drawing the scene? Could be that the regular display mode does not take these feature into account (this is a wild guess though)

Cheers,

                Carsten

From: Дарья Николаева [mailto:dar...@gm...]
Sent: Monday, November 30, 2015 9:58 AM
To: pym...@li...
Subject: [PyMOL] light reposition


Hello,



I want to change the position of my light sources.



First I set the number of light sources:

>set light_count, 3



Then I attempt to reposition the light source, e.g., #2:

>set light2, [x, y, z]



The problem is - I see no changes to the scene.



The question: How to use the "set light(2-8)" command or is there any

other way to reposition light sources?



Thank you,

Darya

Hi Smith -

I’m not quite sure what you mean by "axis of a subunit."  If you mean the principal axis of that selection of atoms, `orient my_selection` will get it aligned along one of the axes.  Then you can create pseudoatoms on that axis and create a dash between them with the distance command.

# Get it lined up with the viewport axes.
select domain, chain A and resi 1-100
orient domain

# Here I’m assuming this put the long axis of the domain along the
# x axis.  We move the view along the x axis, and place pseudoatoms
# at the viewport center in two places.  You can change the length of the
# displayed axis based on how far you move.
move x, -10
pseudoatom ps1
move x, 20
pseudoatom ps2
move x, -10
distance axis, ps1, ps2

This is a bit clumsy and not a rigorous approach, but it will work for any other kind of vector you want to show, as long as you can get it aligned with one of the view axes.

Cheers,
Jared

—
Jared Sampson
Graduate Student
Department of Biochemistry and Molecular Biophysics
Columbia University

On Nov 29, 2015, at 7:42 AM, Smith Liu <smi...@16...<mailto:smi...@16...>> wrote:

Dear All,

Will you please show me how to display an axis of a subunit or a domain by pymol?

Smith



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Hello,


I want to change the position of my light sources.


First I set the number of light sources:

>set light_count, 3


Then I attempt to reposition the light source, e.g., #2:

>set light2, [x, y, z]


The problem is - I see no changes to the scene.


The question: How to use the "set light(2-8)" command or is there any

other way to reposition light sources?


Thank you,

Darya

Smith,

Let's take this off-list. I will reply to you directly. We can send a summary to the list once it's working for you.

Cheers,
  Thomas

On 29 Nov 2015, at 22:13, Smith Liu <smi...@16...> wrote:

> Dear Thomas,
> 
> I do not know I still do something wrong.
> 
> First I load a PDB in pymol, then I input orient (with orient input the molecule really moved significantly in display), then I input transform_by_camera_rotation, then I input save /tmp/withneworientation.pdb, the withneworientation.pdb was really saved, but the newly saved withneworientation.pdb has the all atom orientations (x,y,z) exactly same as those of the original PDB I initially input to the pymol for the process I obtained the withneworientation.pdb.
> 
> Smith

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear Thomas,


I do not know I still do something wrong.


First I load a PDB in pymol, then I input orient (with orient input the molecule really moved significantly in display), then I input transform_by_camera_rotation, then I input save /tmp/withneworientation.pdb, the withneworientation.pdb was really saved, but the newly saved withneworientation.pdb has the all atom orientations (x,y,z) exactly same as those of the original PDB I initially input to the pymol for the process I obtained the withneworientation.pdb.




Smith







At 2015-11-30 08:08:52, "Thomas Holder" <tho...@sc...> wrote:
>Hi Smith, and everybody who tried to help you so far,
>
>Short answer: copy and paste this into the PyMOL command line, it will save the view-transformed object to "transformed.pdb" in your home folder.
>
>cv=list(cmd.get_view())
>cmd.transform_selection("all", \
>  cv[0:3]+[0.0]+ \
>  cv[3:6]+[0.0]+ \
>  cv[6:9]+[0.0]+ \
>  cv[12:15]+[1.0], transpose=1)
>cmd.save('~/transformed.pdb')
>
>To comment on the many emails that have been posted so far:
>
>1) I think you haven't used the script correct. Instead of "run save_trannsforme.py all, newpdb.pdb", you have to do "run save_transformed.py", followed by "save_transformed all, newpdb.pdb"
>2) The script is actually wrong (missing transpose=1)
>3) A correct solution has been posted for example here:
>https://sourceforge.net/p/pymol/mailman/message/27824450/
>
>Hope that helps.
>
>Cheers,
>  Thomas
>
>On 28 Nov 2015, at 02:52, Jordan Willis <jwi...@gm...> wrote:
>
>> Yes, but what you are describing, saving a new view is your purpose. All orient does is move the camera. It does not do anything to the x,y,z coordinates of the PDB. 
>>> On Nov 27, 2015, at 11:49 PM, Smith Liu <smi...@16...> wrote:
>>> 
>>> Dear Jordan, 
>>> 
>>> To save a new view is not my purpose, my purpose is to save a new set of PDB. For example， if the original PDB does not orient well by pymol by default, first I input "orient", and I want to save a set of new pdb, when I display by pymol the new pdb, it will display as "oriented“. Is any way we can get this oriented pdb?
>>> 
>>> Smith
>>> 
>>> 
>>> At 2015-11-28 15:37:10, "Jordan Willis" <jwi...@gm...> wrote:
>>> get view takes in camera coordinates. You can’t open a PDB and it have know anything about the camera view. You will have to grab the view, save it somewhere, and then load it. You can’t code a view change within the PDB. 
>>> 
>>> 
>>>> On Nov 27, 2015, at 11:27 PM, Smith Liu <smi...@16...> wrote:
>>>> 
>>>> Dear Jordan,
>>>> 
>>>> My purpose is, once you move a molecule in pymol, I want to save a new pdb, when we open the new pdb, pymol will display the new position as default.
>>>> 
>>>> The script is
>>>> 
>>>> "# Adds the command save_transformed
>>>> # Usage: save_transformed object, file
>>>> def save_transformed(object,file):
>>>>     m = cmd.get_view(0)
>>>>     ttt = [m[0], m[1], m[2], 0.0,
>>>>            m[3], m[4], m[5], 0.0,
>>>>            m[6], m[7], m[8], 0.0,
>>>>            0.0,   0.0,  0.0, 1.0]
>>>>     cmd.transform_object(object,ttt)
>>>>     cmd.save(file,object)
>>>> cmd.extend('save_transformed',save_transformed)"
>>>> 
>>>> shown in http://pymolwiki.org/index.php/Modeling_and_Editing_Structures
>>>> 
>>>> Here I notice that once load a pdb, you move it a little, then you input "get_view", you will get the matrix like
>>>> 0.448818117, 0.886667669, -0.111277729
>>>> -0.889764965, 0.454960942,  0.036454394
>>>> 
>>>> which should be the m[0] to m[5] in the above script.
>>>> 
>>>> In addition, in http://www.pymolwiki.org/index.php/Transform_odb, there is also a transcript. For matrix it uses *.odb file. Is this *.odb  same as the get_view matrix, if not, can we convert get_view matrix to *.odb?
>>>> 
>>>> Besides, in http://www.pymolwiki.org/index.php/Transform_selection there is another script.
>>>> 
>>>> I do not know how to use this scripts to realize my purpose.
>>>> 
>>>> Smith
>>>> 
>>>> 
>>>> 
>>>> At 2015-11-28 15:07:18, "Jordan Willis" <jwi...@gm...> wrote:
>>>> very possible, can you send me the script?
>>>>> On Nov 27, 2015, at 10:58 PM, Smith Liu <smi...@16...> wrote:
>>>>> 
>>>>> By Jordan,
>>>>> 
>>>>> by
>>>>> 
>>>>> find ~/ -name “newpdb.pdb” or by
>>>>> 
>>>>> find / -name “newpdb.pdb”
>>>>> 
>>>>> still does not work. Is any possibility the original "save_transformed.py" does not work?
>>>>> 
>>>>> 
>>>>> Smith
>>>>> 
>>>>> 
>>>>> At 2015-11-28 13:11:25, "Jordan Willis" <jwi...@gm...> wrote:
>>>>> try running 
>>>>> 
>>>>> 
>>>>> find ~/ -name “newpdb.pdb” 
>>>>> 
>>>>> 
>>>>>> On Nov 27, 2015, at 9:08 PM, Smith Liu <smi...@16...> wrote:
>>>>>> 
>>>>>> 
>>>>>> Dear All,
>>>>>> 
>>>>>> Osvaldo is new here for this question, so I repeat it a little. By pymol I open a pdb and orient it and I want to save the oriented pdb. First I input command "orient" after load the pdb, then I input command "run save_trannsforme.py all, newpdb.pdb". I have tried to locate the newpdb.pdb by locate newpdb.pdb or find newpdb.pdb, even as the root user, but I cannot find the outpur newpdb.pdb. My pymol is Linux Open-Source PyMOL 1.6.X.
>>>>>> 
>>>>>> I am looking forward  to getting a reply from you on how to get the oriented pdb, which should be different from the original PDB I load.
>>>>>> 
>>>>>> Smith
>>>>>> 
>>>>>> 
>>>>>> At 2015-11-28 00:44:07, "Shane Caldwell" <sha...@gm...> wrote:
>>>>>> Hi Smith,
>>>>>> 
>>>>>> It will be in whatever folder pymol is launched from. If you launched pymol from a specific place, it will be that folder. If not, it might be in the system files for pymol, which will depend on your operating system and architecture.
>>>>>> 
>>>>>> Shane
>>>>>> 
>>>>>> 
>>>>>> Shane Caldwell
>>>>>> McGill University
>>>>>> 
>>>>>> On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <smi...@16...> wrote:
>>>>>> Dear All，
>>>>>> 
>>>>>> Once a molecule displayed in pymol, first I input command "orient", then I input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the oriented newpdb.pdb.
>>>>>> 
>>>>>> Will you please show me how to get the oriented newpdb.pdb?
>>>>>> 
>>>>>> Smith
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> At 2015-11-26 18:58:48, "Spencer Bliven" <spe...@gm...> wrote:
>>>>>> Smith–
>>>>>> 
>>>>>> The code is intended to be saved to a file ("save_transformed.py") and then loaded into pymol using `run /path/to/save_transformed.py`. There's some general info on running pymol scripts: Simple_Scripting Running_Scripts
>>>>>> 
>>>>>> The script defines a new command which can be run e.g. `save_transformed <object>, <file>`. You don't have to replace anything in the script yourself.
>>>>>> 
>>>>>> Note that the save_transformed command modifies the object it's run on, so you might want to run it on a backup copy by first calling `create <object>_backup, <object>`
>>>>>> 
>>>>>> -Spencer
>>>>>> 
>>>>>> On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smi...@16...> wrote:
>>>>>> Dear All,
>>>>>> 
>>>>>> For get view, we get something like
>>>>>> 
>>>>>>  set_view (\
>>>>>>        0.999876618,   -0.000452542,   -0.015699286,\
>>>>>>        0.000446742,    0.999999821,   -0.000372844,\
>>>>>>        0.015699454,    0.000365782,    0.999876678,\
>>>>>>        0.000000000,    0.000000000, -150.258514404,\
>>>>>>        11.842411041,   20.648729324,    8.775371552,\
>>>>>>        118.464958191,  182.052062988,    0.000000000 )
>>>>>>  
>>>>>> For save trasformed pdb file, we need sonething like
>>>>>> 
>>>>>> ttt = [m[0], m[1], m[2], 0.0,
>>>>>>            m[3], m[4], m[5], 0.0,
>>>>>>            m[6], m[7], m[8], 0.0,
>>>>>>            0.0,   0.0,  0.0, 1.0]
>>>>>> Will you please show me how to replace m[0], m[1].... from what we get by get_view? Which item is which item?
>>>>>> 
>>>>>> In addition, for the save_transformed.py, the last sentence is "cmd.extend('save_transformed',save_transformed)". Should we replace the second save_transformed with something, for example *.pdb? Ortherwise how to get the output modified PDB?
>>>>>> 
>>>>>> 
>>>>>> I am looking forward to getting a reply from you.
>>>>>> 
>>>>>> Smith
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> At 2015-11-26 14:24:15, "Andreas Forster" <doc...@gm...> wrote:
>>>>>> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
>>>>>> 
>>>>>> 
>>>>>> Andreas
>>>>>> 
>>>>>> 
>>>>>> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16...> wrote:
>>>>>> Dear Shane,
>>>>>> 
>>>>>> 
>>>>>> get_view is a nice command. Is any way to change the original PDB based on what we get by set_view to get the new pdb?
>>>>>> 
>>>>>> Smith
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm...> wrote:
>>>>>> Hi Smith,
>>>>>> 
>>>>>> You can type 
>>>>>> 
>>>>>> >get_view
>>>>>> 
>>>>>> and copy the output into a txt file for later use. The output set_view command will return the window to the same camera settings
>>>>>> 
>>>>>> Shane
>>>>>> 
>>>>>> Shane Caldwell
>>>>>> McGill University
>>>>>> 
>>>>>> On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16...> wrote:
>>>>>> Dear All,
>>>>>> 
>>>>>> Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented?
>>>>>> 
>>>>>> Smith
>
>-- 
>Thomas Holder
>PyMOL Principal Developer
>Schrödinger, Inc.
>

Hi Smith, and everybody who tried to help you so far,

Short answer: copy and paste this into the PyMOL command line, it will save the view-transformed object to "transformed.pdb" in your home folder.

cv=list(cmd.get_view())
cmd.transform_selection("all", \
  cv[0:3]+[0.0]+ \
  cv[3:6]+[0.0]+ \
  cv[6:9]+[0.0]+ \
  cv[12:15]+[1.0], transpose=1)
cmd.save('~/transformed.pdb')

To comment on the many emails that have been posted so far:

1) I think you haven't used the script correct. Instead of "run save_trannsforme.py all, newpdb.pdb", you have to do "run save_transformed.py", followed by "save_transformed all, newpdb.pdb"
2) The script is actually wrong (missing transpose=1)
3) A correct solution has been posted for example here:
https://sourceforge.net/p/pymol/mailman/message/27824450/

Hope that helps.

Cheers,
  Thomas

On 28 Nov 2015, at 02:52, Jordan Willis <jwi...@gm...> wrote:

> Yes, but what you are describing, saving a new view is your purpose. All orient does is move the camera. It does not do anything to the x,y,z coordinates of the PDB. 
>> On Nov 27, 2015, at 11:49 PM, Smith Liu <smi...@16...> wrote:
>> 
>> Dear Jordan, 
>> 
>> To save a new view is not my purpose, my purpose is to save a new set of PDB. For example， if the original PDB does not orient well by pymol by default, first I input "orient", and I want to save a set of new pdb, when I display by pymol the new pdb, it will display as "oriented“. Is any way we can get this oriented pdb?
>> 
>> Smith
>> 
>> 
>> At 2015-11-28 15:37:10, "Jordan Willis" <jwi...@gm...> wrote:
>> get view takes in camera coordinates. You can’t open a PDB and it have know anything about the camera view. You will have to grab the view, save it somewhere, and then load it. You can’t code a view change within the PDB. 
>> 
>> 
>>> On Nov 27, 2015, at 11:27 PM, Smith Liu <smi...@16...> wrote:
>>> 
>>> Dear Jordan,
>>> 
>>> My purpose is, once you move a molecule in pymol, I want to save a new pdb, when we open the new pdb, pymol will display the new position as default.
>>> 
>>> The script is
>>> 
>>> "# Adds the command save_transformed
>>> # Usage: save_transformed object, file
>>> def save_transformed(object,file):
>>>     m = cmd.get_view(0)
>>>     ttt = [m[0], m[1], m[2], 0.0,
>>>            m[3], m[4], m[5], 0.0,
>>>            m[6], m[7], m[8], 0.0,
>>>            0.0,   0.0,  0.0, 1.0]
>>>     cmd.transform_object(object,ttt)
>>>     cmd.save(file,object)
>>> cmd.extend('save_transformed',save_transformed)"
>>> 
>>> shown in http://pymolwiki.org/index.php/Modeling_and_Editing_Structures
>>> 
>>> Here I notice that once load a pdb, you move it a little, then you input "get_view", you will get the matrix like
>>> 0.448818117, 0.886667669, -0.111277729
>>> -0.889764965, 0.454960942,  0.036454394
>>> 
>>> which should be the m[0] to m[5] in the above script.
>>> 
>>> In addition, in http://www.pymolwiki.org/index.php/Transform_odb, there is also a transcript. For matrix it uses *.odb file. Is this *.odb  same as the get_view matrix, if not, can we convert get_view matrix to *.odb?
>>> 
>>> Besides, in http://www.pymolwiki.org/index.php/Transform_selection there is another script.
>>> 
>>> I do not know how to use this scripts to realize my purpose.
>>> 
>>> Smith
>>> 
>>> 
>>> 
>>> At 2015-11-28 15:07:18, "Jordan Willis" <jwi...@gm...> wrote:
>>> very possible, can you send me the script?
>>>> On Nov 27, 2015, at 10:58 PM, Smith Liu <smi...@16...> wrote:
>>>> 
>>>> By Jordan,
>>>> 
>>>> by
>>>> 
>>>> find ~/ -name “newpdb.pdb” or by
>>>> 
>>>> find / -name “newpdb.pdb”
>>>> 
>>>> still does not work. Is any possibility the original "save_transformed.py" does not work?
>>>> 
>>>> 
>>>> Smith
>>>> 
>>>> 
>>>> At 2015-11-28 13:11:25, "Jordan Willis" <jwi...@gm...> wrote:
>>>> try running 
>>>> 
>>>> 
>>>> find ~/ -name “newpdb.pdb” 
>>>> 
>>>> 
>>>>> On Nov 27, 2015, at 9:08 PM, Smith Liu <smi...@16...> wrote:
>>>>> 
>>>>> 
>>>>> Dear All,
>>>>> 
>>>>> Osvaldo is new here for this question, so I repeat it a little. By pymol I open a pdb and orient it and I want to save the oriented pdb. First I input command "orient" after load the pdb, then I input command "run save_trannsforme.py all, newpdb.pdb". I have tried to locate the newpdb.pdb by locate newpdb.pdb or find newpdb.pdb, even as the root user, but I cannot find the outpur newpdb.pdb. My pymol is Linux Open-Source PyMOL 1.6.X.
>>>>> 
>>>>> I am looking forward  to getting a reply from you on how to get the oriented pdb, which should be different from the original PDB I load.
>>>>> 
>>>>> Smith
>>>>> 
>>>>> 
>>>>> At 2015-11-28 00:44:07, "Shane Caldwell" <sha...@gm...> wrote:
>>>>> Hi Smith,
>>>>> 
>>>>> It will be in whatever folder pymol is launched from. If you launched pymol from a specific place, it will be that folder. If not, it might be in the system files for pymol, which will depend on your operating system and architecture.
>>>>> 
>>>>> Shane
>>>>> 
>>>>> 
>>>>> Shane Caldwell
>>>>> McGill University
>>>>> 
>>>>> On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <smi...@16...> wrote:
>>>>> Dear All，
>>>>> 
>>>>> Once a molecule displayed in pymol, first I input command "orient", then I input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the oriented newpdb.pdb.
>>>>> 
>>>>> Will you please show me how to get the oriented newpdb.pdb?
>>>>> 
>>>>> Smith
>>>>> 
>>>>> 
>>>>> 
>>>>> At 2015-11-26 18:58:48, "Spencer Bliven" <spe...@gm...> wrote:
>>>>> Smith–
>>>>> 
>>>>> The code is intended to be saved to a file ("save_transformed.py") and then loaded into pymol using `run /path/to/save_transformed.py`. There's some general info on running pymol scripts: Simple_Scripting Running_Scripts
>>>>> 
>>>>> The script defines a new command which can be run e.g. `save_transformed <object>, <file>`. You don't have to replace anything in the script yourself.
>>>>> 
>>>>> Note that the save_transformed command modifies the object it's run on, so you might want to run it on a backup copy by first calling `create <object>_backup, <object>`
>>>>> 
>>>>> -Spencer
>>>>> 
>>>>> On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smi...@16...> wrote:
>>>>> Dear All,
>>>>> 
>>>>> For get view, we get something like
>>>>> 
>>>>>  set_view (\
>>>>>        0.999876618,   -0.000452542,   -0.015699286,\
>>>>>        0.000446742,    0.999999821,   -0.000372844,\
>>>>>        0.015699454,    0.000365782,    0.999876678,\
>>>>>        0.000000000,    0.000000000, -150.258514404,\
>>>>>        11.842411041,   20.648729324,    8.775371552,\
>>>>>        118.464958191,  182.052062988,    0.000000000 )
>>>>>  
>>>>> For save trasformed pdb file, we need sonething like
>>>>> 
>>>>> ttt = [m[0], m[1], m[2], 0.0,
>>>>>            m[3], m[4], m[5], 0.0,
>>>>>            m[6], m[7], m[8], 0.0,
>>>>>            0.0,   0.0,  0.0, 1.0]
>>>>> Will you please show me how to replace m[0], m[1].... from what we get by get_view? Which item is which item?
>>>>> 
>>>>> In addition, for the save_transformed.py, the last sentence is "cmd.extend('save_transformed',save_transformed)". Should we replace the second save_transformed with something, for example *.pdb? Ortherwise how to get the output modified PDB?
>>>>> 
>>>>> 
>>>>> I am looking forward to getting a reply from you.
>>>>> 
>>>>> Smith
>>>>> 
>>>>> 
>>>>> 
>>>>> At 2015-11-26 14:24:15, "Andreas Forster" <doc...@gm...> wrote:
>>>>> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
>>>>> 
>>>>> 
>>>>> Andreas
>>>>> 
>>>>> 
>>>>> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16...> wrote:
>>>>> Dear Shane,
>>>>> 
>>>>> 
>>>>> get_view is a nice command. Is any way to change the original PDB based on what we get by set_view to get the new pdb?
>>>>> 
>>>>> Smith
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm...> wrote:
>>>>> Hi Smith,
>>>>> 
>>>>> You can type 
>>>>> 
>>>>> >get_view
>>>>> 
>>>>> and copy the output into a txt file for later use. The output set_view command will return the window to the same camera settings
>>>>> 
>>>>> Shane
>>>>> 
>>>>> Shane Caldwell
>>>>> McGill University
>>>>> 
>>>>> On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16...> wrote:
>>>>> Dear All,
>>>>> 
>>>>> Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented?
>>>>> 
>>>>> Smith

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear All,


Will you please show me how to display an axis of a subunit or a domain by pymol?


Smith

Yes, but what you are describing, saving a new view is your purpose. All orient does is move the camera. It does not do anything to the x,y,z coordinates of the PDB. 
> On Nov 27, 2015, at 11:49 PM, Smith Liu <smi...@16...> wrote:
> 
> Dear Jordan, 
> 
> To save a new view is not my purpose, my purpose is to save a new set of PDB. For example， if the original PDB does not orient well by pymol by default, first I input "orient", and I want to save a set of new pdb, when I display by pymol the new pdb, it will display as "oriented“. Is any way we can get this oriented pdb?
> 
> Smith
> 
> 
> 
> 
> 
> At 2015-11-28 15:37:10, "Jordan Willis" <jwi...@gm...> wrote:
> get view takes in camera coordinates. You can’t open a PDB and it have know anything about the camera view. You will have to grab the view, save it somewhere, and then load it. You can’t code a view change within the PDB. 
> 
> 
>> On Nov 27, 2015, at 11:27 PM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>> 
>> Dear Jordan,
>> 
>> My purpose is, once you move a molecule in pymol, I want to save a new pdb, when we open the new pdb, pymol will display the new position as default.
>> 
>> The script is
>> 
>> "# Adds the command save_transformed
>> # Usage: save_transformed object, file
>> def save_transformed(object,file):
>>     m = cmd.get_view(0)
>>     ttt = [m[0], m[1], m[2], 0.0,
>>            m[3], m[4], m[5], 0.0,
>>            m[6], m[7], m[8], 0.0,
>>            0.0,   0.0,  0.0, 1.0]
>>     cmd.transform_object(object,ttt)
>>     cmd.save(file,object)
>> cmd.extend('save_transformed',save_transformed)"
>> 
>> shown in http://pymolwiki.org/index.php/Modeling_and_Editing_Structures <" rel="nofollow">http://pymolwiki.org/index.php/Modeling_and_Editing_Structures>
>> 
>> Here I notice that once load a pdb, you move it a little, then you input "get_view", you will get the matrix like
>> 0.448818117, 0.886667669, -0.111277729
>> -0.889764965, 0.454960942,  0.036454394
>> 
>> which should be the m[0] to m[5] in the above script.
>> 
>> In addition, in http://www.pymolwiki.org/index.php/Transform_odb <," rel="nofollow">http://www.pymolwiki.org/index.php/Transform_odb>, there is also a transcript. For matrix it uses *.odb file. Is this *.odb  same as the get_view matrix, if not, can we convert get_view matrix to *.odb?
>> 
>> Besides, in http://www.pymolwiki.org/index.php/Transform_selection <" rel="nofollow">http://www.pymolwiki.org/index.php/Transform_selection> there is another script.
>> 
>> I do not know how to use this scripts to realize my purpose.
>> 
>> Smith
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> At 2015-11-28 15:07:18, "Jordan Willis" <jwi...@gm... <mailto:jwi...@gm...>> wrote:
>> very possible, can you send me the script?
>>> On Nov 27, 2015, at 10:58 PM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>>> 
>>> By Jordan,
>>> 
>>> by
>>> 
>>> find ~/ -name “newpdb.pdb” or by
>>> 
>>> find / -name “newpdb.pdb”
>>> 
>>> still does not work. Is any possibility the original "save_transformed.py" does not work?
>>> 
>>> 
>>> Smith
>>> 
>>> 
>>> 
>>> 
>>> 
>>> At 2015-11-28 13:11:25, "Jordan Willis" <jwi...@gm... <mailto:jwi...@gm...>> wrote:
>>> try running 
>>> 
>>> 
>>> find ~/ -name “newpdb.pdb” 
>>> 
>>> 
>>>> On Nov 27, 2015, at 9:08 PM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>>>> 
>>>> 
>>>> Dear All,
>>>> 
>>>> Osvaldo is new here for this question, so I repeat it a little. By pymol I open a pdb and orient it and I want to save the oriented pdb. First I input command "orient" after load the pdb, then I input command "run save_trannsforme.py all, newpdb.pdb". I have tried to locate the newpdb.pdb by locate newpdb.pdb or find newpdb.pdb, even as the root user, but I cannot find the outpur newpdb.pdb. My pymol is Linux Open-Source PyMOL 1.6.X.
>>>> 
>>>> I am looking forward  to getting a reply from you on how to get the oriented pdb, which should be different from the original PDB I load.
>>>> 
>>>> Smith
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> At 2015-11-28 00:44:07, "Shane Caldwell" <sha...@gm... <mailto:sha...@gm...>> wrote:
>>>> Hi Smith,
>>>> 
>>>> It will be in whatever folder pymol is launched from. If you launched pymol from a specific place, it will be that folder. If not, it might be in the system files for pymol, which will depend on your operating system and architecture.
>>>> 
>>>> Shane
>>>> 
>>>> 
>>>> Shane Caldwell
>>>> McGill University
>>>> 
>>>> On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>>>> Dear All，
>>>> 
>>>> Once a molecule displayed in pymol, first I input command "orient", then I input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the oriented newpdb.pdb.
>>>> 
>>>> Will you please show me how to get the oriented newpdb.pdb?
>>>> 
>>>> Smith
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> At 2015-11-26 18:58:48, "Spencer Bliven" <spe...@gm... <mailto:spe...@gm...>> wrote:
>>>> Smith–
>>>> 
>>>> The code is intended to be saved to a file ("save_transformed.py") and then loaded into pymol using `run /path/to/save_transformed.py`. There's some general info on running pymol scripts: Simple_Scripting <" rel="nofollow">http://pymolwiki.org/index.php/Simple_Scripting> Running_Scripts <" rel="nofollow">http://pymolwiki.org/index.php/Running_Scripts>
>>>> 
>>>> The script defines a new command which can be run e.g. `save_transformed <object>, <file>`. You don't have to replace anything in the script yourself.
>>>> 
>>>> Note that the save_transformed command modifies the object it's run on, so you might want to run it on a backup copy by first calling `create <object>_backup, <object>`
>>>> 
>>>> -Spencer
>>>> 
>>>> On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>>>> Dear All,
>>>> 
>>>> For get view, we get something like
>>>> 
>>>>  set_view (\
>>>>        0.999876618,   -0.000452542,   -0.015699286,\
>>>>        0.000446742,    0.999999821,   -0.000372844,\
>>>>        0.015699454,    0.000365782,    0.999876678,\
>>>>        0.000000000,    0.000000000, -150.258514404,\
>>>>        11.842411041,   20.648729324,    8.775371552,\
>>>>        118.464958191,  182.052062988,    0.000000000 )
>>>>  
>>>> For save trasformed pdb file, we need sonething like
>>>> 
>>>> ttt = [m[0], m[1], m[2], 0.0,
>>>>            m[3], m[4], m[5], 0.0,
>>>>            m[6], m[7], m[8], 0.0,
>>>>            0.0,   0.0,  0.0, 1.0]
>>>> Will you please show me how to replace m[0], m[1].... from what we get by get_view? Which item is which item?
>>>> 
>>>> In addition, for the save_transformed.py, the last sentence is "cmd.extend('save_transformed',save_transformed)". Should we replace the second save_transformed with something, for example *.pdb? Ortherwise how to get the output modified PDB?
>>>> 
>>>> 
>>>> I am looking forward to getting a reply from you.
>>>> 
>>>> Smith
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> At 2015-11-26 14:24:15, "Andreas Forster" <doc...@gm... <mailto:doc...@gm...>> wrote:
>>>> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures <" rel="nofollow">http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures>
>>>> 
>>>> 
>>>> Andreas
>>>> 
>>>> 
>>>> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>>>> Dear Shane,
>>>> 
>>>> 
>>>> get_view is a nice command. Is any way to change the original PDB based on what we get by set_view to get the new pdb?
>>>> 
>>>> Smith
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm... <mailto:sha...@gm...>> wrote:
>>>> Hi Smith,
>>>> 
>>>> You can type 
>>>> 
>>>> >get_view
>>>> 
>>>> and copy the output into a txt file for later use. The output set_view command will return the window to the same camera settings
>>>> 
>>>> Shane
>>>> 
>>>> Shane Caldwell
>>>> McGill University
>>>> 
>>>> On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>>>> Dear All,
>>>> 
>>>> Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented?
>>>> 
>>>> Smith
>>>> 
>>>> 
>>>>  
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>>> Use one codebase in this all-in-one HTML5 development environment.
>>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 <" rel="nofollow">http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140>
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users>
>>>> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
>>>> 
>>>> 
>>>> 
>>>>  
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>>> Use one codebase in this all-in-one HTML5 development environment.
>>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 <" rel="nofollow">http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140>
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users>
>>>> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
>>>> 
>>>> 
>>>> 
>>>>  
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>>> Use one codebase in this all-in-one HTML5 development environment.
>>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 <" rel="nofollow">http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140>
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users>
>>>> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
>>>> 
>>>> 
>>>> 
>>>>  
>>>> 
>>>> 
>>>> 
>>>>  
>>>> ------------------------------------------------------------------------------
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users>
>>>> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
>>> 
>>> 
>>>  
>> 
>> 
>> 
>>  
> 
> 
> 
>  

Dear Jordan,


To save a new view is not my purpose, my purpose is to save a new set of PDB. For example， if the original PDB does not orient well by pymol by default, first I input "orient", and I want to save a set of new pdb, when I display by pymol the new pdb, it will display as "oriented“. Is any way we can get this oriented pdb?


Smith







At 2015-11-28 15:37:10, "Jordan Willis" <jwi...@gm...> wrote:
get view takes in camera coordinates. You can’t open a PDB and it have know anything about the camera view. You will have to grab the view, save it somewhere, and then load it. You can’t code a view change within the PDB. 




On Nov 27, 2015, at 11:27 PM, Smith Liu <smi...@16...> wrote:


Dear Jordan,


My purpose is, once you move a molecule in pymol, I want to save a new pdb, when we open the new pdb, pymol will display the new position as default.


The script is


"# Adds the command save_transformed
# Usage: save_transformed object, file
def save_transformed(object,file):
    m = cmd.get_view(0)
    ttt = [m[0], m[1], m[2], 0.0,
           m[3], m[4], m[5], 0.0,
           m[6], m[7], m[8], 0.0,
           0.0,   0.0,  0.0, 1.0]
    cmd.transform_object(object,ttt)
    cmd.save(file,object)
cmd.extend('save_transformed',save_transformed)"


shown in http://pymolwiki.org/index.php/Modeling_and_Editing_Structures


Here I notice that once load a pdb, you move it a little, then you input "get_view", you will get the matrix like
0.448818117, 0.886667669, -0.111277729
-0.889764965, 0.454960942,  0.036454394


which should be the m[0] to m[5] in the above script.


In addition, in http://www.pymolwiki.org/index.php/Transform_odb, there is also a transcript. For matrix it uses *.odb file. Is this *.odb  same as the get_view matrix, if not, can we convert get_view matrix to *.odb?


Besides, in http://www.pymolwiki.org/index.php/Transform_selection there is another script.


I do not know how to use this scripts to realize my purpose.


Smith












At 2015-11-28 15:07:18, "Jordan Willis" <jwi...@gm...> wrote:
very possible, can you send me the script?

On Nov 27, 2015, at 10:58 PM, Smith Liu <smi...@16...> wrote:


By Jordan,


by


find ~/ -name “newpdb.pdb” or by


find / -name “newpdb.pdb”


still does not work. Is any possibility the original "save_transformed.py" does not work?




Smith







At 2015-11-28 13:11:25, "Jordan Willis" <jwi...@gm...> wrote:
try running 




find ~/ -name “newpdb.pdb” 




On Nov 27, 2015, at 9:08 PM, Smith Liu <smi...@16...> wrote:



Dear All,


Osvaldo is new here for this question, so I repeat it a little. By pymol I open a pdb and orient it and I want to save the oriented pdb. First I input command "orient" after load the pdb, then I input command "run save_trannsforme.py all, newpdb.pdb". I have tried to locate the newpdb.pdb by locate newpdb.pdb or find newpdb.pdb, even as the root user, but I cannot find the outpur newpdb.pdb. My pymol is Linux Open-Source PyMOL 1.6.X.


I am looking forward  to getting a reply from you on how to get the oriented pdb, which should be different from the original PDB I load.


Smith









At 2015-11-28 00:44:07, "Shane Caldwell" <sha...@gm...> wrote:

Hi Smith,


It will be in whatever folder pymol is launched from. If you launched pymol from a specific place, it will be that folder. If not, it might be in the system files for pymol, which will depend on your operating system and architecture.


Shane





Shane Caldwell

McGill University


On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <smi...@16...> wrote:

Dear All，


Once a molecule displayed in pymol, first I input command "orient", then I input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the oriented newpdb.pdb.


Will you please show me how to get the oriented newpdb.pdb?


Smith







At 2015-11-26 18:58:48, "Spencer Bliven" <spe...@gm...> wrote:

Smith–


The code is intended to be saved to a file ("save_transformed.py") and then loaded into pymol using `run /path/to/save_transformed.py`. There's some general info on running pymol scripts: Simple_ScriptingRunning_Scripts


The script defines a new command which can be run e.g. `save_transformed <object>, <file>`. You don't have to replace anything in the script yourself.


Note that the save_transformed command modifies the object it's run on, so you might want to run it on a backup copy by first calling `create <object>_backup, <object>`


-Spencer



On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smi...@16...> wrote:

Dear All,


For get view, we get something like


 set_view (\
       0.999876618,   -0.000452542,   -0.015699286,\
       0.000446742,    0.999999821,   -0.000372844,\
       0.015699454,    0.000365782,    0.999876678,\
       0.000000000,    0.000000000, -150.258514404,\
       11.842411041,   20.648729324,    8.775371552,\
       118.464958191,  182.052062988,    0.000000000 )
 
For save trasformed pdb file, we need sonething like


ttt = [m[0], m[1], m[2], 0.0,
           m[3], m[4], m[5], 0.0,
           m[6], m[7], m[8], 0.0,
           0.0,   0.0,  0.0, 1.0]
Will you please show me how to replace m[0], m[1].... from what we get by get_view? Which item is which item?


In addition, for the save_transformed.py, the last sentence is "cmd.extend('save_transformed',save_transformed)". Should we replace the second save_transformed with something, for example *.pdb? Ortherwise how to get the output modified PDB?



I am looking forward to getting a reply from you.


Smith



















At 2015-11-26 14:24:15, "Andreas Forster" <doc...@gm...> wrote:

http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures





Andreas




On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16...> wrote:


Dear Shane,



get_view is a nice command. Is any way to change the original PDB based on what we get by set_view to get the new pdb?


Smith








At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm...> wrote:

Hi Smith,


You can type

>get_view


and copy the output into a txt file for later use. The output set_view command will return the window to the same camera settings


Shane



Shane Caldwell

McGill University


On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16...> wrote:

Dear All,


Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented?


Smith



 


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get view takes in camera coordinates. You can’t open a PDB and it have know anything about the camera view. You will have to grab the view, save it somewhere, and then load it. You can’t code a view change within the PDB. 


> On Nov 27, 2015, at 11:27 PM, Smith Liu <smi...@16...> wrote:
> 
> Dear Jordan,
> 
> My purpose is, once you move a molecule in pymol, I want to save a new pdb, when we open the new pdb, pymol will display the new position as default.
> 
> The script is
> 
> "# Adds the command save_transformed
> # Usage: save_transformed object, file
> def save_transformed(object,file):
>     m = cmd.get_view(0)
>     ttt = [m[0], m[1], m[2], 0.0,
>            m[3], m[4], m[5], 0.0,
>            m[6], m[7], m[8], 0.0,
>            0.0,   0.0,  0.0, 1.0]
>     cmd.transform_object(object,ttt)
>     cmd.save(file,object)
> cmd.extend('save_transformed',save_transformed)"
> 
> shown in http://pymolwiki.org/index.php/Modeling_and_Editing_Structures <" rel="nofollow">http://pymolwiki.org/index.php/Modeling_and_Editing_Structures>
> 
> Here I notice that once load a pdb, you move it a little, then you input "get_view", you will get the matrix like
> 0.448818117, 0.886667669, -0.111277729
> -0.889764965, 0.454960942,  0.036454394
> 
> which should be the m[0] to m[5] in the above script.
> 
> In addition, in http://www.pymolwiki.org/index.php/Transform_odb <," rel="nofollow">http://www.pymolwiki.org/index.php/Transform_odb>, there is also a transcript. For matrix it uses *.odb file. Is this *.odb  same as the get_view matrix, if not, can we convert get_view matrix to *.odb?
> 
> Besides, in http://www.pymolwiki.org/index.php/Transform_selection <" rel="nofollow">http://www.pymolwiki.org/index.php/Transform_selection> there is another script.
> 
> I do not know how to use this scripts to realize my purpose.
> 
> Smith
> 
> 
> 
> 
> 
> 
> 
> 
> At 2015-11-28 15:07:18, "Jordan Willis" <jwi...@gm...> wrote:
> very possible, can you send me the script?
>> On Nov 27, 2015, at 10:58 PM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>> 
>> By Jordan,
>> 
>> by
>> 
>> find ~/ -name “newpdb.pdb” or by
>> 
>> find / -name “newpdb.pdb”
>> 
>> still does not work. Is any possibility the original "save_transformed.py" does not work?
>> 
>> 
>> Smith
>> 
>> 
>> 
>> 
>> 
>> At 2015-11-28 13:11:25, "Jordan Willis" <jwi...@gm... <mailto:jwi...@gm...>> wrote:
>> try running 
>> 
>> 
>> find ~/ -name “newpdb.pdb” 
>> 
>> 
>>> On Nov 27, 2015, at 9:08 PM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>>> 
>>> 
>>> Dear All,
>>> 
>>> Osvaldo is new here for this question, so I repeat it a little. By pymol I open a pdb and orient it and I want to save the oriented pdb. First I input command "orient" after load the pdb, then I input command "run save_trannsforme.py all, newpdb.pdb". I have tried to locate the newpdb.pdb by locate newpdb.pdb or find newpdb.pdb, even as the root user, but I cannot find the outpur newpdb.pdb. My pymol is Linux Open-Source PyMOL 1.6.X.
>>> 
>>> I am looking forward  to getting a reply from you on how to get the oriented pdb, which should be different from the original PDB I load.
>>> 
>>> Smith
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> At 2015-11-28 00:44:07, "Shane Caldwell" <sha...@gm... <mailto:sha...@gm...>> wrote:
>>> Hi Smith,
>>> 
>>> It will be in whatever folder pymol is launched from. If you launched pymol from a specific place, it will be that folder. If not, it might be in the system files for pymol, which will depend on your operating system and architecture.
>>> 
>>> Shane
>>> 
>>> 
>>> Shane Caldwell
>>> McGill University
>>> 
>>> On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>>> Dear All，
>>> 
>>> Once a molecule displayed in pymol, first I input command "orient", then I input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the oriented newpdb.pdb.
>>> 
>>> Will you please show me how to get the oriented newpdb.pdb?
>>> 
>>> Smith
>>> 
>>> 
>>> 
>>> 
>>> 
>>> At 2015-11-26 18:58:48, "Spencer Bliven" <spe...@gm... <mailto:spe...@gm...>> wrote:
>>> Smith–
>>> 
>>> The code is intended to be saved to a file ("save_transformed.py") and then loaded into pymol using `run /path/to/save_transformed.py`. There's some general info on running pymol scripts: Simple_Scripting <" rel="nofollow">http://pymolwiki.org/index.php/Simple_Scripting> Running_Scripts <" rel="nofollow">http://pymolwiki.org/index.php/Running_Scripts>
>>> 
>>> The script defines a new command which can be run e.g. `save_transformed <object>, <file>`. You don't have to replace anything in the script yourself.
>>> 
>>> Note that the save_transformed command modifies the object it's run on, so you might want to run it on a backup copy by first calling `create <object>_backup, <object>`
>>> 
>>> -Spencer
>>> 
>>> On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>>> Dear All,
>>> 
>>> For get view, we get something like
>>> 
>>>  set_view (\
>>>        0.999876618,   -0.000452542,   -0.015699286,\
>>>        0.000446742,    0.999999821,   -0.000372844,\
>>>        0.015699454,    0.000365782,    0.999876678,\
>>>        0.000000000,    0.000000000, -150.258514404,\
>>>        11.842411041,   20.648729324,    8.775371552,\
>>>        118.464958191,  182.052062988,    0.000000000 )
>>>  
>>> For save trasformed pdb file, we need sonething like
>>> 
>>> ttt = [m[0], m[1], m[2], 0.0,
>>>            m[3], m[4], m[5], 0.0,
>>>            m[6], m[7], m[8], 0.0,
>>>            0.0,   0.0,  0.0, 1.0]
>>> Will you please show me how to replace m[0], m[1].... from what we get by get_view? Which item is which item?
>>> 
>>> In addition, for the save_transformed.py, the last sentence is "cmd.extend('save_transformed',save_transformed)". Should we replace the second save_transformed with something, for example *.pdb? Ortherwise how to get the output modified PDB?
>>> 
>>> 
>>> I am looking forward to getting a reply from you.
>>> 
>>> Smith
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> At 2015-11-26 14:24:15, "Andreas Forster" <doc...@gm... <mailto:doc...@gm...>> wrote:
>>> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures <" rel="nofollow">http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures>
>>> 
>>> 
>>> Andreas
>>> 
>>> 
>>> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>>> Dear Shane,
>>> 
>>> 
>>> get_view is a nice command. Is any way to change the original PDB based on what we get by set_view to get the new pdb?
>>> 
>>> Smith
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm... <mailto:sha...@gm...>> wrote:
>>> Hi Smith,
>>> 
>>> You can type 
>>> 
>>> >get_view
>>> 
>>> and copy the output into a txt file for later use. The output set_view command will return the window to the same camera settings
>>> 
>>> Shane
>>> 
>>> Shane Caldwell
>>> McGill University
>>> 
>>> On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>>> Dear All,
>>> 
>>> Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented?
>>> 
>>> Smith
>>> 
>>> 
>>>  
>>> 
>>> ------------------------------------------------------------------------------
>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>> Use one codebase in this all-in-one HTML5 development environment.
>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
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>>> _______________________________________________
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>>> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
>>> 
>>> 
>>> 
>>>  
>>> 
>>> ------------------------------------------------------------------------------
>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>> Use one codebase in this all-in-one HTML5 development environment.
>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 <" rel="nofollow">http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140>
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>>> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
>>> 
>>> 
>>> 
>>>  
>>> 
>>> ------------------------------------------------------------------------------
>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>> Use one codebase in this all-in-one HTML5 development environment.
>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 <" rel="nofollow">http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140>
>>> _______________________________________________
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>>> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
>>> 
>>> 
>>> 
>>>  
>>> 
>>> 
>>> 
>>>  
>>> ------------------------------------------------------------------------------
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users>
>>> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
>> 
>> 
>>  
> 
> 
> 
>  

Dear Jordan,


My purpose is, once you move a molecule in pymol, I want to save a new pdb, when we open the new pdb, pymol will display the new position as default.


The script is


"# Adds the command save_transformed
# Usage: save_transformed object, file
def save_transformed(object,file):
    m = cmd.get_view(0)
    ttt = [m[0], m[1], m[2], 0.0,
           m[3], m[4], m[5], 0.0,
           m[6], m[7], m[8], 0.0,
           0.0,   0.0,  0.0, 1.0]
    cmd.transform_object(object,ttt)
    cmd.save(file,object)
cmd.extend('save_transformed',save_transformed)"


shown in http://pymolwiki.org/index.php/Modeling_and_Editing_Structures


Here I notice that once load a pdb, you move it a little, then you input "get_view", you will get the matrix like
0.448818117, 0.886667669, -0.111277729
-0.889764965, 0.454960942,  0.036454394


which should be the m[0] to m[5] in the above script.


In addition, in http://www.pymolwiki.org/index.php/Transform_odb, there is also a transcript. For matrix it uses *.odb file. Is this *.odb  same as the get_view matrix, if not, can we convert get_view matrix to *.odb?


Besides, in http://www.pymolwiki.org/index.php/Transform_selection there is another script.


I do not know how to use this scripts to realize my purpose.


Smith












At 2015-11-28 15:07:18, "Jordan Willis" <jwi...@gm...> wrote:
very possible, can you send me the script?

On Nov 27, 2015, at 10:58 PM, Smith Liu <smi...@16...> wrote:


By Jordan,


by


find ~/ -name “newpdb.pdb” or by


find / -name “newpdb.pdb”


still does not work. Is any possibility the original "save_transformed.py" does not work?




Smith







At 2015-11-28 13:11:25, "Jordan Willis" <jwi...@gm...> wrote:
try running 




find ~/ -name “newpdb.pdb” 




On Nov 27, 2015, at 9:08 PM, Smith Liu <smi...@16...> wrote:



Dear All,


Osvaldo is new here for this question, so I repeat it a little. By pymol I open a pdb and orient it and I want to save the oriented pdb. First I input command "orient" after load the pdb, then I input command "run save_trannsforme.py all, newpdb.pdb". I have tried to locate the newpdb.pdb by locate newpdb.pdb or find newpdb.pdb, even as the root user, but I cannot find the outpur newpdb.pdb. My pymol is Linux Open-Source PyMOL 1.6.X.


I am looking forward  to getting a reply from you on how to get the oriented pdb, which should be different from the original PDB I load.


Smith









At 2015-11-28 00:44:07, "Shane Caldwell" <sha...@gm...> wrote:

Hi Smith,


It will be in whatever folder pymol is launched from. If you launched pymol from a specific place, it will be that folder. If not, it might be in the system files for pymol, which will depend on your operating system and architecture.


Shane





Shane Caldwell

McGill University


On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <smi...@16...> wrote:

Dear All，


Once a molecule displayed in pymol, first I input command "orient", then I input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the oriented newpdb.pdb.


Will you please show me how to get the oriented newpdb.pdb?


Smith







At 2015-11-26 18:58:48, "Spencer Bliven" <spe...@gm...> wrote:

Smith–


The code is intended to be saved to a file ("save_transformed.py") and then loaded into pymol using `run /path/to/save_transformed.py`. There's some general info on running pymol scripts: Simple_ScriptingRunning_Scripts


The script defines a new command which can be run e.g. `save_transformed <object>, <file>`. You don't have to replace anything in the script yourself.


Note that the save_transformed command modifies the object it's run on, so you might want to run it on a backup copy by first calling `create <object>_backup, <object>`


-Spencer



On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smi...@16...> wrote:

Dear All,


For get view, we get something like


 set_view (\
       0.999876618,   -0.000452542,   -0.015699286,\
       0.000446742,    0.999999821,   -0.000372844,\
       0.015699454,    0.000365782,    0.999876678,\
       0.000000000,    0.000000000, -150.258514404,\
       11.842411041,   20.648729324,    8.775371552,\
       118.464958191,  182.052062988,    0.000000000 )
 
For save trasformed pdb file, we need sonething like


ttt = [m[0], m[1], m[2], 0.0,
           m[3], m[4], m[5], 0.0,
           m[6], m[7], m[8], 0.0,
           0.0,   0.0,  0.0, 1.0]
Will you please show me how to replace m[0], m[1].... from what we get by get_view? Which item is which item?


In addition, for the save_transformed.py, the last sentence is "cmd.extend('save_transformed',save_transformed)". Should we replace the second save_transformed with something, for example *.pdb? Ortherwise how to get the output modified PDB?



I am looking forward to getting a reply from you.


Smith



















At 2015-11-26 14:24:15, "Andreas Forster" <doc...@gm...> wrote:

http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures





Andreas




On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16...> wrote:


Dear Shane,



get_view is a nice command. Is any way to change the original PDB based on what we get by set_view to get the new pdb?


Smith








At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm...> wrote:

Hi Smith,


You can type

>get_view


and copy the output into a txt file for later use. The output set_view command will return the window to the same camera settings


Shane



Shane Caldwell

McGill University


On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16...> wrote:

Dear All,


Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented?


Smith



 


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Give your users amazing mobile app experiences with Intel(R) XDK.
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Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
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Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
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very possible, can you send me the script?
> On Nov 27, 2015, at 10:58 PM, Smith Liu <smi...@16...> wrote:
> 
> By Jordan,
> 
> by
> 
> find ~/ -name “newpdb.pdb” or by
> 
> find / -name “newpdb.pdb”
> 
> still does not work. Is any possibility the original "save_transformed.py" does not work?
> 
> 
> Smith
> 
> 
> 
> 
> 
> At 2015-11-28 13:11:25, "Jordan Willis" <jwi...@gm...> wrote:
> try running 
> 
> 
> find ~/ -name “newpdb.pdb” 
> 
> 
>> On Nov 27, 2015, at 9:08 PM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>> 
>> 
>> Dear All,
>> 
>> Osvaldo is new here for this question, so I repeat it a little. By pymol I open a pdb and orient it and I want to save the oriented pdb. First I input command "orient" after load the pdb, then I input command "run save_trannsforme.py all, newpdb.pdb". I have tried to locate the newpdb.pdb by locate newpdb.pdb or find newpdb.pdb, even as the root user, but I cannot find the outpur newpdb.pdb. My pymol is Linux Open-Source PyMOL 1.6.X.
>> 
>> I am looking forward  to getting a reply from you on how to get the oriented pdb, which should be different from the original PDB I load.
>> 
>> Smith
>> 
>> 
>> 
>> 
>> 
>> 
>> At 2015-11-28 00:44:07, "Shane Caldwell" <sha...@gm... <mailto:sha...@gm...>> wrote:
>> Hi Smith,
>> 
>> It will be in whatever folder pymol is launched from. If you launched pymol from a specific place, it will be that folder. If not, it might be in the system files for pymol, which will depend on your operating system and architecture.
>> 
>> Shane
>> 
>> 
>> Shane Caldwell
>> McGill University
>> 
>> On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>> Dear All，
>> 
>> Once a molecule displayed in pymol, first I input command "orient", then I input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the oriented newpdb.pdb.
>> 
>> Will you please show me how to get the oriented newpdb.pdb?
>> 
>> Smith
>> 
>> 
>> 
>> 
>> 
>> At 2015-11-26 18:58:48, "Spencer Bliven" <spe...@gm... <mailto:spe...@gm...>> wrote:
>> Smith–
>> 
>> The code is intended to be saved to a file ("save_transformed.py") and then loaded into pymol using `run /path/to/save_transformed.py`. There's some general info on running pymol scripts: Simple_Scripting <" rel="nofollow">http://pymolwiki.org/index.php/Simple_Scripting> Running_Scripts <" rel="nofollow">http://pymolwiki.org/index.php/Running_Scripts>
>> 
>> The script defines a new command which can be run e.g. `save_transformed <object>, <file>`. You don't have to replace anything in the script yourself.
>> 
>> Note that the save_transformed command modifies the object it's run on, so you might want to run it on a backup copy by first calling `create <object>_backup, <object>`
>> 
>> -Spencer
>> 
>> On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>> Dear All,
>> 
>> For get view, we get something like
>> 
>>  set_view (\
>>        0.999876618,   -0.000452542,   -0.015699286,\
>>        0.000446742,    0.999999821,   -0.000372844,\
>>        0.015699454,    0.000365782,    0.999876678,\
>>        0.000000000,    0.000000000, -150.258514404,\
>>        11.842411041,   20.648729324,    8.775371552,\
>>        118.464958191,  182.052062988,    0.000000000 )
>>  
>> For save trasformed pdb file, we need sonething like
>> 
>> ttt = [m[0], m[1], m[2], 0.0,
>>            m[3], m[4], m[5], 0.0,
>>            m[6], m[7], m[8], 0.0,
>>            0.0,   0.0,  0.0, 1.0]
>> Will you please show me how to replace m[0], m[1].... from what we get by get_view? Which item is which item?
>> 
>> In addition, for the save_transformed.py, the last sentence is "cmd.extend('save_transformed',save_transformed)". Should we replace the second save_transformed with something, for example *.pdb? Ortherwise how to get the output modified PDB?
>> 
>> 
>> I am looking forward to getting a reply from you.
>> 
>> Smith
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> At 2015-11-26 14:24:15, "Andreas Forster" <doc...@gm... <mailto:doc...@gm...>> wrote:
>> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures <" rel="nofollow">http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures>
>> 
>> 
>> Andreas
>> 
>> 
>> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>> Dear Shane,
>> 
>> 
>> get_view is a nice command. Is any way to change the original PDB based on what we get by set_view to get the new pdb?
>> 
>> Smith
>> 
>> 
>> 
>> 
>> 
>> 
>> At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm... <mailto:sha...@gm...>> wrote:
>> Hi Smith,
>> 
>> You can type 
>> 
>> >get_view
>> 
>> and copy the output into a txt file for later use. The output set_view command will return the window to the same camera settings
>> 
>> Shane
>> 
>> Shane Caldwell
>> McGill University
>> 
>> On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
>> Dear All,
>> 
>> Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented?
>> 
>> Smith
>> 
>> 
>>  
>> 
>> ------------------------------------------------------------------------------
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 <" rel="nofollow">http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users>
>> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
>> 
>> 
>> 
>>  
>> 
>> ------------------------------------------------------------------------------
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 <" rel="nofollow">http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users>
>> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
>> 
>> 
>> 
>>  
>> 
>> ------------------------------------------------------------------------------
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 <" rel="nofollow">http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>)
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>> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
>> 
>> 
>> 
>>  
>> 
>> 
>> 
>>  
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users>
>> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
> 
> 
>  

By Jordan,


by


find ~/ -name “newpdb.pdb” or by


find / -name “newpdb.pdb”


still does not work. Is any possibility the original "save_transformed.py" does not work?




Smith







At 2015-11-28 13:11:25, "Jordan Willis" <jwi...@gm...> wrote:
try running 




find ~/ -name “newpdb.pdb” 




On Nov 27, 2015, at 9:08 PM, Smith Liu <smi...@16...> wrote:



Dear All,


Osvaldo is new here for this question, so I repeat it a little. By pymol I open a pdb and orient it and I want to save the oriented pdb. First I input command "orient" after load the pdb, then I input command "run save_trannsforme.py all, newpdb.pdb". I have tried to locate the newpdb.pdb by locate newpdb.pdb or find newpdb.pdb, even as the root user, but I cannot find the outpur newpdb.pdb. My pymol is Linux Open-Source PyMOL 1.6.X.


I am looking forward  to getting a reply from you on how to get the oriented pdb, which should be different from the original PDB I load.


Smith









At 2015-11-28 00:44:07, "Shane Caldwell" <sha...@gm...> wrote:

Hi Smith,


It will be in whatever folder pymol is launched from. If you launched pymol from a specific place, it will be that folder. If not, it might be in the system files for pymol, which will depend on your operating system and architecture.


Shane





Shane Caldwell

McGill University


On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <smi...@16...> wrote:

Dear All，


Once a molecule displayed in pymol, first I input command "orient", then I input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the oriented newpdb.pdb.


Will you please show me how to get the oriented newpdb.pdb?


Smith







At 2015-11-26 18:58:48, "Spencer Bliven" <spe...@gm...> wrote:

Smith–


The code is intended to be saved to a file ("save_transformed.py") and then loaded into pymol using `run /path/to/save_transformed.py`. There's some general info on running pymol scripts: Simple_ScriptingRunning_Scripts


The script defines a new command which can be run e.g. `save_transformed <object>, <file>`. You don't have to replace anything in the script yourself.


Note that the save_transformed command modifies the object it's run on, so you might want to run it on a backup copy by first calling `create <object>_backup, <object>`


-Spencer



On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smi...@16...> wrote:

Dear All,


For get view, we get something like


 set_view (\
       0.999876618,   -0.000452542,   -0.015699286,\
       0.000446742,    0.999999821,   -0.000372844,\
       0.015699454,    0.000365782,    0.999876678,\
       0.000000000,    0.000000000, -150.258514404,\
       11.842411041,   20.648729324,    8.775371552,\
       118.464958191,  182.052062988,    0.000000000 )
 
For save trasformed pdb file, we need sonething like


ttt = [m[0], m[1], m[2], 0.0,
           m[3], m[4], m[5], 0.0,
           m[6], m[7], m[8], 0.0,
           0.0,   0.0,  0.0, 1.0]
Will you please show me how to replace m[0], m[1].... from what we get by get_view? Which item is which item?


In addition, for the save_transformed.py, the last sentence is "cmd.extend('save_transformed',save_transformed)". Should we replace the second save_transformed with something, for example *.pdb? Ortherwise how to get the output modified PDB?



I am looking forward to getting a reply from you.


Smith



















At 2015-11-26 14:24:15, "Andreas Forster" <doc...@gm...> wrote:

http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures





Andreas




On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16...> wrote:


Dear Shane,



get_view is a nice command. Is any way to change the original PDB based on what we get by set_view to get the new pdb?


Smith








At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm...> wrote:

Hi Smith,


You can type

>get_view


and copy the output into a txt file for later use. The output set_view command will return the window to the same camera settings


Shane



Shane Caldwell

McGill University


On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16...> wrote:

Dear All,


Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented?


Smith



 


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try running 


find ~/ -name “newpdb.pdb” 


> On Nov 27, 2015, at 9:08 PM, Smith Liu <smi...@16...> wrote:
> 
> 
> Dear All,
> 
> Osvaldo is new here for this question, so I repeat it a little. By pymol I open a pdb and orient it and I want to save the oriented pdb. First I input command "orient" after load the pdb, then I input command "run save_trannsforme.py all, newpdb.pdb". I have tried to locate the newpdb.pdb by locate newpdb.pdb or find newpdb.pdb, even as the root user, but I cannot find the outpur newpdb.pdb. My pymol is Linux Open-Source PyMOL 1.6.X.
> 
> I am looking forward  to getting a reply from you on how to get the oriented pdb, which should be different from the original PDB I load.
> 
> Smith
> 
> 
> 
> 
> 
> 
> At 2015-11-28 00:44:07, "Shane Caldwell" <sha...@gm...> wrote:
> Hi Smith,
> 
> It will be in whatever folder pymol is launched from. If you launched pymol from a specific place, it will be that folder. If not, it might be in the system files for pymol, which will depend on your operating system and architecture.
> 
> Shane
> 
> 
> Shane Caldwell
> McGill University
> 
> On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
> Dear All，
> 
> Once a molecule displayed in pymol, first I input command "orient", then I input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the oriented newpdb.pdb.
> 
> Will you please show me how to get the oriented newpdb.pdb?
> 
> Smith
> 
> 
> 
> 
> 
> At 2015-11-26 18:58:48, "Spencer Bliven" <spe...@gm... <mailto:spe...@gm...>> wrote:
> Smith–
> 
> The code is intended to be saved to a file ("save_transformed.py") and then loaded into pymol using `run /path/to/save_transformed.py`. There's some general info on running pymol scripts: Simple_Scripting <" rel="nofollow">http://pymolwiki.org/index.php/Simple_Scripting> Running_Scripts <" rel="nofollow">http://pymolwiki.org/index.php/Running_Scripts>
> 
> The script defines a new command which can be run e.g. `save_transformed <object>, <file>`. You don't have to replace anything in the script yourself.
> 
> Note that the save_transformed command modifies the object it's run on, so you might want to run it on a backup copy by first calling `create <object>_backup, <object>`
> 
> -Spencer
> 
> On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
> Dear All,
> 
> For get view, we get something like
> 
>  set_view (\
>        0.999876618,   -0.000452542,   -0.015699286,\
>        0.000446742,    0.999999821,   -0.000372844,\
>        0.015699454,    0.000365782,    0.999876678,\
>        0.000000000,    0.000000000, -150.258514404,\
>        11.842411041,   20.648729324,    8.775371552,\
>        118.464958191,  182.052062988,    0.000000000 )
>  
> For save trasformed pdb file, we need sonething like
> 
> ttt = [m[0], m[1], m[2], 0.0,
>            m[3], m[4], m[5], 0.0,
>            m[6], m[7], m[8], 0.0,
>            0.0,   0.0,  0.0, 1.0]
> Will you please show me how to replace m[0], m[1].... from what we get by get_view? Which item is which item?
> 
> In addition, for the save_transformed.py, the last sentence is "cmd.extend('save_transformed',save_transformed)". Should we replace the second save_transformed with something, for example *.pdb? Ortherwise how to get the output modified PDB?
> 
> 
> I am looking forward to getting a reply from you.
> 
> Smith
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> At 2015-11-26 14:24:15, "Andreas Forster" <doc...@gm... <mailto:doc...@gm...>> wrote:
> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures <" rel="nofollow">http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures>
> 
> 
> Andreas
> 
> 
> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
> Dear Shane,
> 
> 
> get_view is a nice command. Is any way to change the original PDB based on what we get by set_view to get the new pdb?
> 
> Smith
> 
> 
> 
> 
> 
> 
> At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm... <mailto:sha...@gm...>> wrote:
> Hi Smith,
> 
> You can type 
> 
> >get_view
> 
> and copy the output into a txt file for later use. The output set_view command will return the window to the same camera settings
> 
> Shane
> 
> Shane Caldwell
> McGill University
> 
> On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16... <mailto:smi...@16...>> wrote:
> Dear All,
> 
> Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented?
> 
> Smith
> 
> 
>  
> 
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
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> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
> 
> 
> 
>  
> 
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 <" rel="nofollow">http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140>
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> 
> 
> 
>  
> 
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 <" rel="nofollow">http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140>
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> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
> 
> 
> 
>  
> 
> 
> 
>  
> ------------------------------------------------------------------------------
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> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Dear All,


Osvaldo is new here for this question, so I repeat it a little. By pymol I open a pdb and orient it and I want to save the oriented pdb. First I input command "orient" after load the pdb, then I input command "run save_trannsforme.py all, newpdb.pdb". I have tried to locate the newpdb.pdb by locate newpdb.pdb or find newpdb.pdb, even as the root user, but I cannot find the outpur newpdb.pdb. My pymol is Linux Open-Source PyMOL 1.6.X.


I am looking forward  to getting a reply from you on how to get the oriented pdb, which should be different from the original PDB I load.


Smith









At 2015-11-28 00:44:07, "Shane Caldwell" <sha...@gm...> wrote:

Hi Smith,


It will be in whatever folder pymol is launched from. If you launched pymol from a specific place, it will be that folder. If not, it might be in the system files for pymol, which will depend on your operating system and architecture.


Shane





Shane Caldwell

McGill University


On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <smi...@16...> wrote:

Dear All，


Once a molecule displayed in pymol, first I input command "orient", then I input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the oriented newpdb.pdb.


Will you please show me how to get the oriented newpdb.pdb?


Smith







At 2015-11-26 18:58:48, "Spencer Bliven" <spe...@gm...> wrote:

Smith–


The code is intended to be saved to a file ("save_transformed.py") and then loaded into pymol using `run /path/to/save_transformed.py`. There's some general info on running pymol scripts: Simple_ScriptingRunning_Scripts


The script defines a new command which can be run e.g. `save_transformed <object>, <file>`. You don't have to replace anything in the script yourself.


Note that the save_transformed command modifies the object it's run on, so you might want to run it on a backup copy by first calling `create <object>_backup, <object>`


-Spencer



On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smi...@16...> wrote:

Dear All,


For get view, we get something like


 set_view (\
       0.999876618,   -0.000452542,   -0.015699286,\
       0.000446742,    0.999999821,   -0.000372844,\
       0.015699454,    0.000365782,    0.999876678,\
       0.000000000,    0.000000000, -150.258514404,\
       11.842411041,   20.648729324,    8.775371552,\
       118.464958191,  182.052062988,    0.000000000 )
 
For save trasformed pdb file, we need sonething like


ttt = [m[0], m[1], m[2], 0.0,
           m[3], m[4], m[5], 0.0,
           m[6], m[7], m[8], 0.0,
           0.0,   0.0,  0.0, 1.0]
Will you please show me how to replace m[0], m[1].... from what we get by get_view? Which item is which item?


In addition, for the save_transformed.py, the last sentence is "cmd.extend('save_transformed',save_transformed)". Should we replace the second save_transformed with something, for example *.pdb? Ortherwise how to get the output modified PDB?



I am looking forward to getting a reply from you.


Smith



















At 2015-11-26 14:24:15, "Andreas Forster" <doc...@gm...> wrote:

http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures





Andreas




On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16...> wrote:


Dear Shane,



get_view is a nice command. Is any way to change the original PDB based on what we get by set_view to get the new pdb?


Smith








At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm...> wrote:

Hi Smith,


You can type

>get_view


and copy the output into a txt file for later use. The output set_view command will return the window to the same camera settings


Shane



Shane Caldwell

McGill University


On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16...> wrote:

Dear All,


Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented?


Smith




 


------------------------------------------------------------------------------
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Hi Smith,

It will be in whatever folder pymol is launched from. If you launched pymol
from a specific place, it will be that folder. If not, it might be in the
system files for pymol, which will depend on your operating system and
architecture.

Shane


Shane Caldwell
McGill University

On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <smi...@16...> wrote:

> Dear All，
>
> Once a molecule displayed in pymol, first I input command "orient", then I
> input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the
> oriented newpdb.pdb.
>
> Will you please show me how to get the oriented newpdb.pdb?
>
> Smith
>
>
>
>
>
> At 2015-11-26 18:58:48, "Spencer Bliven" <spe...@gm...> wrote:
>
> Smith–
>
> The code is intended to be saved to a file ("save_transformed.py") and
> then loaded into pymol using `run /path/to/save_transformed.py`. There's
> some general info on running pymol scripts: Simple_Scripting
> <" rel="nofollow">http://pymolwiki.org/index.php/Simple_Scripting> Running_Scripts
> <" rel="nofollow">http://pymolwiki.org/index.php/Running_Scripts>
>
> The script defines a new command which can be run e.g. `save_transformed
> <object>, <file>`. You don't have to replace anything in the script
> yourself.
>
> Note that the save_transformed command modifies the object it's run on, so
> you might want to run it on a backup copy by first calling `create
> <object>_backup, <object>`
>
> -Spencer
>
> On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smi...@16...> wrote:
>
>> Dear All,
>>
>> For get view, we get something like
>>
>>  set_view (\
>>        0.999876618,   -0.000452542,   -0.015699286,\
>>        0.000446742,    0.999999821,   -0.000372844,\
>>        0.015699454,    0.000365782,    0.999876678,\
>>        0.000000000,    0.000000000, -150.258514404,\
>>        11.842411041,   20.648729324,    8.775371552,\
>>        118.464958191,  182.052062988,    0.000000000 )
>>
>> For save trasformed pdb file, we need sonething like
>>
>> ttt = [m[0], m[1], m[2], 0.0,
>>            m[3], m[4], m[5], 0.0,
>>            m[6], m[7], m[8], 0.0,
>>            0.0,   0.0,  0.0, 1.0]
>> Will you please show me how to replace m[0], m[1].... from what we get by
>> get_view? Which item is which item?
>>
>> In addition, for the save_transformed.py, the last sentence is
>> "cmd.extend('save_transformed',save_transformed)". Should we replace the
>> second save_transformed with something, for example *.pdb? Ortherwise how
>> to get the output modified PDB?
>>
>>
>> I am looking forward to getting a reply from you.
>>
>> Smith
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> At 2015-11-26 14:24:15, "Andreas Forster" <doc...@gm...> wrote:
>>
>> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
>>
>>
>> Andreas
>>
>>
>> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16...> wrote:
>>
>>> Dear Shane,
>>>
>>> get_view is a nice command. Is any way to change the original PDB based
>>> on what we get by set_view to get the new pdb?
>>>
>>> Smith
>>>
>>>
>>>
>>>
>>>
>>>
>>> At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm...>
>>> wrote:
>>>
>>> Hi Smith,
>>>
>>> You can type
>>>
>>> >get_view
>>>
>>> and copy the output into a txt file for later use. The output set_view
>>> command will return the window to the same camera settings
>>>
>>> Shane
>>>
>>> Shane Caldwell
>>> McGill University
>>>
>>> On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16...> wrote:
>>>
>>>> Dear All,
>>>>
>>>> Suppose the original PDB was not oriented. Once we have it oriented by
>>>> pymol, is any way we can save the new PDB oriented?
>>>>
>>>> Smith
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>>> Use one codebase in this all-in-one HTML5 development environment.
>>>> Design, debug & build mobile apps & 2D/3D high-impact games for
>>>> multiple OSs.
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyM...@li...)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>> Use one codebase in this all-in-one HTML5 development environment.
>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>>> OSs.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>> OSs.
>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
>
>

Dear All，


Once a molecule displayed in pymol, first I input command "orient", then I input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the oriented newpdb.pdb.


Will you please show me how to get the oriented newpdb.pdb?


Smith







At 2015-11-26 18:58:48, "Spencer Bliven" <spe...@gm...> wrote:

Smith–


The code is intended to be saved to a file ("save_transformed.py") and then loaded into pymol using `run /path/to/save_transformed.py`. There's some general info on running pymol scripts: Simple_ScriptingRunning_Scripts


The script defines a new command which can be run e.g. `save_transformed <object>, <file>`. You don't have to replace anything in the script yourself.


Note that the save_transformed command modifies the object it's run on, so you might want to run it on a backup copy by first calling `create <object>_backup, <object>`


-Spencer



On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smi...@16...> wrote:

Dear All,


For get view, we get something like


 set_view (\
       0.999876618,   -0.000452542,   -0.015699286,\
       0.000446742,    0.999999821,   -0.000372844,\
       0.015699454,    0.000365782,    0.999876678,\
       0.000000000,    0.000000000, -150.258514404,\
       11.842411041,   20.648729324,    8.775371552,\
       118.464958191,  182.052062988,    0.000000000 )
 
For save trasformed pdb file, we need sonething like


ttt = [m[0], m[1], m[2], 0.0,
           m[3], m[4], m[5], 0.0,
           m[6], m[7], m[8], 0.0,
           0.0,   0.0,  0.0, 1.0]
Will you please show me how to replace m[0], m[1].... from what we get by get_view? Which item is which item?


In addition, for the save_transformed.py, the last sentence is "cmd.extend('save_transformed',save_transformed)". Should we replace the second save_transformed with something, for example *.pdb? Ortherwise how to get the output modified PDB?



I am looking forward to getting a reply from you.


Smith



















At 2015-11-26 14:24:15, "Andreas Forster" <doc...@gm...> wrote:

http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures





Andreas




On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16...> wrote:


Dear Shane,



get_view is a nice command. Is any way to change the original PDB based on what we get by set_view to get the new pdb?


Smith








At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm...> wrote:

Hi Smith,


You can type

>get_view


and copy the output into a txt file for later use. The output set_view command will return the window to the same camera settings


Shane



Shane Caldwell

McGill University


On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16...> wrote:

Dear All,


Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented?


Smith




 


------------------------------------------------------------------------------
Go from Idea to Many App Stores Faster with Intel(R) XDK
Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
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_______________________________________________
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Archives: http://www.mail-archive.com/pym...@li...







 


------------------------------------------------------------------------------
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Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
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------------------------------------------------------------------------------
Go from Idea to Many App Stores Faster with Intel(R) XDK
Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
_______________________________________________
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Archives: http://www.mail-archive.com/pym...@li...

Smith–

The code is intended to be saved to a file ("save_transformed.py") and then
loaded into pymol using `run /path/to/save_transformed.py`. There's some
general info on running pymol scripts: Simple_Scripting
<" rel="nofollow">http://pymolwiki.org/index.php/Simple_Scripting> Running_Scripts
<" rel="nofollow">http://pymolwiki.org/index.php/Running_Scripts>

The script defines a new command which can be run e.g. `save_transformed
<object>, <file>`. You don't have to replace anything in the script
yourself.

Note that the save_transformed command modifies the object it's run on, so
you might want to run it on a backup copy by first calling `create
<object>_backup, <object>`

-Spencer

On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smi...@16...> wrote:

> Dear All,
>
> For get view, we get something like
>
>  set_view (\
>        0.999876618,   -0.000452542,   -0.015699286,\
>        0.000446742,    0.999999821,   -0.000372844,\
>        0.015699454,    0.000365782,    0.999876678,\
>        0.000000000,    0.000000000, -150.258514404,\
>        11.842411041,   20.648729324,    8.775371552,\
>        118.464958191,  182.052062988,    0.000000000 )
>
> For save trasformed pdb file, we need sonething like
>
> ttt = [m[0], m[1], m[2], 0.0,
>            m[3], m[4], m[5], 0.0,
>            m[6], m[7], m[8], 0.0,
>            0.0,   0.0,  0.0, 1.0]
> Will you please show me how to replace m[0], m[1].... from what we get by
> get_view? Which item is which item?
>
> In addition, for the save_transformed.py, the last sentence is
> "cmd.extend('save_transformed',save_transformed)". Should we replace the
> second save_transformed with something, for example *.pdb? Ortherwise how
> to get the output modified PDB?
>
>
> I am looking forward to getting a reply from you.
>
> Smith
>
>
>
>
>
>
>
>
>
> At 2015-11-26 14:24:15, "Andreas Forster" <doc...@gm...> wrote:
>
> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
>
>
> Andreas
>
>
> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16...> wrote:
>
>> Dear Shane,
>>
>> get_view is a nice command. Is any way to change the original PDB based
>> on what we get by set_view to get the new pdb?
>>
>> Smith
>>
>>
>>
>>
>>
>>
>> At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm...>
>> wrote:
>>
>> Hi Smith,
>>
>> You can type
>>
>> >get_view
>>
>> and copy the output into a txt file for later use. The output set_view
>> command will return the window to the same camera settings
>>
>> Shane
>>
>> Shane Caldwell
>> McGill University
>>
>> On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16...> wrote:
>>
>>> Dear All,
>>>
>>> Suppose the original PDB was not oriented. Once we have it oriented by
>>> pymol, is any way we can save the new PDB oriented?
>>>
>>> Smith
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>> Use one codebase in this all-in-one HTML5 development environment.
>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>>> OSs.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>> OSs.
>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
> OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Dear All,


For get view, we get something like


 set_view (\
       0.999876618,   -0.000452542,   -0.015699286,\
       0.000446742,    0.999999821,   -0.000372844,\
       0.015699454,    0.000365782,    0.999876678,\
       0.000000000,    0.000000000, -150.258514404,\
       11.842411041,   20.648729324,    8.775371552,\
       118.464958191,  182.052062988,    0.000000000 )
 
For save trasformed pdb file, we need sonething like


ttt = [m[0], m[1], m[2], 0.0,
           m[3], m[4], m[5], 0.0,
           m[6], m[7], m[8], 0.0,
           0.0,   0.0,  0.0, 1.0]
Will you please show me how to replace m[0], m[1].... from what we get by get_view? Which item is which item?


In addition, for the save_transformed.py, the last sentence is "cmd.extend('save_transformed',save_transformed)". Should we replace the second save_transformed with something, for example *.pdb? Ortherwise how to get the output modified PDB?



I am looking forward to getting a reply from you.


Smith



















At 2015-11-26 14:24:15, "Andreas Forster" <doc...@gm...> wrote:

http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures





Andreas




On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16...> wrote:


Dear Shane,



get_view is a nice command. Is any way to change the original PDB based on what we get by set_view to get the new pdb?


Smith








At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm...> wrote:

Hi Smith,


You can type

>get_view


and copy the output into a txt file for later use. The output set_view command will return the window to the same camera settings


Shane



Shane Caldwell

McGill University


On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16...> wrote:

Dear All,


Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented?


Smith




 


------------------------------------------------------------------------------
Go from Idea to Many App Stores Faster with Intel(R) XDK
Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
_______________________________________________
PyMOL-users mailing list (PyM...@li...)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pym...@li...







 


------------------------------------------------------------------------------
Go from Idea to Many App Stores Faster with Intel(R) XDK
Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
_______________________________________________
PyMOL-users mailing list (PyM...@li...)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pym...@li...

http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures


Andreas


On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smi...@16...> wrote:

> Dear Shane,
>
> get_view is a nice command. Is any way to change the original PDB based on
> what we get by set_view to get the new pdb?
>
> Smith
>
>
>
>
>
>
> At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm...>
> wrote:
>
> Hi Smith,
>
> You can type
>
> >get_view
>
> and copy the output into a txt file for later use. The output set_view
> command will return the window to the same camera settings
>
> Shane
>
> Shane Caldwell
> McGill University
>
> On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16...> wrote:
>
>> Dear All,
>>
>> Suppose the original PDB was not oriented. Once we have it oriented by
>> pymol, is any way we can save the new PDB oriented?
>>
>> Smith
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>> OSs.
>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
> OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Dear Shane,



get_view is a nice command. Is any way to change the original PDB based on what we get by set_view to get the new pdb?


Smith








At 2015-11-26 03:54:32, "Shane Caldwell" <sha...@gm...> wrote:

Hi Smith,


You can type

>get_view


and copy the output into a txt file for later use. The output set_view command will return the window to the same camera settings


Shane



Shane Caldwell

McGill University


On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16...> wrote:

Dear All,


Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented?


Smith




 


------------------------------------------------------------------------------
Go from Idea to Many App Stores Faster with Intel(R) XDK
Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
_______________________________________________
PyMOL-users mailing list (PyM...@li...)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pym...@li...

http://pymolwiki.org/index.php/Save ??

-David

> On Nov 24, 2015, at 9:45 PM, Smith Liu <smi...@16...> wrote:
> 
> Dear All,
> 
> Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented?
> 
> Smith
> 
> 
>  
> 
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hi Smith,

You can type

>get_view

and copy the output into a txt file for later use. The output set_view
command will return the window to the same camera settings

Shane

Shane Caldwell
McGill University

On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smi...@16...> wrote:

> Dear All,
>
> Suppose the original PDB was not oriented. Once we have it oriented by
> pymol, is any way we can save the new PDB oriented?
>
> Smith
>
>
>
>
>
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
> OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Dear All,


Suppose the original PDB was not oriented. Once we have it oriented by pymol, is any way we can save the new PDB oriented?


Smith