pymol-users Mailing List for PyMOL Molecular Graphics System

Hi All,
I have a protein, which is colored by rmsd.
The .pml coloring scripts have been produced by ProSmart.
The color spectrum is white, yellow and red, where red denotes the
highest rmsd value.
Does anyone knows how to select only these AAs, which are colored in red?
thanks

Hi,
I am using the cmd.load_coords function in my script, which does the following:
1-do some calculations with coordinates. I want to use the new coordinates as input for another program, for which I only have an executable that reads .pdb files. So my approach is:
2-Use load_coords to apply the new set of coordinates (numpy array) to a pymol object
3-Write this object out as .pdb and use as input for other program
4-get result
5-do some other stuff
In principle, this seems to work - but:
I am using multiprocessing with 10 processes. Most times that I run the script, 8 or 9 processes run fine but one or two simply stop doing anything at step 2. I found that this line is the culprit:
...
cmd.load_coords(complex, "complex")
....
This also happens about once in 10 runs when I use just 1 process.
 
It seems that the function sometimes does not return any result - any idea why this happens?
Thank you and all the best,
Gregor

Hi,
I am using the cmd.load_coords function in my script, which does the following:
1-do some calculations with coordinates. Next, I want to use the new set of coordinates as input for another program, for which I only have an executable that reads .pdb files. So my approach is:
2-Use cmd.load_coords to apply the new set of coordinates (numpy array) to an existing pymol object
3-Write this modified object out as .pdb and use as input for other program
4-get result
5-do some other stuff
In principle, this seems to work - but:
I am using multiprocessing with 10 processes. Most times when I run the script, 8 or 9 processes run fine but one or two simply stop doing anything at step 2. I found that this line is the culprit:
...
cmd.load_coords(complex, "complex")
....
This also happens about once in 10 runs when I use just 1 process.
 
It seems that the function sometimes does not return any result - any idea why this happens?
Thank you and all the best,
Gregor

Dear Jordan
Comparing the two images, it looks to me that they differ in the cartoon loop settings applied to produce the cartoon: https://pymolwiki.org/index.php/Cartoon_smooth_loops <https://pymolwiki.org/index.php/Cartoon_smooth_loops>,
as well as the helix representation and cartoon highlight color
However, normally, if you copy an object, e.g. using the create commands, or even with <cntl>C / <cntl>V, the copy keeps all representation settings - how do you copy the object?
best regards
Annemarie
____________________________________________________________
Dr. Annemarie Honegger
Dept. of Biochemistry
Zürich University
Winterthurerstrasse 190
8057 Zürich
Switzerland
e-mail: hon...@bi...
phone: +41 44 635 55 62
fax: +41 44 635 57 12 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: 2017年8月24日 14:24:34 -0700
> From: "J.R. W" <jwi...@gm...>
> To: pymol-users <pym...@li...>
> Subject: [PyMOL] Copy object distorts cartoon backbone.
> Message-ID: <506...@gm...>
> Content-Type: text/plain; charset="utf-8"
> 
> I have a trimeric structure. It looks great when I show it in a cartoon object. As soon as I copy one of the chains to an object, the backbone immediately distorts. The residues perfectly align with the parent object. Does anyone know what?s happening? Can I copy the representation of the parent object too? Please see the attached pictures from the parent object and the copied object.
> 
> 
> 
> Jordan
> 
> 
> https://drive.google.com/file/d/0BzArdal219l4MFBGQTNqN2dydFE/view?usp=sharing <https://drive.google.com/file/d/0BzArdal219l4MFBGQTNqN2dydFE/view?usp=sharing>
> 

I’m so sorry to spam. The answer is set cartoon_smooth_loops 1
Jordan
> On Aug 24, 2017, at 2:24 PM, J.R. W <jwi...@gm...> wrote:
> 
> I have a trimeric structure. It looks great when I show it in a cartoon object. As soon as I copy one of the chains to an object, the backbone immediately distorts. The residues perfectly align with the parent object. Does anyone know what’s happening? Can I copy the representation of the parent object too? Please see the attached pictures from the parent object and the copied object.
> 
> 
> 
> Jordan
> 
> 
> https://drive.google.com/file/d/0BzArdal219l4MFBGQTNqN2dydFE/view?usp=sharing <https://drive.google.com/file/d/0BzArdal219l4MFBGQTNqN2dydFE/view?usp=sharing>
> 

I have a trimeric structure. It looks great when I show it in a cartoon object. As soon as I copy one of the chains to an object, the backbone immediately distorts. The residues perfectly align with the parent object. Does anyone know what’s happening? Can I copy the representation of the parent object too? Please see the attached pictures from the parent object and the copied object.
Jordan
https://drive.google.com/file/d/0BzArdal219l4MFBGQTNqN2dydFE/view?usp=sharing <https://drive.google.com/file/d/0BzArdal219l4MFBGQTNqN2dydFE/view?usp=sharing>

Hi Hari,
In Incentive PyMOL, the entity id is loaded into the "entity_id" atom property, which is available as p.entity_id in the selection language and in iterate/alter. Since Open-Source PyMOL doesn't support arbitrary atom properties yet, we also populate the "custom" property with the same value. So this should work:
# all PyMOL versions
select 5S, custom 58
# Incentive PyMOL only
select 5S, p.entity_id in 58
See also:
https://pymol.org/d/properties#selection_language
Cheers,
 Thomas
> On Aug 23, 2017, at 10:38 PM, hari jayaram <ha...@gm...> wrote:
> 
> Hi all,
> I am trying to select a particular chain ( the 5S RNA) within the E.coli ribosome cif file ( pdb ID 4V69)
> 
> The sequence info page at rcsb indicates that this chain has the information given below. I dont know the chain id or segid for this chain and in general have not worked with cif files inside pymol.
> 
> How do I select polymer 58 inside this cif structure.
> Thanks in advance
> Hari
> 
> 
> Chain Info
> 
> Polymer: 58
> Length: 117 residues
> Chain Type: polyribonucleotide
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi all,
I am trying to select a particular chain ( the 5S RNA) within the E.coli
ribosome cif file ( pdb ID 4V69)
The sequence info page at rcsb indicates that this chain has the
information given below. I dont know the chain id or segid for this chain
and in general have not worked with cif files inside pymol.
How do I select polymer 58 inside this cif structure.
Thanks in advance
Hari
Chain InfoPolymer: 58
Length: 117 residues
Chain Type: polyribonucleotide

University of Massachusetts Medical SchoolPost Doctoral Associate in Worcester, Massachusetts
A postdoctoral position is available in the Schiffer laboratory at UMass Medical School to work on structural biology of proteins related to viral infections and drug resistance. UMass Medical School is home to a newly built state-of-the-art cryo-EM facility, with a vibrant research community in structural biology. To learn about the Schiffer Lab and research program, please visit:
http://www.umassmed.edu/schifferlab
Applicant must have (or expect to obtain shortly) a Ph.D. in Biochemistry, Biophysics, or a related field. Previous experience and excellent skills in protein crystallography are required, including: protein expression/purification, protein crystallization, data collection, structure determination and analysis (and familiarity with the latest generation software in the field). Additional experience in the following areas is a plus: small molecule binding to proteins, molecular dynamics simulations, and enzyme kinetics. Crystal structures will include potential co-crystal structures with small molecules, nucleic acids and protein-protein complexes. The candidate is expected to complement crystallographic data with biochemical and biophysical assays, work closely with a diverse interdisciplinary research team, and be motivated to acquire new experimental and computational skills – including potentially cryo-EM.
MINIMUM QUALIFICATIONS:
A Ph.D. degree in Biochemistry, Biophysics, or a related field
Proficient in Protein Crystallography (protein crystallization, data collection, structure determination and analysis)
Experience in protein expression and purification
Ability to work in a multidisciplinary team environment
Please send a cover letter explaining your fit for the position and your CV to: Sch...@um...

Found it: set cartoon_tube_radius, number
Regards,
Vaheh Oganesyan
www.medimmune.com
From: Oganesyan, Vaheh [mailto:Oga...@Me...]
Sent: Tuesday, August 22, 2017 11:52 AM
To: pym...@li...
Subject: [PyMOL] tube width
Hello PyMOLers,
When presenting in cartoon tube mode how one can change the tube width?
Regards,
Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com
To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.

Hello PyMOLers,
When presenting in cartoon tube mode how one can change the tube width?
Regards,
Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com
To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.

Dear Christoph and David
Thanks for the support and solution. The solution given by Christoph
solved the issue. Now, the plugin manager is running smoothly.
Cheers
Vijay
On 8/22/17, David Hall <li...@co...> wrote:
> See https://sourceforge.net/p/pmw/patches/7/
> <https://sourceforge.net/p/pmw/patches/7/>
>
>> On Aug 21, 2017, at 10:32 PM, Vijay Masand <vij...@gm...> wrote:
>>
>> Dear Christoph
>> Thank you for the help. I followed your suggestion, but no success.
>> However, a new line is appearing now at the bottom of the error
>> message, here is the complete error message:
>>
>> Error: 1
>> TypeError Exception in Tk callback
>> Function: <function addPluginManagerMenuItem.<locals>.plugin_manager
>> at 0x000001B40CB228C8> (type: <class 'function'>)
>> Args: ()
>> Traceback (innermost last):
>> File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwBase.py",
>> line 1776, in __call__
>> return self.func(*args)
>> File "C:\Python36\lib\site-packages\pymol\plugins\legacysupport.py",
>> line 73, in plugin_manager
>> managergui.manager_dialog()
>> File "C:\Python36\lib\site-packages\pymol\plugins\managergui.py",
>> line 47, in manager_dialog
>> dialog = PluginManager(get_tk_root())
>> File "C:\Python36\lib\site-packages\pymol\plugins\managergui.py",
>> line 129, in __init__
>> notebook = Pmw.NoteBook(master)
>> File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwNoteBook.py",
>> line 60, in __init__
>> Pmw.Color.bordercolors(self, self['hull_background'])
>> File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwColor.py",
>> line 359, in bordercolors
>> '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),
>> TypeError: %x format: an integer is required, not float
>>
>> Regards
>> Vijay
>>
>> On 8/21/17, Christoph Gohlke <cg...@uc...> wrote:
>>> This message is eligible for Automatic Cleanup! (cg...@uc...)
>>> Add cleanup rule:
>>> https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Fkey%3DfjHYRYsu4KQHdU%252Ba%252BEcpBy5T890XwH5qjqDEd3FM6vA%253D%26token%3DvR75mOOuK9HSGhlUEWqQjF3KfnruxVIgFHwynqDNRMahVjOodkgbk0QRSdL3WLRXex4P5VnWowp%252BvpfF1%252BCu1%252FmCNcAaYuOLpU6eWPtjWTBuvuraePHhZ8Bh7k282k3QNHqPcw2tAhY%253D&tc_serial=32224636974&tc_rand=1319549807&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
>>> More info:
>>> http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=32224636974&tc_rand=1319549807&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
>>>
>>
>>
>> --
>> Assistant Professor
>> Department of Chemistry,
>> Vidya Bharati College, Amravati, 444 602
>> Maharashtra, India.
>> Phone number- +91-9403312628
>> https://sites.google.com/site/vijaymasand/
>>
>> ------------------------------------------------------------------------------
>> 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...
>
>
-- 
Assistant Professor
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/

Hi caver plugin users,
I've made a modified version of the plugin which simplifies the installation process. See https://pymolwiki.org/index.php/Caver3
Cheers,
 Thomas
> On Aug 21, 2017, at 2:15 PM, Thomas Holder <tho...@sc...> wrote:
> 
> Hi Raag,
> 
> If you follow these instructions, the caver plugin should work for you:
> 
> https://pymolwiki.org/index.php/Caver3
> 
> Cheers,
> Thomas
> 
>> On Aug 14, 2017, at 8:52 AM, Raag Saluja <sal...@gm...> wrote:
>> 
>> Hi!
>> 
>> I'm using MacPyMOL (PyMOL 1.7.4.5 Edu Incentive Product) and have been trying to install the Caver plugin.
>> However, it gives an error saying that it has been installed but
>> initialization failed. Please help!
>> 
>> Regards,
>> Raag
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

See https://sourceforge.net/p/pmw/patches/7/ <https://sourceforge.net/p/pmw/patches/7/> 
> On Aug 21, 2017, at 10:32 PM, Vijay Masand <vij...@gm...> wrote:
> 
> Dear Christoph
> Thank you for the help. I followed your suggestion, but no success.
> However, a new line is appearing now at the bottom of the error
> message, here is the complete error message:
> 
> Error: 1
> TypeError Exception in Tk callback
> Function: <function addPluginManagerMenuItem.<locals>.plugin_manager
> at 0x000001B40CB228C8> (type: <class 'function'>)
> Args: ()
> Traceback (innermost last):
> File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwBase.py",
> line 1776, in __call__
> return self.func(*args)
> File "C:\Python36\lib\site-packages\pymol\plugins\legacysupport.py",
> line 73, in plugin_manager
> managergui.manager_dialog()
> File "C:\Python36\lib\site-packages\pymol\plugins\managergui.py",
> line 47, in manager_dialog
> dialog = PluginManager(get_tk_root())
> File "C:\Python36\lib\site-packages\pymol\plugins\managergui.py",
> line 129, in __init__
> notebook = Pmw.NoteBook(master)
> File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwNoteBook.py",
> line 60, in __init__
> Pmw.Color.bordercolors(self, self['hull_background'])
> File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwColor.py",
> line 359, in bordercolors
> '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),
> TypeError: %x format: an integer is required, not float
> 
> Regards
> Vijay
> 
> On 8/21/17, Christoph Gohlke <cg...@uc...> wrote:
>> This message is eligible for Automatic Cleanup! (cg...@uc...)
>> Add cleanup rule:
>> https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Fkey%3DfjHYRYsu4KQHdU%252Ba%252BEcpBy5T890XwH5qjqDEd3FM6vA%253D%26token%3DvR75mOOuK9HSGhlUEWqQjF3KfnruxVIgFHwynqDNRMahVjOodkgbk0QRSdL3WLRXex4P5VnWowp%252BvpfF1%252BCu1%252FmCNcAaYuOLpU6eWPtjWTBuvuraePHhZ8Bh7k282k3QNHqPcw2tAhY%253D&tc_serial=32224636974&tc_rand=1319549807&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
>> More info:
>> http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=32224636974&tc_rand=1319549807&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
>> 
> 
> 
> -- 
> Assistant Professor
> Department of Chemistry,
> Vidya Bharati College, Amravati, 444 602
> Maharashtra, India.
> Phone number- +91-9403312628
> https://sites.google.com/site/vijaymasand/
> 
> ------------------------------------------------------------------------------
> 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 Christoph
Thank you for the help. I followed your suggestion, but no success.
However, a new line is appearing now at the bottom of the error
message, here is the complete error message:
Error: 1
TypeError Exception in Tk callback
 Function: <function addPluginManagerMenuItem.<locals>.plugin_manager
at 0x000001B40CB228C8> (type: <class 'function'>)
 Args: ()
Traceback (innermost last):
 File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwBase.py",
line 1776, in __call__
 return self.func(*args)
 File "C:\Python36\lib\site-packages\pymol\plugins\legacysupport.py",
line 73, in plugin_manager
 managergui.manager_dialog()
 File "C:\Python36\lib\site-packages\pymol\plugins\managergui.py",
line 47, in manager_dialog
 dialog = PluginManager(get_tk_root())
 File "C:\Python36\lib\site-packages\pymol\plugins\managergui.py",
line 129, in __init__
 notebook = Pmw.NoteBook(master)
 File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwNoteBook.py",
line 60, in __init__
 Pmw.Color.bordercolors(self, self['hull_background'])
 File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwColor.py",
line 359, in bordercolors
 '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),
TypeError: %x format: an integer is required, not float
Regards
Vijay
On 8/21/17, Christoph Gohlke <cg...@uc...> wrote:
> This message is eligible for Automatic Cleanup! (cg...@uc...)
> Add cleanup rule:
> https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Fkey%3DfjHYRYsu4KQHdU%252Ba%252BEcpBy5T890XwH5qjqDEd3FM6vA%253D%26token%3DvR75mOOuK9HSGhlUEWqQjF3KfnruxVIgFHwynqDNRMahVjOodkgbk0QRSdL3WLRXex4P5VnWowp%252BvpfF1%252BCu1%252FmCNcAaYuOLpU6eWPtjWTBuvuraePHhZ8Bh7k282k3QNHqPcw2tAhY%253D&tc_serial=32224636974&tc_rand=1319549807&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
> More info:
> http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=32224636974&tc_rand=1319549807&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
>
-- 
Assistant Professor
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/

Hello,
try to uninstall Pmw and reinstall it using Pmw-2.0.1-py3-none-any.whl 
from <http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol>.
C:\Python36\python.exe -m pip uninstall Pmw
C:\Python36\python.exe -m pip install Pmw-2.0.1-py3-none-any.whl
Christoph
On 8/21/2017 8:27 AM, Vijay Masand wrote:
> Dear PyMOL Users
> Today, I installed PyMOL 1.8.7 with Python 3.6 on Windows 10. But,
> unfortunatelt facing one issue with Plugin Manager. The error is as
> following:
> 
> Error: 1
> TypeError Exception in Tk callback
> Function: <function addPluginManagerMenuItem.<locals>.plugin_manager
> at 0x0000019192E818C8> (type: <class 'function'>)
> Args: ()
> Traceback (innermost last):
> File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwBase.py",
> line 1776, in __call__
> return self.func(*args)
> File "C:\Python36\lib\site-packages\pymol\plugins\legacysupport.py",
> line 73, in plugin_manager
> managergui.manager_dialog()
> File "C:\Python36\lib\site-packages\pymol\plugins\managergui.py",
> line 47, in manager_dialog
> dialog = PluginManager(get_tk_root())
> File "C:\Python36\lib\site-packages\pymol\plugins\managergui.py",
> line 129, in __init__
> notebook = Pmw.NoteBook(master)
> File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwNoteBook.py",
> line 60, in __init__
> Pmw.Color.bordercolors(self, self['hull_background'])
> File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwColor.py",
> line 359, in bordercolors
> '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),
> 
> Any solution?
> Thanks in advance.
> From
> Vijay
> 

Dear PyMOL Users
Today, I installed PyMOL 1.8.7 with Python 3.6 on Windows 10. But,
unfortunatelt facing one issue with Plugin Manager. The error is as
following:
Error: 1
TypeError Exception in Tk callback
 Function: <function addPluginManagerMenuItem.<locals>.plugin_manager
at 0x0000019192E818C8> (type: <class 'function'>)
 Args: ()
Traceback (innermost last):
 File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwBase.py",
line 1776, in __call__
 return self.func(*args)
 File "C:\Python36\lib\site-packages\pymol\plugins\legacysupport.py",
line 73, in plugin_manager
 managergui.manager_dialog()
 File "C:\Python36\lib\site-packages\pymol\plugins\managergui.py",
line 47, in manager_dialog
 dialog = PluginManager(get_tk_root())
 File "C:\Python36\lib\site-packages\pymol\plugins\managergui.py",
line 129, in __init__
 notebook = Pmw.NoteBook(master)
 File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwNoteBook.py",
line 60, in __init__
 Pmw.Color.bordercolors(self, self['hull_background'])
 File "C:\Python36\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwColor.py",
line 359, in bordercolors
 '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),
Any solution?
Thanks in advance.
From
Vijay
-- 
Assistant Professor
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/

Hi Gianluca,
Interesting observation. As far as I can tell, PyMOL reads the data correct from all files. I'll contact the MMTF folks and suggest to change their assembly ordering.
Cheers,
 Thomas
> On Aug 18, 2017, at 6:34 PM, Gianluca Tomasello <gia...@gm...> wrote:
> 
> Hi, I was trying to set assembly 1 and load 1C0K (and other structures) in pdb, cif and mmtf format. I noticed that when I split_states and get each model, model_0001 of cif and pdb format corresponds to model_0002 of mmtf format. 
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Raag,
If you follow these instructions, the caver plugin should work for you:
https://pymolwiki.org/index.php/Caver3
Cheers,
 Thomas
> On Aug 14, 2017, at 8:52 AM, Raag Saluja <sal...@gm...> wrote:
> 
> Hi!
> 
> I'm using MacPyMOL (PyMOL 1.7.4.5 Edu Incentive Product) and have been trying to install the Caver plugin.
> However, it gives an error saying that it has been installed but
> initialization failed. Please help!
> 
> Regards,
> Raag
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi, I was trying to set assembly 1 and load 1C0K (and other structures) in
pdb, cif and mmtf format. I noticed that when I split_states and get each
model, model_0001 of cif and pdb format corresponds to model_0002 of mmtf
format.

Dear PyMOL Users,
It gives me an immense pleasure to inform you that our group has
developed a new plugin to calculate 11,145 molecular descriptors for
small molecules. This is an attempt to add new dimension to PyMOL. The
research article describing 'PyDescriptor' has been published in
Chemometrics and Intelligent Laboratory Systems. For more details please refer:
Vijay H. Masand, Vesna Rastija, "PyDescriptor: A new PyMOL plugin for
calculating thousands of easily understandable molecular descriptors",
Chemometrics and Intelligent Laboratory Systems, 169, (2017), 12–18.
I hope it will be useful to a good number of PyMOL users.
Cheers
Vijay
-- 
Assistant Professor
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/

Hi!
I'm using MacPyMOL (PyMOL 1.7.4.5 Edu Incentive Product) and have been
trying to install the Caver plugin.
However, it gives an error saying that it has been installed but
initialization failed. Please help!
Regards,
Raag

Hi!
I'm using MacPyMOL and have been trying to install the Caver plugin.
However, it gives an error saying that it has been installed but
initialization failed. Please guide!
Regards,
Raag

Hi,
 I also had some problem with this. The "trick", I believe, is to
compile/install pymol with:
python2.7 setup.py build install --home=path_to_pymol/
--install-lib=path_to_pymol/modules/ --install-scripts=path_to_pymol/
 The part you are interested in is the modules. I needed to install
something called msgpack-c before compiling pymol.
 In addition, you need to add path_to_pymol/modules/ to your python
paths. You can add these to the .bashrc file:
export PYMOL_PATH=path_to_pymol/
export PYTHONPATH=$PYTHONPATH:$PYMOL_PATH/modules:
Have fun!
Leandro
On Tue, Jul 25, 2017 at 8:27 PM, Vivien Schoonenberg <
viv...@gm...> wrote:
> Hi all,
>
>
>
> I have been trying for a while, but cannot seem to figure out how to
> install pymol on my unix server so that I can run pymol from within a
> python script. (So that I can use it with the command ‘ import pymol’. I
> did manage to do this on my windows with a wheel, but don’t know how to
> solve it on my unix system)
>
>
>
> Any tips would be very welcome!
>
>
>
> Thanks,
>
> Vivien
>
> ------------------------------------------------------------
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>

Hi,
I have a problem after upgrading to Windows 10 Enterprise that I am hoping someone might be able to help with. I have tried to install Pymol using both Python 27 and 35 but both have the same problem, which is why I think it has to do with Windows.
Everything is running smoothly but if I click using the mouse on either the background or a residue Pymol stalls (Pymol not responding) and the cursor becomes a running circle. After maybe 10-15 seconds the residue is selected and I can work again. If I use commands instead I can select without a stall. Do anyone have an idea what could be causing this?
Thanks very much,
Klaus