pymol-users Mailing List for PyMOL Molecular Graphics System

Hello, Illustrious Members!
I have a query:
Let us assume one is in possession of a particular named organic reaction.
In that reaction a set of reactants change into a set of products.
It is very easy to observe in those named reactions as to which bonds
have broken down to form other newer bonds.
Is it possible in Pymol to determine Individual Bond Dissociation
Energy for any such Bond of those reactants and products?
Regards

Hi Marko,

You may want to tweak ray_trace_gain setting:

https://pymolwiki.org/index.php/Ray_Trace_Gain

- Piotr

On Thu, May 25, 2017 at 6:53 AM, Marko Hyvonen <mh...@ca...> wrote:
> Hello Pymolers,
>
> I seem to fail to find the setting (which I recall having used before)
> to get stronger/thicker outlines in ray traced images when using mode 1,
> 2 and 3, in particular when rendering larger images. The lines seem to
> be defined as pixels, as they get thinner the bigger the image is. Is is
> possible to define this, and if so, how?
>
> many thanks in advance, Marko
>
> --
>
> Marko Hyvonen
> Department of Biochemistry, University of Cambridge
> mh...@ca...
> +44-(0)1223-766 044
> @HyvonenGroup
> http://www-cryst.bioc.cam.ac.uk/groups/hyvonen
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hello Pymolers,

I seem to fail to find the setting (which I recall having used before) 
to get stronger/thicker outlines in ray traced images when using mode 1, 
2 and 3, in particular when rendering larger images. The lines seem to 
be defined as pixels, as they get thinner the bigger the image is. Is is 
possible to define this, and if so, how?

many thanks in advance, Marko

-- 

Marko Hyvonen
Department of Biochemistry, University of Cambridge
mh...@ca...
+44-(0)1223-766 044
@HyvonenGroup
http://www-cryst.bioc.cam.ac.uk/groups/hyvonen
  

> 
> Message: 4
> Date: Wed, 24 May 2017 16:45:23 +0800 (GMT+08:00)
> From: ??? <liu...@si...>
> Subject: [PyMOL] show surface on pymol
> To: pym...@li...
> Message-ID:
> 	<1c6...@si...>
> Content-Type: text/plain; charset="gbk"
> 
> 
> Dear Madem/Sir,
> 
> I am a user of Pymol software. Pymol facilitates me a lot during my study. I have a problem and maybe need your help. I want to show surface of a ligand in which there is a methylated lysine. Other residues are OK except the methylated lysine. Could you help me to deal with this problem? Should I install any plugin that can recognize molecules like methylated lysine or anything? Thanks a lot.
> 
> Yanchao Liu
> 
> Shanghai Institute of Biochemistry and Cell Biology.
> 
> Shanghai Institutes for Biological Sciences.
> 
> Chinese Academy of Sciences. 
> 
> 320 Yueyang Road ,Shanghai 200031,China.

Dear Yanchao Liu

Try “set surface_mode,1”
With the default surface mode 0, heteroatom are not included in the surface, with surface mode 1 they are.
Of course, if you have other heterosexual-compounds like ligands and buffer components in the same object,
you might first want to either remove these or extract them to a different object.

Annemarie

It sounds like you may need to change surface mode to include hets

https://pymolwiki.org/index.php/Surface_mode

-David

> On May 24, 2017, at 4:45 AM, 刘艳超 <liu...@si...> wrote:
> 
> 
> Dear Madem/Sir,
> 
> I am a user of Pymol software. Pymol facilitates me a lot during my study. I have a problem and maybe need your help. I want to show surface of a ligand in which there is a methylated lysine. Other residues are OK except the methylated lysine. Could you help me to deal with this problem? Should I install any plugin that can recognize molecules like methylated lysine or anything? Thanks a lot.
> 
> Yanchao Liu
> 
> Shanghai Institute of Biochemistry and Cell Biology.
> 
> Shanghai Institutes for Biological Sciences.
> 
> Chinese Academy of Sciences.
> 
> 320 Yueyang Road ,Shanghai 200031,China.
> 
> 
>  
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> 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 Madem/Sir,

I am a user of Pymol software. Pymol facilitates me a lot during my study. I have a problem and maybe need your help. I want to show surface of a ligand in which there is a methylated lysine. Other residues are OK except the methylated lysine. Could you help me to deal with this problem? Should I install any plugin that can recognize molecules like methylated lysine or anything? Thanks a lot.

Yanchao Liu

Shanghai Institute of Biochemistry and Cell Biology.

Shanghai Institutes for Biological Sciences.

Chinese Academy of Sciences.

320 Yueyang Road ,Shanghai 200031,China.



 

Hi Chi,

The file needs a .py extension to be recognized as a Python script. Microsoft Windows can be tricky when it comes to changing a file extension. I recommend to follow these steps when downloading a Python file from the PyMOLWiki:

1) Visit https://pymolwiki.org/index.php/Get_raw_distances
2) Box on the right side, right click on "Download get_raw_distances.py"
3) "Save Link As..." or "Save target as..." (depends on browser)
    File name: get_raw_distances.py
    Save as type: PY File

Hope that helps.

Cheers,
  Thomas

> On May 19, 2017, at 9:41 PM, Chi Celestine <chi...@ph...> wrote:
> 
> Dear Thomas, 
> Many thanks! I copied and saved the script as a dot txt but can not run it from file> run  on pymol. Do I need yo save the file in a special folder? I am actually really new with pymol and not vey good in scripting
> 
> Thanks for your understanding 
> 
> Sincerely 
> Chi
> -------------------------------------------------
> Celestine Chi, PhD
> ETH Zürich 
> Laboratory for Physical Chemistry
> Vladimir-Prelog-Weg 2 HCI F 222
> CH-8093 Zürich
> Email: chi...@ph...
> tele: 004144 63 37510
> 
>> On May 19, 2017, at 5:33 PM, Thomas Holder <tho...@sc...> wrote:
>> 
>> Hi Celestine,
>> 
>> Did you run the "get_raw_distances.py" script first? You can do that by:
>> 
>> run https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py
>> 
>> Or better: Download it to your computer and run it from there ("run" command or "File > Run Script..." from the menu).
>> 
>> After running the script, you can use the "get_raw_distances" command.
>> 
>> Cheers,
>>  Thomas
>> 
>>> On May 19, 2017, at 2:26 PM, Chi Celestine <chi...@ph...> wrote:
>>> 
>>> Hi Thomas,
>>> I am also interesting in getting bond distances between two pairs of molecule. I tried running the commands to suggested but I get an error message e.g 
>>> When I tried the following (see below) the fist command was well executed but the second gave an error message “ SyntaxError: invalid syntax”
>>> 
>>> I got a similar error message when I tried to execute  this command D = get_raw_distances("distname”)  as well 
>>> 
>>> 
>>> Sincerely,
>>> Celestine 
>>> 
>>> Example
>>> fetch 2xwu, async=0
>>> 
>>> 
>>> 
>>> # interface polar contacts
>>> distance iface_hbonds, chain A, chain B, mode=2
>>> 
>>> 
>>> 
>>> # dump (model,index) information
>>> get_raw_distances iface_hbonds
>>> 
>>> 
>>> -------------------------------------------------
>>> Celestine Chi, PhD
>>> ETH Zürich 
>>> Laboratory for Physical Chemistry
>>> Vladimir-Prelog-Weg 2 HCI F 222
>>> CH-8093 Zürich
>>> Email: chi...@ph...
>>> tele: 004144 63 37510
>>> 
>>>> On May 19, 2017, at 1:16 PM, Thomas Holder <tho...@sc...> wrote:
>>>> 
>>>> Hi Ahmad,
>>>> 
>>>> Unfortunately there is no proper API for this. But I can think of two approaches. Note that the results can differ because the two method do slightly different h-bond detection!
>>>> 
>>>> 1) Use "cmd.find_pairs" with mode=1 on "donors" and "acceptors" selection. Example:
>>>> 
>>>> sele1 = "chain A & (donors | acceptors)"
>>>> sele2 = "chain B & (donors | acceptors)"
>>>> radius = 3.5
>>>> D = cmd.find_pairs(sele1, sele2, mode=1, cutoff=radius)
>>>> print("number of h-bonds:", len(D))
>>>> 
>>>> 1) Use "cmd.distance" and the "get_raw_distances" script. Example:
>>>> 
>>>> run https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py
>>>> 
>>>> sele1 = "chain A"
>>>> sele2 = "chain B"
>>>> radius = 3.5
>>>> cmd.distance("distname", sele1, sele2, mode=2, cutoff=radius)
>>>> D = get_raw_distances("distname")
>>>> print("number of h-bonds:", len(D))
>>>> 
>>>> See also:
>>>> https://pymolwiki.org/index.php/Get_raw_distances
>>>> https://pymolwiki.org/index.php/Distance
>>>> https://pymolwiki.org/index.php/Find_pairs
>>>> 
>>>> Hope that helps.
>>>> 
>>>> Cheers,
>>>> Thomas
>>>> 
>>>>> On May 5, 2017, at 5:08 AM, Ahmad Abdelzaher <und...@gm...> wrote:
>>>>> 
>>>>> I know I can can find the hydrogen bond interactions between a
>>>>> selection and surrounding residues within a certain radius. I would
>>>>> like to find a way to retrieve the actual count of those interactions
>>>>> per residue. How can I do it in the API?
>>>>> 
>>>>> Regards.

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear Thomas,
Many thanks! I copied and saved the script as a dot txt but can not run it from file> run  on pymol. Do I need yo save the file in a special folder? I am actually really new with pymol and not vey good in scripting

Thanks for your understanding

Sincerely
Chi
-------------------------------------------------
Celestine Chi, PhD
ETH Zürich
Laboratory for Physical Chemistry
Vladimir-Prelog-Weg 2 HCI F 222
CH-8093 Zürich
Email: chi...@ph...<mailto:chi...@ph...>
tele: 004144 63 37510

On May 19, 2017, at 5:33 PM, Thomas Holder <tho...@sc...<mailto:tho...@sc...>> wrote:

Hi Celestine,

Did you run the "get_raw_distances.py" script first? You can do that by:

run https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py

Or better: Download it to your computer and run it from there ("run" command or "File > Run Script..." from the menu).

After running the script, you can use the "get_raw_distances" command.

Cheers,
 Thomas

On May 19, 2017, at 2:26 PM, Chi Celestine <chi...@ph...<mailto:chi...@ph...>> wrote:

Hi Thomas,
I am also interesting in getting bond distances between two pairs of molecule. I tried running the commands to suggested but I get an error message e.g
When I tried the following (see below) the fist command was well executed but the second gave an error message “ SyntaxError: invalid syntax”

I got a similar error message when I tried to execute  this command D = get_raw_distances("distname”)  as well


Sincerely,
Celestine

Example
fetch 2xwu, async=0



# interface polar contacts
distance iface_hbonds, chain A, chain B, mode=2



# dump (model,index) information
get_raw_distances iface_hbonds


-------------------------------------------------
Celestine Chi, PhD
ETH Zürich
Laboratory for Physical Chemistry
Vladimir-Prelog-Weg 2 HCI F 222
CH-8093 Zürich
Email: chi...@ph...<mailto:chi...@ph...>
tele: 004144 63 37510

On May 19, 2017, at 1:16 PM, Thomas Holder <tho...@sc...<mailto:tho...@sc...>> wrote:

Hi Ahmad,

Unfortunately there is no proper API for this. But I can think of two approaches. Note that the results can differ because the two method do slightly different h-bond detection!

1) Use "cmd.find_pairs" with mode=1 on "donors" and "acceptors" selection. Example:

sele1 = "chain A & (donors | acceptors)"
sele2 = "chain B & (donors | acceptors)"
radius = 3.5
D = cmd.find_pairs(sele1, sele2, mode=1, cutoff=radius)
print("number of h-bonds:", len(D))

1) Use "cmd.distance" and the "get_raw_distances" script. Example:

run https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py

sele1 = "chain A"
sele2 = "chain B"
radius = 3.5
cmd.distance("distname", sele1, sele2, mode=2, cutoff=radius)
D = get_raw_distances("distname")
print("number of h-bonds:", len(D))

See also:
https://pymolwiki.org/index.php/Get_raw_distances
https://pymolwiki.org/index.php/Distance
https://pymolwiki.org/index.php/Find_pairs

Hope that helps.

Cheers,
Thomas

On May 5, 2017, at 5:08 AM, Ahmad Abdelzaher <und...@gm...> wrote:

I know I can can find the hydrogen bond interactions between a
selection and surrounding residues within a certain radius. I would
like to find a way to retrieve the actual count of those interactions
per residue. How can I do it in the API?

Regards.

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Anke -

Try `as surface`, which is the equivalent of `hide everything; show surface`. 

Hope that helps.

Cheers,
Jared

Sent from my iPhone

> On May 19, 2017, at 6:43 AM, Anke Schultz <ank...@tu...> wrote:
> 
> Hi Thomas,
> 
> thanks for the explanation on adjusting view, it works fine. This leaves 
> me with one question: How do I get a .wrl-file containing only faces? 
> Using "show surface" and setting surface_type to 2 (triangles) gives me 
> sticks and spheres in the .wrl-file (sticks as edges, spheres at the 
> ends of every edge).
> 
> Cheers,
> 
> Anke
> 
> 
>> Am 19.05.2017 um 10:38 schrieb Thomas Holder:
>> Hi Anke,
>> 
>> The obvious difference I can see in your two samples is that the first one contains sticks and spheres representations, and the second one only has faces (could be surface or cartoon).
>> 
>> The other difference is the viewport z position (zoom distance), which is 0.0 in the second sample. This can be set as follows before exporting the file (note that the molecule might not be visible anymore, it could be behind the camera):
>> 
>> view = list(cmd.get_view())
>> view[11] = 0.0
>> cmd.set_view(view)
>> 
>> Hope that helps.
>> 
>> Cheers,
>>   Thomas
>> 
>>> On May 17, 2017, at 4:27 PM, Anke Schultz <ank...@tu...> wrote:
>>> 
>>> Hi all,
>>> 
>>> I've been experimenting with exporting surface meshes as .wrl-files. I played with the geometry_export_mode setting and the set_view() options, since I wanted to get the surface's coordinates corresponding to the atom's coordinates of the sd-file I imported to pymol initially. I realized that by exporting .wrl-format I got the camera-view instead of the "real" coordinates as long as I left everything else on default. This resulted in a shift between atom- and surface-coordinates.
>>> 
>>> While playing around to align camera and reality, I somehow managed to change the way my .wrl-file looked in the end and it seems to be exactly what I was looking for. I have tried for two days now, but unfortunately I can't reproduce my steps leading to this special .wrl-file.
>>> 
>>> This is (part of) a .wrl-file without changing default settings:
>>> ###############################################################
>>> #VRML V2.0 utf8
>>> 
>>> Viewpoint {
>>>  position 0 0 20.39730644
>>>  orientation 1 0 0 0
>>>  description "Z view"
>>>  fieldOfView 0.465421
>>> }
>>> DirectionalLight {
>>>  direction -0.348155 -0.348155   -0.870
>>> }
>>> NavigationInfo {
>>>  headlight TRUE
>>>  type "EXAMINE"
>>> }
>>> Transform {
>>>  translation -1.820169 2.166291 -3.211221
>>>  rotation -0.199343 0.000000 0.979930 2.401556
>>>  children [
>>>   Shape {
>>>    geometry Cylinder {
>>>     radius 0.024352
>>>     height 0.139351
>>>     bottom FALSE
>>>     top    FALSE
>>>    }
>>>    appearance Appearance {
>>>    material Material { diffuseColor 0.9000 0.9000 0.9000
>>>                        specularColor 0.8 0.8 0.8
>>>                        shininess 0.8 }
>>>    }
>>>   }
>>>   Transform {
>>>    translation 0.0 0.069676 0.0
>>>    children Shape {
>>>     geometry Sphere { radius 0.024352 }
>>>     appearance Appearance {
>>>    material Material { diffuseColor 0.9000 0.9000 0.9000
>>>                        specularColor 0.8 0.8 0.8
>>>                        shininess 0.8 }
>>>     }
>>>    }
>>>   }
>>>   Transform {
>>>    translation 0.0 -0.069676 0.0
>>>    children Shape {
>>>     geometry Sphere { radius 0.024352 }
>>>     appearance Appearance {
>>>    material Material { diffuseColor 0.9000 0.9000 0.9000
>>>                        specularColor 0.8 0.8 0.8
>>>                        shininess 0.8 }
>>>     }
>>>    }
>>>   }
>>>  ]
>>> }
>>> Transform {
>>>  translation -1.906664 2.148911 -3.187284
>>>  rotation 0.635566 0.000000 0.772046 0.994256
>>> [...]
>>> ###############################################################
>>> 
>>> And this is (part of) the special .wrl-file I mysteriously created:
>>> 
>>> ###############################################################
>>> #VRML V2.0 utf8
>>> 
>>> Viewpoint {
>>>  position 0 0 -0.00000000
>>>  orientation 1 0 0 0
>>>  description "Z view"
>>>  fieldOfView 0.465421
>>> }
>>> DirectionalLight {
>>>  direction -0.348155 -0.348155   -0.870
>>> }
>>> NavigationInfo {
>>>  headlight TRUE
>>>  type "EXAMINE"
>>> }
>>> Shape {
>>>  appearance Appearance {
>>>   material Material { diffuseColor 1.0 1.0 1.0 }
>>>  }
>>>  geometry IndexedFaceSet {
>>>   coord Coordinate {
>>>    point [
>>> 1.121935 1.360173 -0.410155,
>>> 1.840800 1.307029 -0.904629,
>>> 1.445710 1.051540 -1.083943,
>>> 1.301289 0.550209 -1.380068,
>>> 1.445710 1.051540 -1.083943,
>>> 1.840800 1.307029 -0.904629,
>>> 2.165471 0.781700 -1.754629,
>>> 1.301289 0.550209 -1.380068,
>>> 1.840800 1.307029 -0.904629,
>>> 2.693056 1.515260 -1.343787,
>>> 2.165471 0.781700 -1.754629,
>>> 1.840800 1.307029 -0.904629,
>>> [...]
>>> ###############################################################
>>> 
>>> If anyone knows the way to this .wrl-format, I would really appreciate your help.
>>> I'm using Pymol Version 1.8.6.0 on Ubuntu.
>>> 
>>> Thanks in advance,
>>> Anke
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>> 
>> 
> 
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> 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 Celestine,

Did you run the "get_raw_distances.py" script first? You can do that by:

run https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py

Or better: Download it to your computer and run it from there ("run" command or "File > Run Script..." from the menu).

After running the script, you can use the "get_raw_distances" command.

Cheers,
  Thomas

> On May 19, 2017, at 2:26 PM, Chi Celestine <chi...@ph...> wrote:
> 
> Hi Thomas,
> I am also interesting in getting bond distances between two pairs of molecule. I tried running the commands to suggested but I get an error message e.g 
> When I tried the following (see below) the fist command was well executed but the second gave an error message “ SyntaxError: invalid syntax”
> 
> I got a similar error message when I tried to execute  this command D = get_raw_distances("distname”)  as well 
> 
> 
> Sincerely,
> Celestine 
> 
> Example
> fetch 2xwu, async=0
> 
> 
> 
> # interface polar contacts
> distance iface_hbonds, chain A, chain B, mode=2
> 
> 
> 
> # dump (model,index) information
> get_raw_distances iface_hbonds
> 
>  
> -------------------------------------------------
> Celestine Chi, PhD
> ETH Zürich 
> Laboratory for Physical Chemistry
> Vladimir-Prelog-Weg 2 HCI F 222
> CH-8093 Zürich
> Email: chi...@ph...
> tele: 004144 63 37510
> 
>> On May 19, 2017, at 1:16 PM, Thomas Holder <tho...@sc...> wrote:
>> 
>> Hi Ahmad,
>> 
>> Unfortunately there is no proper API for this. But I can think of two approaches. Note that the results can differ because the two method do slightly different h-bond detection!
>> 
>> 1) Use "cmd.find_pairs" with mode=1 on "donors" and "acceptors" selection. Example:
>> 
>> sele1 = "chain A & (donors | acceptors)"
>> sele2 = "chain B & (donors | acceptors)"
>> radius = 3.5
>> D = cmd.find_pairs(sele1, sele2, mode=1, cutoff=radius)
>> print("number of h-bonds:", len(D))
>> 
>> 1) Use "cmd.distance" and the "get_raw_distances" script. Example:
>> 
>> run https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py
>> 
>> sele1 = "chain A"
>> sele2 = "chain B"
>> radius = 3.5
>> cmd.distance("distname", sele1, sele2, mode=2, cutoff=radius)
>> D = get_raw_distances("distname")
>> print("number of h-bonds:", len(D))
>> 
>> See also:
>> https://pymolwiki.org/index.php/Get_raw_distances
>> https://pymolwiki.org/index.php/Distance
>> https://pymolwiki.org/index.php/Find_pairs
>> 
>> Hope that helps.
>> 
>> Cheers,
>>  Thomas
>> 
>>> On May 5, 2017, at 5:08 AM, Ahmad Abdelzaher <und...@gm...> wrote:
>>> 
>>> I know I can can find the hydrogen bond interactions between a
>>> selection and surrounding residues within a certain radius. I would
>>> like to find a way to retrieve the actual count of those interactions
>>> per residue. How can I do it in the API?
>>> 
>>> Regards.

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Thomas,

that's the trick, thank you so much, you saved me a ton of work!

Best,

Anke


Am 19.05.2017 um 13:15 schrieb Thomas Holder:
> Hi Anke,
>
> surface_type 0 will produce faces (solid triangles).
>
> There are no triangle faces in surface_type 2, only edges.
>
> Thomas
>
>> On May 19, 2017, at 12:43 PM, Anke Schultz <ank...@tu...> wrote:
>>
>> Hi Thomas,
>>
>> thanks for the explanation on adjusting view, it works fine. This leaves me with one question: How do I get a .wrl-file containing only faces? Using "show surface" and setting surface_type to 2 (triangles) gives me sticks and spheres in the .wrl-file (sticks as edges, spheres at the ends of every edge).
>>
>> Cheers,
>>
>> Anke
>>
>>
>> Am 19.05.2017 um 10:38 schrieb Thomas Holder:
>>> Hi Anke,
>>>
>>> The obvious difference I can see in your two samples is that the first one contains sticks and spheres representations, and the second one only has faces (could be surface or cartoon).
>>>
>>> The other difference is the viewport z position (zoom distance), which is 0.0 in the second sample. This can be set as follows before exporting the file (note that the molecule might not be visible anymore, it could be behind the camera):
>>>
>>> view = list(cmd.get_view())
>>> view[11] = 0.0
>>> cmd.set_view(view)
>>>
>>> Hope that helps.
>>>
>>> Cheers,
>>>    Thomas
>>>
>>>> On May 17, 2017, at 4:27 PM, Anke Schultz <ank...@tu...> wrote:
>>>>
>>>> Hi all,
>>>>
>>>> I've been experimenting with exporting surface meshes as .wrl-files. I played with the geometry_export_mode setting and the set_view() options, since I wanted to get the surface's coordinates corresponding to the atom's coordinates of the sd-file I imported to pymol initially. I realized that by exporting .wrl-format I got the camera-view instead of the "real" coordinates as long as I left everything else on default. This resulted in a shift between atom- and surface-coordinates.
>>>>
>>>> While playing around to align camera and reality, I somehow managed to change the way my .wrl-file looked in the end and it seems to be exactly what I was looking for. I have tried for two days now, but unfortunately I can't reproduce my steps leading to this special .wrl-file.
>>>>
>>>> This is (part of) a .wrl-file without changing default settings:
>>>> ###############################################################
>>>> #VRML V2.0 utf8
>>>>
>>>> Viewpoint {
>>>>   position 0 0 20.39730644
>>>>   orientation 1 0 0 0
>>>>   description "Z view"
>>>>   fieldOfView 0.465421
>>>> }
>>>> DirectionalLight {
>>>>   direction -0.348155 -0.348155   -0.870
>>>> }
>>>> NavigationInfo {
>>>>   headlight TRUE
>>>>   type "EXAMINE"
>>>> }
>>>> Transform {
>>>>   translation -1.820169 2.166291 -3.211221
>>>>   rotation -0.199343 0.000000 0.979930 2.401556
>>>>   children [
>>>>    Shape {
>>>>     geometry Cylinder {
>>>>      radius 0.024352
>>>>      height 0.139351
>>>>      bottom FALSE
>>>>      top    FALSE
>>>>     }
>>>>     appearance Appearance {
>>>>     material Material { diffuseColor 0.9000 0.9000 0.9000
>>>>                         specularColor 0.8 0.8 0.8
>>>>                         shininess 0.8 }
>>>>     }
>>>>    }
>>>>    Transform {
>>>>     translation 0.0 0.069676 0.0
>>>>     children Shape {
>>>>      geometry Sphere { radius 0.024352 }
>>>>      appearance Appearance {
>>>>     material Material { diffuseColor 0.9000 0.9000 0.9000
>>>>                         specularColor 0.8 0.8 0.8
>>>>                         shininess 0.8 }
>>>>      }
>>>>     }
>>>>    }
>>>>    Transform {
>>>>     translation 0.0 -0.069676 0.0
>>>>     children Shape {
>>>>      geometry Sphere { radius 0.024352 }
>>>>      appearance Appearance {
>>>>     material Material { diffuseColor 0.9000 0.9000 0.9000
>>>>                         specularColor 0.8 0.8 0.8
>>>>                         shininess 0.8 }
>>>>      }
>>>>     }
>>>>    }
>>>>   ]
>>>> }
>>>> Transform {
>>>>   translation -1.906664 2.148911 -3.187284
>>>>   rotation 0.635566 0.000000 0.772046 0.994256
>>>> [...]
>>>> ###############################################################
>>>>
>>>> And this is (part of) the special .wrl-file I mysteriously created:
>>>>
>>>> ###############################################################
>>>> #VRML V2.0 utf8
>>>>
>>>> Viewpoint {
>>>>   position 0 0 -0.00000000
>>>>   orientation 1 0 0 0
>>>>   description "Z view"
>>>>   fieldOfView 0.465421
>>>> }
>>>> DirectionalLight {
>>>>   direction -0.348155 -0.348155   -0.870
>>>> }
>>>> NavigationInfo {
>>>>   headlight TRUE
>>>>   type "EXAMINE"
>>>> }
>>>> Shape {
>>>>   appearance Appearance {
>>>>    material Material { diffuseColor 1.0 1.0 1.0 }
>>>>   }
>>>>   geometry IndexedFaceSet {
>>>>    coord Coordinate {
>>>>     point [
>>>> 1.121935 1.360173 -0.410155,
>>>> 1.840800 1.307029 -0.904629,
>>>> 1.445710 1.051540 -1.083943,
>>>> 1.301289 0.550209 -1.380068,
>>>> 1.445710 1.051540 -1.083943,
>>>> 1.840800 1.307029 -0.904629,
>>>> 2.165471 0.781700 -1.754629,
>>>> 1.301289 0.550209 -1.380068,
>>>> 1.840800 1.307029 -0.904629,
>>>> 2.693056 1.515260 -1.343787,
>>>> 2.165471 0.781700 -1.754629,
>>>> 1.840800 1.307029 -0.904629,
>>>> [...]
>>>> ###############################################################
>>>>
>>>> If anyone knows the way to this .wrl-format, I would really appreciate your help.
>>>> I'm using Pymol Version 1.8.6.0 on Ubuntu.
>>>>
>>>> Thanks in advance,
>>>> Anke
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Hi Thomas,
I am also interesting in getting bond distances between two pairs of molecule. I tried running the commands to suggested but I get an error message e.g
When I tried the following (see below) the fist command was well executed but the second gave an error message “ SyntaxError: invalid syntax”

I got a similar error message when I tried to execute  this command D = get_raw_distances("distname”)  as well


Sincerely,
Celestine

Example

fetch 2xwu, async=0

# interface polar contacts
distance iface_hbonds, chain A, chain B, mode=2

# dump (model,index) information
get_raw_distances iface_hbonds


-------------------------------------------------
Celestine Chi, PhD
ETH Zürich
Laboratory for Physical Chemistry
Vladimir-Prelog-Weg 2 HCI F 222
CH-8093 Zürich
Email: chi...@ph...<mailto:chi...@ph...>
tele: 004144 63 37510

On May 19, 2017, at 1:16 PM, Thomas Holder <tho...@sc...<mailto:tho...@sc...>> wrote:

Hi Ahmad,

Unfortunately there is no proper API for this. But I can think of two approaches. Note that the results can differ because the two method do slightly different h-bond detection!

1) Use "cmd.find_pairs" with mode=1 on "donors" and "acceptors" selection. Example:

sele1 = "chain A & (donors | acceptors)"
sele2 = "chain B & (donors | acceptors)"
radius = 3.5
D = cmd.find_pairs(sele1, sele2, mode=1, cutoff=radius)
print("number of h-bonds:", len(D))

1) Use "cmd.distance" and the "get_raw_distances" script. Example:

run https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py

sele1 = "chain A"
sele2 = "chain B"
radius = 3.5
cmd.distance("distname", sele1, sele2, mode=2, cutoff=radius)
D = get_raw_distances("distname")
print("number of h-bonds:", len(D))

See also:
https://pymolwiki.org/index.php/Get_raw_distances
https://pymolwiki.org/index.php/Distance
https://pymolwiki.org/index.php/Find_pairs

Hope that helps.

Cheers,
 Thomas

On May 5, 2017, at 5:08 AM, Ahmad Abdelzaher <und...@gm...> wrote:

I know I can can find the hydrogen bond interactions between a
selection and surrounding residues within a certain radius. I would
like to find a way to retrieve the actual count of those interactions
per residue. How can I do it in the API?

Regards.

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Hi Ahmad,

Unfortunately there is no proper API for this. But I can think of two approaches. Note that the results can differ because the two method do slightly different h-bond detection!

1) Use "cmd.find_pairs" with mode=1 on "donors" and "acceptors" selection. Example:

sele1 = "chain A & (donors | acceptors)"
sele2 = "chain B & (donors | acceptors)"
radius = 3.5
D = cmd.find_pairs(sele1, sele2, mode=1, cutoff=radius)
print("number of h-bonds:", len(D))

1) Use "cmd.distance" and the "get_raw_distances" script. Example:

run https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py

sele1 = "chain A"
sele2 = "chain B"
radius = 3.5
cmd.distance("distname", sele1, sele2, mode=2, cutoff=radius)
D = get_raw_distances("distname")
print("number of h-bonds:", len(D))

See also:
https://pymolwiki.org/index.php/Get_raw_distances
https://pymolwiki.org/index.php/Distance
https://pymolwiki.org/index.php/Find_pairs

Hope that helps.

Cheers,
  Thomas

> On May 5, 2017, at 5:08 AM, Ahmad Abdelzaher <und...@gm...> wrote:
> 
> I know I can can find the hydrogen bond interactions between a
> selection and surrounding residues within a certain radius. I would
> like to find a way to retrieve the actual count of those interactions
> per residue. How can I do it in the API?
> 
> Regards.

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Anke,

surface_type 0 will produce faces (solid triangles).

There are no triangle faces in surface_type 2, only edges.

Thomas

> On May 19, 2017, at 12:43 PM, Anke Schultz <ank...@tu...> wrote:
> 
> Hi Thomas,
> 
> thanks for the explanation on adjusting view, it works fine. This leaves me with one question: How do I get a .wrl-file containing only faces? Using "show surface" and setting surface_type to 2 (triangles) gives me sticks and spheres in the .wrl-file (sticks as edges, spheres at the ends of every edge).
> 
> Cheers,
> 
> Anke
> 
> 
> Am 19.05.2017 um 10:38 schrieb Thomas Holder:
>> Hi Anke,
>> 
>> The obvious difference I can see in your two samples is that the first one contains sticks and spheres representations, and the second one only has faces (could be surface or cartoon).
>> 
>> The other difference is the viewport z position (zoom distance), which is 0.0 in the second sample. This can be set as follows before exporting the file (note that the molecule might not be visible anymore, it could be behind the camera):
>> 
>> view = list(cmd.get_view())
>> view[11] = 0.0
>> cmd.set_view(view)
>> 
>> Hope that helps.
>> 
>> Cheers,
>>   Thomas
>> 
>>> On May 17, 2017, at 4:27 PM, Anke Schultz <ank...@tu...> wrote:
>>> 
>>> Hi all,
>>> 
>>> I've been experimenting with exporting surface meshes as .wrl-files. I played with the geometry_export_mode setting and the set_view() options, since I wanted to get the surface's coordinates corresponding to the atom's coordinates of the sd-file I imported to pymol initially. I realized that by exporting .wrl-format I got the camera-view instead of the "real" coordinates as long as I left everything else on default. This resulted in a shift between atom- and surface-coordinates.
>>> 
>>> While playing around to align camera and reality, I somehow managed to change the way my .wrl-file looked in the end and it seems to be exactly what I was looking for. I have tried for two days now, but unfortunately I can't reproduce my steps leading to this special .wrl-file.
>>> 
>>> This is (part of) a .wrl-file without changing default settings:
>>> ###############################################################
>>> #VRML V2.0 utf8
>>> 
>>> Viewpoint {
>>>  position 0 0 20.39730644
>>>  orientation 1 0 0 0
>>>  description "Z view"
>>>  fieldOfView 0.465421
>>> }
>>> DirectionalLight {
>>>  direction -0.348155 -0.348155   -0.870
>>> }
>>> NavigationInfo {
>>>  headlight TRUE
>>>  type "EXAMINE"
>>> }
>>> Transform {
>>>  translation -1.820169 2.166291 -3.211221
>>>  rotation -0.199343 0.000000 0.979930 2.401556
>>>  children [
>>>   Shape {
>>>    geometry Cylinder {
>>>     radius 0.024352
>>>     height 0.139351
>>>     bottom FALSE
>>>     top    FALSE
>>>    }
>>>    appearance Appearance {
>>>    material Material { diffuseColor 0.9000 0.9000 0.9000
>>>                        specularColor 0.8 0.8 0.8
>>>                        shininess 0.8 }
>>>    }
>>>   }
>>>   Transform {
>>>    translation 0.0 0.069676 0.0
>>>    children Shape {
>>>     geometry Sphere { radius 0.024352 }
>>>     appearance Appearance {
>>>    material Material { diffuseColor 0.9000 0.9000 0.9000
>>>                        specularColor 0.8 0.8 0.8
>>>                        shininess 0.8 }
>>>     }
>>>    }
>>>   }
>>>   Transform {
>>>    translation 0.0 -0.069676 0.0
>>>    children Shape {
>>>     geometry Sphere { radius 0.024352 }
>>>     appearance Appearance {
>>>    material Material { diffuseColor 0.9000 0.9000 0.9000
>>>                        specularColor 0.8 0.8 0.8
>>>                        shininess 0.8 }
>>>     }
>>>    }
>>>   }
>>>  ]
>>> }
>>> Transform {
>>>  translation -1.906664 2.148911 -3.187284
>>>  rotation 0.635566 0.000000 0.772046 0.994256
>>> [...]
>>> ###############################################################
>>> 
>>> And this is (part of) the special .wrl-file I mysteriously created:
>>> 
>>> ###############################################################
>>> #VRML V2.0 utf8
>>> 
>>> Viewpoint {
>>>  position 0 0 -0.00000000
>>>  orientation 1 0 0 0
>>>  description "Z view"
>>>  fieldOfView 0.465421
>>> }
>>> DirectionalLight {
>>>  direction -0.348155 -0.348155   -0.870
>>> }
>>> NavigationInfo {
>>>  headlight TRUE
>>>  type "EXAMINE"
>>> }
>>> Shape {
>>>  appearance Appearance {
>>>   material Material { diffuseColor 1.0 1.0 1.0 }
>>>  }
>>>  geometry IndexedFaceSet {
>>>   coord Coordinate {
>>>    point [
>>> 1.121935 1.360173 -0.410155,
>>> 1.840800 1.307029 -0.904629,
>>> 1.445710 1.051540 -1.083943,
>>> 1.301289 0.550209 -1.380068,
>>> 1.445710 1.051540 -1.083943,
>>> 1.840800 1.307029 -0.904629,
>>> 2.165471 0.781700 -1.754629,
>>> 1.301289 0.550209 -1.380068,
>>> 1.840800 1.307029 -0.904629,
>>> 2.693056 1.515260 -1.343787,
>>> 2.165471 0.781700 -1.754629,
>>> 1.840800 1.307029 -0.904629,
>>> [...]
>>> ###############################################################
>>> 
>>> If anyone knows the way to this .wrl-format, I would really appreciate your help.
>>> I'm using Pymol Version 1.8.6.0 on Ubuntu.
>>> 
>>> Thanks in advance,
>>> Anke

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Thomas,

thanks for the explanation on adjusting view, it works fine. This leaves 
me with one question: How do I get a .wrl-file containing only faces? 
Using "show surface" and setting surface_type to 2 (triangles) gives me 
sticks and spheres in the .wrl-file (sticks as edges, spheres at the 
ends of every edge).

Cheers,

Anke


Am 19.05.2017 um 10:38 schrieb Thomas Holder:
> Hi Anke,
>
> The obvious difference I can see in your two samples is that the first one contains sticks and spheres representations, and the second one only has faces (could be surface or cartoon).
>
> The other difference is the viewport z position (zoom distance), which is 0.0 in the second sample. This can be set as follows before exporting the file (note that the molecule might not be visible anymore, it could be behind the camera):
>
> view = list(cmd.get_view())
> view[11] = 0.0
> cmd.set_view(view)
>
> Hope that helps.
>
> Cheers,
>    Thomas
>
>> On May 17, 2017, at 4:27 PM, Anke Schultz <ank...@tu...> wrote:
>>
>> Hi all,
>>
>> I've been experimenting with exporting surface meshes as .wrl-files. I played with the geometry_export_mode setting and the set_view() options, since I wanted to get the surface's coordinates corresponding to the atom's coordinates of the sd-file I imported to pymol initially. I realized that by exporting .wrl-format I got the camera-view instead of the "real" coordinates as long as I left everything else on default. This resulted in a shift between atom- and surface-coordinates.
>>
>> While playing around to align camera and reality, I somehow managed to change the way my .wrl-file looked in the end and it seems to be exactly what I was looking for. I have tried for two days now, but unfortunately I can't reproduce my steps leading to this special .wrl-file.
>>
>> This is (part of) a .wrl-file without changing default settings:
>> ###############################################################
>> #VRML V2.0 utf8
>>
>> Viewpoint {
>>   position 0 0 20.39730644
>>   orientation 1 0 0 0
>>   description "Z view"
>>   fieldOfView 0.465421
>> }
>> DirectionalLight {
>>   direction -0.348155 -0.348155   -0.870
>> }
>> NavigationInfo {
>>   headlight TRUE
>>   type "EXAMINE"
>> }
>> Transform {
>>   translation -1.820169 2.166291 -3.211221
>>   rotation -0.199343 0.000000 0.979930 2.401556
>>   children [
>>    Shape {
>>     geometry Cylinder {
>>      radius 0.024352
>>      height 0.139351
>>      bottom FALSE
>>      top    FALSE
>>     }
>>     appearance Appearance {
>>     material Material { diffuseColor 0.9000 0.9000 0.9000
>>                         specularColor 0.8 0.8 0.8
>>                         shininess 0.8 }
>>     }
>>    }
>>    Transform {
>>     translation 0.0 0.069676 0.0
>>     children Shape {
>>      geometry Sphere { radius 0.024352 }
>>      appearance Appearance {
>>     material Material { diffuseColor 0.9000 0.9000 0.9000
>>                         specularColor 0.8 0.8 0.8
>>                         shininess 0.8 }
>>      }
>>     }
>>    }
>>    Transform {
>>     translation 0.0 -0.069676 0.0
>>     children Shape {
>>      geometry Sphere { radius 0.024352 }
>>      appearance Appearance {
>>     material Material { diffuseColor 0.9000 0.9000 0.9000
>>                         specularColor 0.8 0.8 0.8
>>                         shininess 0.8 }
>>      }
>>     }
>>    }
>>   ]
>> }
>> Transform {
>>   translation -1.906664 2.148911 -3.187284
>>   rotation 0.635566 0.000000 0.772046 0.994256
>> [...]
>> ###############################################################
>>
>> And this is (part of) the special .wrl-file I mysteriously created:
>>
>> ###############################################################
>> #VRML V2.0 utf8
>>
>> Viewpoint {
>>   position 0 0 -0.00000000
>>   orientation 1 0 0 0
>>   description "Z view"
>>   fieldOfView 0.465421
>> }
>> DirectionalLight {
>>   direction -0.348155 -0.348155   -0.870
>> }
>> NavigationInfo {
>>   headlight TRUE
>>   type "EXAMINE"
>> }
>> Shape {
>>   appearance Appearance {
>>    material Material { diffuseColor 1.0 1.0 1.0 }
>>   }
>>   geometry IndexedFaceSet {
>>    coord Coordinate {
>>     point [
>> 1.121935 1.360173 -0.410155,
>> 1.840800 1.307029 -0.904629,
>> 1.445710 1.051540 -1.083943,
>> 1.301289 0.550209 -1.380068,
>> 1.445710 1.051540 -1.083943,
>> 1.840800 1.307029 -0.904629,
>> 2.165471 0.781700 -1.754629,
>> 1.301289 0.550209 -1.380068,
>> 1.840800 1.307029 -0.904629,
>> 2.693056 1.515260 -1.343787,
>> 2.165471 0.781700 -1.754629,
>> 1.840800 1.307029 -0.904629,
>> [...]
>> ###############################################################
>>
>> If anyone knows the way to this .wrl-format, I would really appreciate your help.
>> I'm using Pymol Version 1.8.6.0 on Ubuntu.
>>
>> Thanks in advance,
>> Anke
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Hi Kingsley,

The b-factor is a result of the X-ray crystallography experiment. If you have X-ray data, I suggest to consult the CCP4BB mailing list (http://www.ccp4.ac.uk/ccp4bb.php). If you don’t have such data, then you can’t calculate a b-factor.

There are computational methods which analyze a structure for potential flexibility, for example Normal Mode Analysis (NMA). These methods can approximate real b-factors.

If you have an ensemble of structures (e.g. from an MD simulation) you could also calculate the root mean square fluctuation per atom (RMSF), which is related to the b-factor in the sense that it describes a distribution around a center position. See for example “rmsf2b” in the PSICO library: https://github.com/speleo3/pymol-psico/blob/master/psico/editing.py#L69

Cheers,
  Thomas

> On May 8, 2017, at 2:42 PM, Kingsley Theras Primus Dass . <105...@gm...> wrote:
> 
> Hi everyone ! 
> I want to calculate the b-factor for my protein . Can. Anyone tell me how to do b-factor or some tutorial about that. 
> 
> Thanks in advance :)

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Dolev,

The difference is that the menu action only aligns on C-alpha atoms. Since PyMOL 1.8 the menu label says “align > to molecule (*/CA)” to make this more obvious.

The exact command which is executed by the menu action is:

align 4A11 & name CA & polymer, 3W15 & name CA & polymer, object=aln_4A11_to_3W15

The “polymer” selection makes sure that calcium atoms are not included, which also have name CA.

See also:
https://pymolwiki.org/index.php/Align

Cheers,
  Thomas

> On May 18, 2017, at 12:41 PM, do r <dol...@gm...> wrote:
> 
> Hello
> 
> I have noted that using action -> align -> to molecule via the GUI gives (sometimes radically) different result then running align on the same structures via command line.
> 
> For examples, for PDB structures 4A11 and 3W15, the command
> align 4A11,3W15, aligns 1632 atoms and gives an RMSD of 7.538, whereas
> action -> align -> to molecule aligns 375 and gives an RMSD of 24.416.
> I have also seen such differences on other pairs of structures.
> 
> Any explanation of this phenomenon will be most appreciated.
> 
> Thanks in advance
> Dolev Rahat 

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Anke,

The obvious difference I can see in your two samples is that the first one contains sticks and spheres representations, and the second one only has faces (could be surface or cartoon).

The other difference is the viewport z position (zoom distance), which is 0.0 in the second sample. This can be set as follows before exporting the file (note that the molecule might not be visible anymore, it could be behind the camera):

view = list(cmd.get_view())
view[11] = 0.0
cmd.set_view(view)

Hope that helps.

Cheers,
  Thomas

> On May 17, 2017, at 4:27 PM, Anke Schultz <ank...@tu...> wrote:
> 
> Hi all,
> 
> I've been experimenting with exporting surface meshes as .wrl-files. I played with the geometry_export_mode setting and the set_view() options, since I wanted to get the surface's coordinates corresponding to the atom's coordinates of the sd-file I imported to pymol initially. I realized that by exporting .wrl-format I got the camera-view instead of the "real" coordinates as long as I left everything else on default. This resulted in a shift between atom- and surface-coordinates.
> 
> While playing around to align camera and reality, I somehow managed to change the way my .wrl-file looked in the end and it seems to be exactly what I was looking for. I have tried for two days now, but unfortunately I can't reproduce my steps leading to this special .wrl-file.
> 
> This is (part of) a .wrl-file without changing default settings:
> ###############################################################
> #VRML V2.0 utf8
> 
> Viewpoint {
>  position 0 0 20.39730644
>  orientation 1 0 0 0
>  description "Z view"
>  fieldOfView 0.465421
> }
> DirectionalLight {
>  direction -0.348155 -0.348155   -0.870
> }
> NavigationInfo {
>  headlight TRUE
>  type "EXAMINE"
> }
> Transform {
>  translation -1.820169 2.166291 -3.211221
>  rotation -0.199343 0.000000 0.979930 2.401556
>  children [
>   Shape {
>    geometry Cylinder {
>     radius 0.024352
>     height 0.139351
>     bottom FALSE
>     top    FALSE
>    }
>    appearance Appearance {
>    material Material { diffuseColor 0.9000 0.9000 0.9000 
>                        specularColor 0.8 0.8 0.8 
>                        shininess 0.8 }
>    }
>   }
>   Transform {
>    translation 0.0 0.069676 0.0
>    children Shape {
>     geometry Sphere { radius 0.024352 }
>     appearance Appearance {
>    material Material { diffuseColor 0.9000 0.9000 0.9000 
>                        specularColor 0.8 0.8 0.8 
>                        shininess 0.8 }
>     }
>    }
>   }
>   Transform {
>    translation 0.0 -0.069676 0.0
>    children Shape {
>     geometry Sphere { radius 0.024352 }
>     appearance Appearance {
>    material Material { diffuseColor 0.9000 0.9000 0.9000 
>                        specularColor 0.8 0.8 0.8 
>                        shininess 0.8 }
>     }
>    }
>   }
>  ]
> }
> Transform {
>  translation -1.906664 2.148911 -3.187284
>  rotation 0.635566 0.000000 0.772046 0.994256
> [...]
> ###############################################################
> 
> And this is (part of) the special .wrl-file I mysteriously created:
> 
> ###############################################################
> #VRML V2.0 utf8
> 
> Viewpoint {
>  position 0 0 -0.00000000
>  orientation 1 0 0 0
>  description "Z view"
>  fieldOfView 0.465421
> }
> DirectionalLight {
>  direction -0.348155 -0.348155   -0.870
> }
> NavigationInfo {
>  headlight TRUE
>  type "EXAMINE"
> }
> Shape {
>  appearance Appearance {
>   material Material { diffuseColor 1.0 1.0 1.0 }
>  }
>  geometry IndexedFaceSet {
>   coord Coordinate {
>    point [
> 1.121935 1.360173 -0.410155,
> 1.840800 1.307029 -0.904629,
> 1.445710 1.051540 -1.083943,
> 1.301289 0.550209 -1.380068,
> 1.445710 1.051540 -1.083943,
> 1.840800 1.307029 -0.904629,
> 2.165471 0.781700 -1.754629,
> 1.301289 0.550209 -1.380068,
> 1.840800 1.307029 -0.904629,
> 2.693056 1.515260 -1.343787,
> 2.165471 0.781700 -1.754629,
> 1.840800 1.307029 -0.904629,
> [...]
> ###############################################################
> 
> If anyone knows the way to this .wrl-format, I would really appreciate your help.
> I'm using Pymol Version 1.8.6.0 on Ubuntu.
> 
> Thanks in advance,
> Anke

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Marko,

Have you tried this?

select zplane, z > 6.377 and z < 7.139

This works since PyMOL 1.6 (I think).

Cheers,
  Thomas

> On May 19, 2017, at 9:49 AM, Marko Sever <Mar...@ki...> wrote:
> 
> Hello everyone! Could someone help me figure out, how I could do a residue selection along specific z-axis coordinates, for example from 6,377-7,139 on the z-axis, etc..Like that it selects all residues in that plane.
> 
> Marko Sever, PhD student

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hello everyone! Could someone help me figure out, how I could do a residue selection along specific z-axis coordinates, for example from 6,377-7,139 on the z-axis, etc..Like that it selects all residues in that plane.

Marko Sever, PhD student

Hello

I have noted that using action -> align -> to molecule via the GUI gives
(sometimes radically) different result then running align on the same
structures via command line.

For examples, for PDB structures 4A11 and 3W15, the command
align 4A11,3W15, aligns 1632 atoms and gives an RMSD of 7.538, whereas
action -> align -> to molecule aligns 375 and gives an RMSD of 24.416.
I have also seen such differences on other pairs of structures.

Any explanation of this phenomenon will be most appreciated.

Thanks in advance
Dolev Rahat

Hi all,

I've been experimenting with exporting surface meshes as .wrl-files. I 
played with the geometry_export_mode setting and the set_view() options, 
since I wanted to get the surface's coordinates corresponding to the 
atom's coordinates of the sd-file I imported to pymol initially. I 
realized that by exporting .wrl-format I got the camera-view instead of 
the "real" coordinates as long as I left everything else on default. 
This resulted in a shift between atom- and surface-coordinates.

While playing around to align camera and reality, I somehow managed to 
change the way my .wrl-file looked in the end and it seems to be exactly 
what I was looking for. I have tried for two days now, but unfortunately 
I can't reproduce my steps leading to this special .wrl-file.

This is (part of) a .wrl-file without changing default settings:
###############################################################
/#VRML V2.0 utf8

Viewpoint {
  position 0 0 20.39730644
  orientation 1 0 0 0
  description "Z view"
  fieldOfView 0.465421
}
DirectionalLight {
  direction -0.348155 -0.348155   -0.870
}
NavigationInfo {
  headlight TRUE
  type "EXAMINE"
}
Transform {
  translation -1.820169 2.166291 -3.211221
  rotation -0.199343 0.000000 0.979930 2.401556
  children [
   Shape {
    geometry Cylinder {
     radius 0.024352
     height 0.139351
     bottom FALSE
     top    FALSE
    }
    appearance Appearance {
    material Material { diffuseColor 0.9000 0.9000 0.9000
                        specularColor 0.8 0.8 0.8
                        shininess 0.8 }
    }
   }
   Transform {
    translation 0.0 0.069676 0.0
    children Shape {
     geometry Sphere { radius 0.024352 }
     appearance Appearance {
    material Material { diffuseColor 0.9000 0.9000 0.9000
                        specularColor 0.8 0.8 0.8
                        shininess 0.8 }
     }
    }
   }
   Transform {
    translation 0.0 -0.069676 0.0
    children Shape {
     geometry Sphere { radius 0.024352 }
     appearance Appearance {
    material Material { diffuseColor 0.9000 0.9000 0.9000
                        specularColor 0.8 0.8 0.8
                        shininess 0.8 }
     }
    }
   }
  ]
}
Transform {
  translation -1.906664 2.148911 -3.187284
  rotation 0.635566 0.000000 0.772046 0.994256//
//[...]
###############################################################
/
And this is (part of) the special .wrl-file I mysteriously created:

/###############################################################
#VRML V2.0 utf8

Viewpoint {
  position 0 0 -0.00000000
  orientation 1 0 0 0
  description "Z view"
  fieldOfView 0.465421
}
DirectionalLight {
  direction -0.348155 -0.348155   -0.870
}
NavigationInfo {
  headlight TRUE
  type "EXAMINE"
}
Shape {
  appearance Appearance {
   material Material { diffuseColor 1.0 1.0 1.0 }
  }
  geometry IndexedFaceSet {
   coord Coordinate {
    point [
1.121935 1.360173 -0.410155,
1.840800 1.307029 -0.904629,
1.445710 1.051540 -1.083943,
1.301289 0.550209 -1.380068,
1.445710 1.051540 -1.083943,
1.840800 1.307029 -0.904629,
2.165471 0.781700 -1.754629,
1.301289 0.550209 -1.380068,
1.840800 1.307029 -0.904629,
2.693056 1.515260 -1.343787,
2.165471 0.781700 -1.754629,
1.840800 1.307029 -0.904629,
[...]
###############################################################

/If anyone knows the way to this .wrl-format, I would really appreciate 
your help./
/I'm using Pymol Version 1.8.6.0 on Ubuntu./
/
Thanks in advance,
Anke/
/

Hi Junjun,

Yes, representations need to be refreshed. This should do it:

PyMOL> rebuild

Note that "reps" is only available in alter since PyMOL 1.7.4

Of course, to hide all representations, you can also do:

PyMOL> hide everything, resi 84 and name CE1

Cheers,
  Thomas

> On May 15, 2017, at 11:33 AM, liu junjun <lj...@gm...> wrote:
> 
> Hi all,
> 
> I have a question about alter command on "reps" variable. I find reps is zero when object being set with "hide everything". I try to modify one atom's reps to be zero by using the following alter command:
>    alter (resi 84 and name CE1), reps=0
> It seems the reps do changed to 0, but that atom is not being hidden. My question is: do we need to refresh the representation after altering one atom's reps? if yes, how to do that?
> 
> Thanks in advance!
> 
> Junjun

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi all,

I have a question about alter command on "reps" variable. I find reps is
zero when object being set with "hide everything". I try to modify one
atom's reps to be zero by using the following alter command:
   alter (resi 84 and name CE1), reps=0
It seems the reps do changed to 0, but that atom is not being hidden. My
question is: do we need to refresh the representation after altering one
atom's reps? if yes, how to do that?

Thanks in advance!

Junjun

Dear Pymol users,

I have displayed a cavity as a surface in my DNA structure in Pymol and I
am looking to calculate the volume of it. How would one do this in Pymol?

Thank you in advance!

Betty