pymol-users Mailing List for PyMOL Molecular Graphics System

The quick answer is "Don't use an evaluation build".

You have 3 main options:
1) become a sponsor and get builds of the latest code
http://pymol.org/funding.html
2) use the free builds that are several years old http://pymol.org/rel/099/
3) build pymol from source.  There are instructions on
http://www.pymolwiki.org/ for building on windows, mac, and  linux,
and solutions to many common problems you might face can be found by
searching the archives of the list (linked to at the bottom of each
message).  If you run into any problems not discussed in the wiki or
archives, people around here are nice and will likely help you out.

-David

On Thu, Apr 29, 2010 at 6:03 PM, victor kenyon <vic...@gm...> wrote:
> hi all,
> i am an academic using pymol and the new build places a "for
> evaluation only" graphic on top of the rendered structure. not very
> helpful for presentations, publications and the like. how do i
> circumvent this without using chimera to generate my images for pubs.
> thanks.
> victor
>
> ------------------------------------------------------------------------------
> _______________________________________________
> 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 victor,

if you are on windows and need the latest pymol version, please take a look
at christoph's pymol builds (thanks christoph!):

http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol

best,
shiven

On Thu, Apr 29, 2010 at 6:32 PM, Nathaniel Echols <
nat...@gm...> wrote:

> On Thu, Apr 29, 2010 at 3:03 PM, victor kenyon <vic...@gm...>wrote:
>
>> i am an academic using pymol and the new build places a "for
>> evaluation only" graphic on top of the rendered structure. not very
>> helpful for presentations, publications and the like. how do i
>> circumvent this without using chimera to generate my images for pubs.
>>
>
> Use the open-source version, I would be very surprised if that overlays
> anything.   Or download one of the builds of version 0.99, which is missing
> some nifty features but still more than adequate for publication graphics as
> long as you don't need to show anisotropic Bs.
>
> http://www.pymol.org/rel/099/
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

On Thu, Apr 29, 2010 at 3:03 PM, victor kenyon <vic...@gm...> wrote:

> i am an academic using pymol and the new build places a "for
> evaluation only" graphic on top of the rendered structure. not very
> helpful for presentations, publications and the like. how do i
> circumvent this without using chimera to generate my images for pubs.
>

Use the open-source version, I would be very surprised if that overlays
anything.   Or download one of the builds of version 0.99, which is missing
some nifty features but still more than adequate for publication graphics as
long as you don't need to show anisotropic Bs.

http://www.pymol.org/rel/099/

hi all,
i am an academic using pymol and the new build places a "for
evaluation only" graphic on top of the rendered structure. not very
helpful for presentations, publications and the like. how do i
circumvent this without using chimera to generate my images for pubs.
thanks.
victor

Dear Jason,

Thank you for you quick reply!
And This problem is solved!

Yours,
Zhang Cun

On Thu, Apr 29, 2010 at 9:31 PM, Jason Vertrees
<jas...@sc...> wrote:
> Hi Cun,
>
> That's a good start.  Just a couple things needs to be changed.
> First, frames don't track coordinates, states do.  Frames are for
> movies; states are for coordinates.  Next, instead of using center,
> use the origin command with the state parameter specified.  Here's
> example code for 1NMR a multi-state protein, adjust his for your
> application:
>
> python
> cmd.fetch("1nmr", async=0)
> coord=[]
> for i in range(1,cmd.count_states()+1):
>  cmd.origin("i. 1-24", state=i)
>  coord.append(cmd.get_position())
> print coord
> python end
>
> Cheers,
>
> -- Jason
>
> On Thu, Apr 29, 2010 at 8:58 AM, Cun Zhang <apz...@gm...> wrote:
>> hi,
>> I have a pdb file with serveral frames, I hope to get the trajectory
>> of the center of a selected group of atoms.
>> I use the following commands, but return the same coord.
>>
>> cmd.load("a.pdb")
>> coord=[]
>> for i in range(cmd.count_frames()):
>>   cmd.frame(i+1)
>>   cmd.center('id 1-24')
>>   coord.append(cmd.get_position())
>>
>>
>> What should I do?
>>
>> Thank you!
>>
>> Zhang Cun
>>
>> --
>> Blog: http://www.edwardpku.com/cun
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>



-- 
Blog: http://blog.4message.net

Hi Cun,

That's a good start.  Just a couple things needs to be changed.
First, frames don't track coordinates, states do.  Frames are for
movies; states are for coordinates.  Next, instead of using center,
use the origin command with the state parameter specified.  Here's
example code for 1NMR a multi-state protein, adjust his for your
application:

python
cmd.fetch("1nmr", async=0)
coord=[]
for i in range(1,cmd.count_states()+1):
 cmd.origin("i. 1-24", state=i)
 coord.append(cmd.get_position())
print coord
python end

Cheers,

-- Jason

On Thu, Apr 29, 2010 at 8:58 AM, Cun Zhang <apz...@gm...> wrote:
> hi,
> I have a pdb file with serveral frames, I hope to get the trajectory
> of the center of a selected group of atoms.
> I use the following commands, but return the same coord.
>
> cmd.load("a.pdb")
> coord=[]
> for i in range(cmd.count_frames()):
>   cmd.frame(i+1)
>   cmd.center('id 1-24')
>   coord.append(cmd.get_position())
>
>
> What should I do?
>
> Thank you!
>
> Zhang Cun
>
> --
> Blog: http://www.edwardpku.com/cun
>
> ------------------------------------------------------------------------------
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

hi,
I have a pdb file with serveral frames, I hope to get the trajectory
of the center of a selected group of atoms.
I use the following commands, but return the same coord.

cmd.load("a.pdb")
coord=[]
for i in range(cmd.count_frames()):
   cmd.frame(i+1)
   cmd.center('id 1-24')
   coord.append(cmd.get_position())


What should I do?

Thank you!

Zhang Cun

-- 
Blog: http://www.edwardpku.com/cun

Hi Om,

Try doing this:

load subset.sdf
split_states subset, 1
dele subset
set grid_mode, 1
label id 1, model

I am guessing the resulting view is what you had in mind...

You may have to increase the label_size to make the labels visible in
grid_mode with the command:
set label_size, 30

Best,
Shiven



On Tue, Apr 27, 2010 at 4:33 PM, Jason Vertrees <
jas...@sc...> wrote:

> Om,
>
> I suggest you first read about how labels work in PyMOL.  There's some
> great help here http://pymolwiki.org/index.php/Label.  In fact, check
> out the entire PyMOLWiki category for labeling.
>
> To do what I think you want, you could simply do:
>
> load subset.sdf
> set all_states
> label id 1, resn
>
> Good luck,
>
> -- Jason
>
> On Tue, Apr 27, 2010 at 3:33 PM, Om <omp...@gm...> wrote:
> > Hello,
> >
> > I wish to read a SDF file (multiple molecules) into pymol where title of
> the
> > molecule(s) displayed below it. I tried residueName label etc, its not
> > working. I have attached sample file
> >
> > Thanks
> > Om Prakash
> > School of Information Technology,
> > Jawaharlal Nehru University
> > New Delhi-110067
> > India
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> >
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> 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 Carsten,

How about the following:

# create new structures using alt '' and alt 'a'
# and then alt '' and alt 'b'
create confA, yourProtein and (not alt 'b')
create confB, yourProtein and (not alt 'a')

# update representation
hide
show cartoons confA+confB

You can also repeat the name and use state flags to make a two-state protein.

Cheers,

-- Jason

On Tue, Apr 27, 2010 at 3:51 PM, Schubert, Carsten [PRDUS]
<CSC...@it...> wrote:
> Seemingly simple, but I can’t figure it out:
>
> I modeled a loop in 2 alternate conformations and want to display both of
> the conformations in a ribbon or cartoon. The selection “show ribbon, prot
> and alt B” does not do the trick. The selection syntax must be correct since
> “color red, prot and alt B; show lines prot and alt B” works. I could show
> only the backbone atoms in a pinch, but that is not really what I want. Hard
> to imagine that this is a limitation in PyMol nobody noticed over the years.
>
> Cheers
>
>         Carsten
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Om,

I suggest you first read about how labels work in PyMOL.  There's some
great help here http://pymolwiki.org/index.php/Label.  In fact, check
out the entire PyMOLWiki category for labeling.

To do what I think you want, you could simply do:

load subset.sdf
set all_states
label id 1, resn

Good luck,

-- Jason

On Tue, Apr 27, 2010 at 3:33 PM, Om <omp...@gm...> wrote:
> Hello,
>
> I wish to read a SDF file (multiple molecules) into pymol where title of the
> molecule(s) displayed below it. I tried residueName label etc, its not
> working. I have attached sample file
>
> Thanks
> Om Prakash
> School of Information Technology,
> Jawaharlal Nehru University
> New Delhi-110067
> India
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Seemingly simple, but I can't figure it out: 
I modeled a loop in 2 alternate conformations and want to display both
of the conformations in a ribbon or cartoon. The selection "show ribbon,
prot and alt B" does not do the trick. The selection syntax must be
correct since "color red, prot and alt B; show lines prot and alt B"
works. I could show only the backbone atoms in a pinch, but that is not
really what I want. Hard to imagine that this is a limitation in PyMol
nobody noticed over the years.

Cheers

	Carsten

Dear PyMol Users,

I am  trying to install PyMol using Cygwin as described on the PyMol Wiki. I
believe I have installed all the modules for cygwin that the Wiki said are
required, however I am getting the following error message when trying to
run the "python setup.py install" command in the Cygwin bash shell:

$ python setup.py install
running install
running build
running build_py
running build_ext
building 'pymol._cmd' extension
gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
-D_PYMOL_MODULE -DCYGWIN -D_PYMOL_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2
-Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/python2.5 -c
modules/cealign/src/ccealignmodule.cpp -o
build/temp.cygwin-1.7.5-i686-2.5/modules/cealign/src/ccealignmodule.o
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for
Ada/C/ObjC but not for C++
In file included from modules/cealign/src/ccealignmodule.cpp:32:
modules/cealign/src/ccealignmodule.H:38:21: error: jama_lu.h: No such file
or directory
modules/cealign/src/ccealignmodule.H:40:22: error: jama_svd.h: No such file
or directory
modules/cealign/src/ccealignmodule.cpp: In function 'PyObject*
findBest(cePoint*, cePoint*, afp**, int, int, int)':
modules/cealign/src/ccealignmodule.cpp:521: error: 'JAMA' has not been
declared
modules/cealign/src/ccealignmodule.cpp:521: error: expected
primary-expression before 'double'
modules/cealign/src/ccealignmodule.cpp:521: error: expected `;' before
'double'
modules/cealign/src/ccealignmodule.cpp:532: error: 'svd' was not declared in
this scope
modules/cealign/src/ccealignmodule.cpp:543: error: 'JAMA' has not been
declared
modules/cealign/src/ccealignmodule.cpp:543: error: expected
primary-expression before 'double'
modules/cealign/src/ccealignmodule.cpp:543: error: expected `;' before
'double'
modules/cealign/src/ccealignmodule.cpp:544: error: 'JAMA' has not been
declared
modules/cealign/src/ccealignmodule.cpp:544: error: expected
primary-expression before 'double'
modules/cealign/src/ccealignmodule.cpp:544: error: expected `;' before
'double'
modules/cealign/src/ccealignmodule.cpp:546: error: 'LU_W' was not declared
in this scope
modules/cealign/src/ccealignmodule.cpp:546: error: 'LU_Vt' was not declared
in this scope
modules/cealign/src/ccealignmodule.cpp:553: warning: comparison between
signed and unsigned integer expressions
modules/cealign/src/ccealignmodule.cpp: In function 'TNT::Array2D<double>
transpose(const TNT::Array2D<double>&)':
modules/cealign/src/ccealignmodule.cpp:628: warning: comparison between
signed and unsigned integer expressions
modules/cealign/src/ccealignmodule.cpp:629: warning: comparison between
signed and unsigned integer expressions
error: command 'gcc' failed with exit status 1

Maia,

Looks like the Ubuntu package is older.  Bumps just shows the vdw
overlaps, you can work without it.

-- Jason

On Fri, Apr 23, 2010 at 3:02 PM, Maia Cherney <ch...@ua...> wrote:
> Hi Jason,
>
> 1. I am wondering if I have the latest version of pymol. I got it via ubuntu
> package. How do I update the pymol version?
>
> 2. I was trying to do some procedures from the Warren's letter:
>
> Builder use:
>
> (1) activate the builder by clicking on the "Builder" button on the
> upper window
>
> (2) click the "Bumps" checkbox
>
> (3) click the "Sculpt" button
>
>
> When I click on the "Builder" button on the upper window, I do not have the
> "Bumps" checkbox and the "Sculpt" button.
> I have the autopick, the autozoom and the valence checkboxes.
>
> That is why I am wondering if I have the same version of pymol.
>
> Could you also give me some explanation what are  polymer or organic,  byres
> (organic expand 4), and flag fix, not organic
>
>
> Maia
>
>
> Jason Vertrees wrote:
>>
>> Maia,
>>
>>
>>>
>>> 1. How can I undo a plugin. By mistake I tried to plugin a program using
>>> a
>>> wrong file and now I get an error message every time I open pymol.
>>>
>>
>> Newer versions of PyMOL have a menu option to remove plugins: Plugin >
>> Manage Plugins > Remove.  You can also remove a plugin by simply
>> removing the plugin file.  PyMOL stores plugins in the Python
>> distribution's "site-packages/pmg_tk/startup" directory.  My Mac OS X
>> Fink build has them here:
>>   /sw/lib/python2.5/site-packages/pmg_tk/startup/
>> for example.
>>
>> If you're on Mac or Linux you can try
>>  locate pmg_tk/startup
>> or
>>  find / -name yourPlugin.py
>> for hints as to the plugin's installed location.
>>
>>
>>
>>>
>>> 2. Which plugin allows me to move one structure relative to another. (I
>>> want
>>> to do manual docking of one structure into another).
>>>
>>
>> You don't need a plugin to move objects.  Just use SHIFT-middle-mouse
>> button drag, while in editing mode.  If you're starting from one
>> object (eg. protein and ligand come from one file) then split them up:
>>
>> # example
>> fetch 1oky, async=0
>>
>> # the protein and ligand are one object; now make them two
>> extract myLigand, org
>>
>> Now you can move the myLigand object independently of other objects.
>>
>> Good luck,
>>
>> -- Jason
>>
>>
>>>
>>> Maia
>>>
>>> Jason Vertrees wrote:
>>>
>>>>
>>>> PyMOLers,
>>>>
>>>> Due to the popularity of using PyMOL as a portal to other programs and
>>>> integrating programs with PyMOL, we are developing a new Plugin
>>>> Architecture for PyMOL.  We have dedicated a page on the PyMOLWiki
>>>>   http://www.pymolwiki.org/index.php/PluginArchitecture
>>>> for this discussion.
>>>>
>>>> If you have a desire to be involved in how the architecture is
>>>> developed please add your contact information to that page (or email,
>>>> personally).  Even if you don't care much about helping out, you might
>>>> want to stop by and let us know which plugin systems you like and
>>>> which you don't.
>>>>
>>>> Thanks,
>>>>
>>>> -- Jason
>>>>
>>>>
>>>>
>>
>>
>>
>>
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Jason,

1. I am wondering if I have the latest version of pymol. I got it via 
ubuntu package. How do I update the pymol version?

2. I was trying to do some procedures from the Warren's letter:

Builder use:

(1) activate the builder by clicking on the "Builder" button on the
upper window
 
(2) click the "Bumps" checkbox
 
(3) click the "Sculpt" button


When I click on the "Builder" button on the upper window, I do not have 
the "Bumps" checkbox and the "Sculpt" button.
I have the autopick, the autozoom and the valence checkboxes.

That is why I am wondering if I have the same version of pymol.

Could you also give me some explanation what are  polymer or organic,  byres (organic expand 4), and flag fix, not organic


Maia


Jason Vertrees wrote:
> Maia,
>
>   
>> 1. How can I undo a plugin. By mistake I tried to plugin a program using a
>> wrong file and now I get an error message every time I open pymol.
>>     
>
> Newer versions of PyMOL have a menu option to remove plugins: Plugin >
> Manage Plugins > Remove.  You can also remove a plugin by simply
> removing the plugin file.  PyMOL stores plugins in the Python
> distribution's "site-packages/pmg_tk/startup" directory.  My Mac OS X
> Fink build has them here:
>    /sw/lib/python2.5/site-packages/pmg_tk/startup/
> for example.
>
> If you're on Mac or Linux you can try
>   locate pmg_tk/startup
> or
>   find / -name yourPlugin.py
> for hints as to the plugin's installed location.
>
>
>   
>> 2. Which plugin allows me to move one structure relative to another. (I want
>> to do manual docking of one structure into another).
>>     
>
> You don't need a plugin to move objects.  Just use SHIFT-middle-mouse
> button drag, while in editing mode.  If you're starting from one
> object (eg. protein and ligand come from one file) then split them up:
>
> # example
> fetch 1oky, async=0
>
> # the protein and ligand are one object; now make them two
> extract myLigand, org
>
> Now you can move the myLigand object independently of other objects.
>
> Good luck,
>
> -- Jason
>
>   
>> Maia
>>
>> Jason Vertrees wrote:
>>     
>>> PyMOLers,
>>>
>>> Due to the popularity of using PyMOL as a portal to other programs and
>>> integrating programs with PyMOL, we are developing a new Plugin
>>> Architecture for PyMOL.  We have dedicated a page on the PyMOLWiki
>>>    http://www.pymolwiki.org/index.php/PluginArchitecture
>>> for this discussion.
>>>
>>> If you have a desire to be involved in how the architecture is
>>> developed please add your contact information to that page (or email,
>>> personally).  Even if you don't care much about helping out, you might
>>> want to stop by and let us know which plugin systems you like and
>>> which you don't.
>>>
>>> Thanks,
>>>
>>> -- Jason
>>>
>>>
>>>       
>
>
>
>   

Dear all,

I just got a MacBookPro.
I have two questions:
How to get the keyboard shortcuts in coot or pymol up, e.g. <alt>F to
open the file dialog.

and

whenever I connect a zalman 220 (stereo ready) monitor to the mac using
a miniDisplayPort to DVI
adapter, the monitor is not recognized and so it is completely dark. The
Mac does not show the monitor in the dialogues but an error message.

-- 
Joachim

On 23/04/10 10:04, Greg Landrum wrote:
> The best part is that you sent this message, where you tell Dave that
> he shouldn't post unsubscribe requests to the list, to the list.
> 
> 

I recognised that it is a common problem with unsubscriptions from
mailing lists, so a public reminder how to unsubscribe can't be bad.

justin

On 23/04/10 06:00, Charles David Stout wrote:
> Dear PyMol developers,
> 
> PyMol is an awesome program, but I'm a casual user.  Please remove my 
> email address from your bulletin board.
> Thanks
> Dave Stout
> 4-22-10
> 
> da...@sc...
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

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justin

On 23/04/10 06:00, Charles David Stout wrote:
> Dear PyMol developers,
> 
> PyMol is an awesome program, but I'm a casual user.  Please remove my 
> email address from your bulletin board.
> Thanks
> Dave Stout
> 4-22-10
> 
> da...@sc...
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
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justin

Dear PyMol developers,

PyMol is an awesome program, but I'm a casual user.  Please remove my 
email address from your bulletin board.
Thanks
Dave Stout
4-22-10

da...@sc...

Thank, Robert, Jason.
Finally I figured this out with your help.

Maia

Robert Campbell wrote:
> Hi Maia,
>
> Just to add to what Jason said:
>
> On Thu, 22 Apr 2010 17:16:41 -0400, Jason Vertrees
> <jas...@sc...> wrote:
>
>   
>>> 2. Which plugin allows me to move one structure relative to another. (I
>>> want to do manual docking of one structure into another).
>>>       
>> You don't need a plugin to move objects.  Just use SHIFT-middle-mouse
>> button drag, while in editing mode.  If you're starting from one
>> object (eg. protein and ligand come from one file) then split them up:
>>     
>
> In case it isn't obvious to you, you can switch between "viewing" mode and
> "editing" mode simply by left clicking in the bottom-right region of the main
> PyMOL window where the mouse button functions are described.
>
> Cheers,
> Rob
>
>   

Hi Maia,

Just to add to what Jason said:

On Thu, 22 Apr 2010 17:16:41 -0400, Jason Vertrees
<jas...@sc...> wrote:

> > 2. Which plugin allows me to move one structure relative to another. (I
> > want to do manual docking of one structure into another).
> 
> You don't need a plugin to move objects.  Just use SHIFT-middle-mouse
> button drag, while in editing mode.  If you're starting from one
> object (eg. protein and ligand come from one file) then split them up:

In case it isn't obvious to you, you can switch between "viewing" mode and
"editing" mode simply by left clicking in the bottom-right region of the main
PyMOL window where the mouse button functions are described.

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Maia,

> 1. How can I undo a plugin. By mistake I tried to plugin a program using a
> wrong file and now I get an error message every time I open pymol.

Newer versions of PyMOL have a menu option to remove plugins: Plugin >
Manage Plugins > Remove.  You can also remove a plugin by simply
removing the plugin file.  PyMOL stores plugins in the Python
distribution's "site-packages/pmg_tk/startup" directory.  My Mac OS X
Fink build has them here:
   /sw/lib/python2.5/site-packages/pmg_tk/startup/
for example.

If you're on Mac or Linux you can try
  locate pmg_tk/startup
or
  find / -name yourPlugin.py
for hints as to the plugin's installed location.


> 2. Which plugin allows me to move one structure relative to another. (I want
> to do manual docking of one structure into another).

You don't need a plugin to move objects.  Just use SHIFT-middle-mouse
button drag, while in editing mode.  If you're starting from one
object (eg. protein and ligand come from one file) then split them up:

# example
fetch 1oky, async=0

# the protein and ligand are one object; now make them two
extract myLigand, org

Now you can move the myLigand object independently of other objects.

Good luck,

-- Jason

>
> Maia
>
> Jason Vertrees wrote:
>>
>> PyMOLers,
>>
>> Due to the popularity of using PyMOL as a portal to other programs and
>> integrating programs with PyMOL, we are developing a new Plugin
>> Architecture for PyMOL.  We have dedicated a page on the PyMOLWiki
>>    http://www.pymolwiki.org/index.php/PluginArchitecture
>> for this discussion.
>>
>> If you have a desire to be involved in how the architecture is
>> developed please add your contact information to that page (or email,
>> personally).  Even if you don't care much about helping out, you might
>> want to stop by and let us know which plugin systems you like and
>> which you don't.
>>
>> Thanks,
>>
>> -- Jason
>>
>>
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Jason,

1. How can I undo a plugin. By mistake I tried to plugin a program using 
a wrong file and now I get an error message every time I open pymol.

2. Which plugin allows me to move one structure relative to another. (I 
want to do manual docking of one structure into another).

Maia

Jason Vertrees wrote:
> PyMOLers,
>
> Due to the popularity of using PyMOL as a portal to other programs and
> integrating programs with PyMOL, we are developing a new Plugin
> Architecture for PyMOL.  We have dedicated a page on the PyMOLWiki
>     http://www.pymolwiki.org/index.php/PluginArchitecture
> for this discussion.
>
> If you have a desire to be involved in how the architecture is
> developed please add your contact information to that page (or email,
> personally).  Even if you don't care much about helping out, you might
> want to stop by and let us know which plugin systems you like and
> which you don't.
>
> Thanks,
>
> -- Jason
>
>   

(s/benchmark/bookmark/)

On Thu, Apr 22, 2010 at 4:12 PM, David Hall <li...@co...> wrote:
> I started a pymolwiki page for this at
> http://www.pymolwiki.org/index.php/Connect_mode so I had something to
> benchmark.  If someone knows what connect_mode=3 does, please fill it
> in.  The code in layer2/ObjectMolecule2.c is probably where to start
> if you want to take a stab at figuring it out.
>
> -David
>
> On Thu, Apr 22, 2010 at 2:43 PM, Jason Vertrees
> <jas...@sc...> wrote:
>> Hi David,
>>
>> Check out the "connect_mode" setting:
>>
>> set connect_mode, 1
>>
>> # no bonds
>>
>> fetch 1cll
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Thu, Apr 22, 2010 at 2:14 PM, David Hall <li...@co...> wrote:
>>> Is it possible to load a pdb file and have pymol skip making bonds?
>>> There's a bunch of undocumented options to load, but I don't think any
>>> of them do what I want.  I have a file where there's a bunch of
>>> jumbled atoms and there's no relation between them, just thousands in
>>> the same place and pymol spends a long time loading it presumably
>>> trying to make these bonds.
>>>
>>> -David
>>>
>>> ------------------------------------------------------------------------------
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) Jas...@sc...
>> (o) +1 (603) 374-7120
>>
>

I started a pymolwiki page for this at
http://www.pymolwiki.org/index.php/Connect_mode so I had something to
benchmark.  If someone knows what connect_mode=3 does, please fill it
in.  The code in layer2/ObjectMolecule2.c is probably where to start
if you want to take a stab at figuring it out.

-David

On Thu, Apr 22, 2010 at 2:43 PM, Jason Vertrees
<jas...@sc...> wrote:
> Hi David,
>
> Check out the "connect_mode" setting:
>
> set connect_mode, 1
>
> # no bonds
>
> fetch 1cll
>
> Cheers,
>
> -- Jason
>
> On Thu, Apr 22, 2010 at 2:14 PM, David Hall <li...@co...> wrote:
>> Is it possible to load a pdb file and have pymol skip making bonds?
>> There's a bunch of undocumented options to load, but I don't think any
>> of them do what I want.  I have a file where there's a bunch of
>> jumbled atoms and there's no relation between them, just thousands in
>> the same place and pymol spends a long time loading it presumably
>> trying to make these bonds.
>>
>> -David
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>