pymol-users Mailing List for PyMOL Molecular Graphics System

Although Mojave was just released, all of our automated and QA tests do
not show anything out of the ordinary. While it's probably still too early
to declare official support, we haven't encountered anything that suggests
users should worry about upgrading with regards to the PyMOL application.
On Fri, Sep 28, 2018 at 2:14 PM Jack Vizelter <ja...@ma...>
wrote:
> Is Mojave then officially supported with PyMol?
>
>
>
>
>
>
>
> *From: *Jarrett Johnson <jar...@sc...>
> *Date: *Friday, September 28, 2018 at 12:59 PM
> *To: *"sa...@um..." <sa...@um...>
> *Cc: *Pymol User list <pym...@li...>
> *Subject: *Re: [PyMOL] Mojave support
>
>
>
> Hi Mark,
>
>
>
> I hope everything is still going well! According to initial tests we ran
> on MacOS 10.14, PyMOL seems to run well. If you or any other users do come
> across any issues, please let us know.
>
>
>
> Thanks,
>
> Jarrett J.
>
>
>
> On Fri, Sep 28, 2018 at 10:02 AM Mark Saper <sa...@um...> wrote:
>
> Hi Tom,
>
> Will PyMOL be supporting macOS Mojave (10.14) anytime soon? 10.14 is
> still supposed to support OpenGL but it is deprecated.
>
> Thanks, Mark
> _______________________________________________
> Mark A. Saper, Ph.D.
> Associate Professor of Biological Chemistry, U-M Medical School
> Room 3220B, MSRB III sa...@um... +1 (734) 764-3353 mobile: (734)
> 276-6505
>
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_pymol-2Dusers&d=DwMFaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=0obZbb_Et6jVC2oTxrGAsSPIfgdjX1evoBw5RwmSZl4&s=k-zdK0kf5ze7wgULrWNxZd9RC6eh37P84usUIFZ1K-o&e=>
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>
>
>
>
> --
>
> Jarrett Johnson
>
> PyMOL Developer
>
> Schrödinger, Inc.
>
-- 
Jarrett Johnson
PyMOL Developer
Schrödinger, Inc.

Is Mojave then officially supported with PyMol?
From: Jarrett Johnson <jar...@sc...>
Date: Friday, September 28, 2018 at 12:59 PM
To: "sa...@um..." <sa...@um...>
Cc: Pymol User list <pym...@li...>
Subject: Re: [PyMOL] Mojave support
Hi Mark,
I hope everything is still going well! According to initial tests we ran on MacOS 10.14, PyMOL seems to run well. If you or any other users do come across any issues, please let us know.
Thanks,
Jarrett J.
On Fri, Sep 28, 2018 at 10:02 AM Mark Saper <sa...@um...<mailto:sa...@um...>> wrote:
Hi Tom,
Will PyMOL be supporting macOS Mojave (10.14) anytime soon? 10.14 is still supposed to support OpenGL but it is deprecated.
Thanks, Mark
_______________________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
Room 3220B, MSRB III sa...@um...<mailto:sa...@um...> +1 (734) 764-3353 mobile: (734) 276-6505
_______________________________________________
PyMOL-users mailing list (PyM...@li...<mailto:PyM...@li...>)
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--
Jarrett Johnson
PyMOL Developer
Schrödinger, Inc.

That’s great to hear! Med school is preparing new core images based on 10.14. 
_____________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
Room 3220B, MSRB III | sa...@um... | +1 (734) 764-3353 
> On Sep 28, 2018, at 12:58 PM, Jarrett Johnson <jar...@sc...> wrote:
> 
> Hi Mark,
> 
> I hope everything is still going well! According to initial tests we ran on MacOS 10.14, PyMOL seems to run well. If you or any other users do come across any issues, please let us know.
> 
> Thanks,
> 
> Jarrett J.
> 
>> On Fri, Sep 28, 2018 at 10:02 AM Mark Saper <sa...@um...> wrote:
>> Hi Tom,
>> 
>> Will PyMOL be supporting macOS Mojave (10.14) anytime soon? 10.14 is still supposed to support OpenGL but it is deprecated.
>> 
>> Thanks, Mark
>> _______________________________________________
>> Mark A. Saper, Ph.D.
>> Associate Professor of Biological Chemistry, U-M Medical School
>> Room 3220B, MSRB III sa...@um... +1 (734) 764-3353 mobile: (734) 276-6505
>> 
>> 
>> 
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
> 
> 
> -- 
> Jarrett Johnson
> PyMOL Developer
> Schrödinger, Inc.

Hi Mark,
I hope everything is still going well! According to initial tests we ran on
MacOS 10.14, PyMOL seems to run well. If you or any other users do come
across any issues, please let us know.
Thanks,
Jarrett J.
On Fri, Sep 28, 2018 at 10:02 AM Mark Saper <sa...@um...> wrote:
> Hi Tom,
>
> Will PyMOL be supporting macOS Mojave (10.14) anytime soon? 10.14 is
> still supposed to support OpenGL but it is deprecated.
>
> Thanks, Mark
> _______________________________________________
> Mark A. Saper, Ph.D.
> Associate Professor of Biological Chemistry, U-M Medical School
> Room 3220B, MSRB III sa...@um... +1 (734) 764-3353 mobile: (734)
> 276-6505
>
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
-- 
Jarrett Johnson
PyMOL Developer
Schrödinger, Inc.

Hi Tom,
Will PyMOL be supporting macOS Mojave (10.14) anytime soon? 10.14 is still supposed to support OpenGL but it is deprecated.
Thanks, Mark
_______________________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
Room 3220B, MSRB III sa...@um... +1 (734) 764-3353 mobile: (734) 276-6505

I would like to use https://github.com/schrodinger/pymol-open-source for my
installation. Instead of using conventional Python, most preferably
Miniconda Python 3, and Miniconda Python 2 if that is not possible, on
CentOS 6. Assuming the dependencies are installed by yum, are there any
procedures in installing to Conda so that it becomes a similar state as
"conda install -c schrodinger pymol" without needing to get a license?
(I'm planning to incorporate as a backend for a distributable pipeline)
Thank you very much.

Dear all,
In recent past in PyMOL one could move the center of the screen using mouse middle button (clock-hold-move). Now middle button invokes zooming. Would anyone know how the center can be moved now?
Thank you.
Regards,
Vaheh Oganesyan, PhD
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.

Hi Ryan,
This problem will most likely be solved if you update your graphics driver. As far as I can tell, your driver version is 5 years old, back then Intel drivers have been quite problematic. 
You can download the latest driver update here:
https://downloadcenter.intel.com/download/27441/Graphics-Intel-Graphics-Driver-for-Windows-7-8-1-15-36-?product=81496
Cheers,
 Thomas
> On Sep 14, 2018, at 4:57 PM, Kung, Ryan <rya...@ul...> wrote:
> 
> Hello all,
> 
> I installed Pymol 2.2.0 for Windows 7 yesterday and I have been running into some problems. Specifically, when I try to open almost any files it almost always crashes. Those files that it does open crash as soon as I select any atoms. On startup my PyMOL prints:
> 
> PyMOL(TM) 2.2.0 - Incentive Product
> Copyright (C) Schrodinger, LLC
> 
> This Executable Build integrates and extends Open-Source PyMOL.
> Detected OpenGL version 4.0. Shaders available.
> GLERROR 0x0500: CShaderPrg::reload begin
> Geometry shaders not available
> Detected GLSL version 4.0.
> OpenGL graphics engine:
> GL_VENDOR: Intel
> GL_RENDERER: Intel(R) HD Graphics 4600
> GL_VERSION: 4.0.0 - Build 9.18.10.3220
> License Expiry date: 26-jan-2021
> Detected 8 CPU cores. Enabled multithreaded rendering.
> 
> To be clear, when I say crashes it has a popup window that says "pythonw.exe has stopped working". I was hoping that someone else had experienced similar problems and had a solution. I have tried uninstalling and reinstalling from both exe installer and zip archive. Neither have fixed the problem. Thanks for your help.
> 
> Ryan Kung
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hello all,
I installed Pymol 2.2.0 for Windows 7 yesterday and I have been running
into some problems. Specifically, when I try to open almost any files it
almost always crashes. Those files that it does open crash as soon as I
select any atoms. On startup my PyMOL prints:
PyMOL(TM) 2.2.0 - Incentive Product
Copyright (C) Schrodinger, LLC
This Executable Build integrates and extends Open-Source PyMOL.
 Detected OpenGL version 4.0. Shaders available.
GLERROR 0x0500: CShaderPrg::reload begin
Geometry shaders not available
Detected GLSL version 4.0.
OpenGL graphics engine:
GL_VENDOR: Intel
GL_RENDERER: Intel(R) HD Graphics 4600
GL_VERSION: 4.0.0 - Build 9.18.10.3220
License Expiry date: 26-jan-2021
Detected 8 CPU cores. Enabled multithreaded rendering.
To be clear, when I say crashes it has a popup window that says
"pythonw.exe has stopped working". I was hoping that someone else had
experienced similar problems and had a solution. I have tried uninstalling
and reinstalling from both exe installer and zip archive. Neither have
fixed the problem. Thanks for your help.
Ryan Kung

Got it, thanks!
On Fri, Sep 14, 2018 at 11:51 AM Thomas Holder <
tho...@sc...> wrote:
> Hi Puneet,
>
> Incentive PyMOL installation instructions:
> https://pymol.org/support#installation
>
> Open-Source PyMOL installation instructions:
> https://pymolwiki.org/index.php/Linux_Install
>
> Cheers,
> Thomas
>
> > On Sep 14, 2018, at 7:08 AM, puneet garg <pun...@gm...> wrote:
> >
> > Hi,
> > Can anyone send me instructions on how to install PyMOL on CentOS 7
> > Thanks
> > --
> > Puneet
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
-- 
Puneet
Structural Biology Lab
Biotechnology Dept.
IIT Madras
Chennai-600036

Hi Puneet,
Incentive PyMOL installation instructions:
https://pymol.org/support#installation
Open-Source PyMOL installation instructions:
https://pymolwiki.org/index.php/Linux_Install
Cheers,
 Thomas
> On Sep 14, 2018, at 7:08 AM, puneet garg <pun...@gm...> wrote:
> 
> Hi,
> Can anyone send me instructions on how to install PyMOL on CentOS 7
> Thanks
> -- 
> Puneet
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi,
Can anyone send me instructions on how to install PyMOL on CentOS 7
Thanks
-- 
Puneet

To verify.
Lei Xu

Hi All,
I'll like to share with you the availability of the following command line scripts:
. PyMOLAlignChains.py
. PyMOLCalculateProperties.py
. PyMOLCalculateRMSD.py
. PyMOLConvertLigandFileFormat.py
. PyMOLConvertPMLToPSE.py
. PyMOLInfoMacromolecules.py
. PyMOLSplitChainsAndLigands.py
. PyMOLVisualizeCryoEMDensity.py
. PyMOLVisualizeElectronDensity.py
. PyMOLVisualizeMacromolecules.py
These scripts are distributed as part of MayaChemTools, a growing collection of command line Perl and Python scripts to support a variety of day-to-day computational discovery needs.
The scripts have been tested using the latest open source release of PyMOL available for both Python2 and Python3. They appear to work as expected, as far as I can tell. An extensive set of documentation is also available for the scripts.
Please visit www.MayaChemTools.org for additional details and to download the package.
Your feedback is welcome. 
Happy scripting,
Manish Sud 
ms...@sa...

07.09.2018 19:00, pym...@li... пишет:
> When launching PyMOL, there should be information regarding your graphics
> settings. Can you provide that for us?
This one?
 Detected OpenGL version 4.6. Shaders available.
 Detected GLSL version 4.60. OpenGL graphics engine: 
  GL_VENDOR:  NVIDIA Corporation 
  GL_RENDERER: GeForce GTX 750 Ti/PCIe/SSE2 
  GL_VERSION: 4.6.0 NVIDIA 390.87 
 Detected 8 CPU cores. Enabled multithreaded rendering.
Anyway, over the weekend after several tries of utterly shamanistic 
actions (rebooting several times, switching back and forth between 
nvidia and nouveau drivers, reinstalling dependencies and rebuilding 
PyMOL) the problem fixed itself. (The graphics settings information 
above was copied when the program was still non-functional)
Thank you for your attention.

Hi Markus,
Is there still a gap (between atoms and cartoon) when you turn on the backbone residues in question?
J
From: Markus Heller <mh...@cd...>
Sent: Thursday, 6 September 2018 6:26 PM
To: pym...@li...
Subject: [PyMOL] Hbond to backbone cartoon
Hi all,
what's the best way to show a hydrogen bond to a backbone atom in the following scenario:
Protein shown as cartoon, ligand as sticks, binding site residues (within 5A of ligand) shown as lines, and sidechain help is on.
If the ligand forms a hydrogen bond with a backbone atom, the dashes don't touch the cartoon, but leave a gap. What's the recommended solution (or workaround) to avoid this gap?
Thanks
Markus

Hi Timofey,
When launching PyMOL, there should be information regarding your graphics
settings. Can you provide that for us?
Jarrett J.
On Thu, Sep 6, 2018 at 9:28 AM, Timofey Tyugashev <tyu...@ni...>
wrote:
> The display window is unable to display anything, shows only distorted
> desktop background, assorted parts of other background applications and so
> on.
> Terminal outputs lines like these after any mouse movement over the window:
>
> Traceback (most recent call last):
> File "/home/timofey/biochem/pymol-svn/lib/python2.7/site-packages/pmg_qt/pymol_gl_widget.py",
> line 151, in mouseMoveEvent
> self.pymol.drag(int(self.fb_scale * ev.x()),
> AttributeError: 'PyMOLGLWidget' object has no attribute 'fb_scale'
>
>
> Open-source PyMOL installed on Linux Mint 19 (nvidia-390 drivers)
> according to Linux_Install page on pymolwiki.
> (python setup.py build install --prefix=~/biochem/pymol-svn
> --use-msgpackc=no)
>
>
> ------------------------------------------------------------
> ------------------
> 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...
-- 
Jarrett Johnson
PyMOL Developer
Schrödinger, Inc.

The display window is unable to display anything, shows only distorted 
desktop background, assorted parts of other background applications and 
so on.
Terminal outputs lines like these after any mouse movement over the window:
Traceback (most recent call last):
  File 
"/home/timofey/biochem/pymol-svn/lib/python2.7/site-packages/pmg_qt/pymol_gl_widget.py", 
line 151, in mouseMoveEvent
   self.pymol.drag(int(self.fb_scale * ev.x()),
AttributeError: 'PyMOLGLWidget' object has no attribute 'fb_scale'
Open-source PyMOL installed on Linux Mint 19 (nvidia-390 drivers) 
according to Linux_Install page on pymolwiki.
(python setup.py build install --prefix=~/biochem/pymol-svn 
--use-msgpackc=no)

Dear Pymol Developers,
Just as an out-there question, I was wondering if Pymol will try to use any
of the real-time ray tracing features in the new Nvidia 20-series cards in
future?
Best wishes
Shintaro

Hi all,
what's the best way to show a hydrogen bond to a backbone atom in the following scenario:
Protein shown as cartoon, ligand as sticks, binding site residues (within 5A of ligand) shown as lines, and sidechain help is on.
If the ligand forms a hydrogen bond with a backbone atom, the dashes don't touch the cartoon, but leave a gap. What's the recommended solution (or workaround) to avoid this gap?
Thanks
Markus

Hi Santrupti,
In Chemoinformatics "heavy atoms" are all non-hydrogen atoms. In crystallography, "heavy atoms" could mean the atoms used for experimental phasing, like selenium.
I hope these examples answer your questions:
# non-hydrogen RMSD
align prot1 & not hydro, prot2 & not hydro, cycles=0
# SE atom RMSD
align prot1 & elem SE, prot2 & elem SE, cycles=0
# backbone RMSD
align prot1 & name N+C+CA+O, prot2 & name N+C+CA+O, cycles=0
# pairwise RMSD for a lot of structures, using Python API
python
import itertools
models = cmd.get_object_list()
for m1, m2 in itertools.combinations(models, 2):
 s1 = m1 + " & name N+C+CA+O"
 s2 = m2 + " & name N+C+CA+O"
 a = cmd.align(s1, s2, cycles=0)
 print("Backbone RMSD for {} and {}: {}".format(m1, m2, a[0]))
python end
Please also read https://pymolwiki.org/index.php/Align
Cheers,
 Thomas
> On Aug 30, 2018, at 10:42 PM, Santrupti Nerli <sn...@uc...> wrote:
> 
> Hi,
> 
> I want to calculate pairwise RMSD for heavy atoms and backbone atoms.
> 
> I see that for backbone, I can use name n+c+ca+o. But, do the same atoms also represent heavy atoms?
> 
> What are the differences between backbone and heavy atoms? How to compute pairwise RMSD for a lot of structures? Can I use align here?
> 
> Thank you very much.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Abhik,
extra_fit calls cmd.align() for all objects in the selection, with target=reference.
Implementation:
https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/fitting.py#L139
Documentation:
https://pymolwiki.org/index.php/Extra_fit
Hope that helps.
Cheers,
 Thomas
> On Aug 22, 2018, at 4:55 PM, abh...@bo... wrote:
> 
> Hello All
> I want to know how the "Extra_fit" option works in pymol (Detail algorithm
> or procedure). Any idea regarding this.
> All suggestions are welcome.
> Thank you.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

A short how-to
https://www.macinchem.org/reviews/3D/augmented.php <https://www.macinchem.org/reviews/3D/augmented.php>
Cheers
Chris
> 
> Message: 1
> Date: 2018年8月31日 12:26:03 -0400
> From: Abel J Baerga Ortiz <abe...@up...>
> To: pym...@li...
> Subject: [PyMOL] PDB structure to .obj or .fbx
> Message-ID:
> 	<CAA...@ma...>
> Content-Type: text/plain; charset="utf-8"
> 
> Hello all,
> 
> Is there any way to convert a .pdb structure to a .obj or .fbx file? I
> would like to incorporate protein structures into virtual reality
> experiences and these are the common formats.
> 
> Abel Baerga Ortiz
> U of Puerto Rico
> 
> -- 
> Abel Baerga Ortiz, PhD.
> Catedr?tico Asociado
> Departamento de Bioqu?mica
> Escuela de Medicina
> Universidad de Puerto Rico
> PO Box 365067
> San Juan, Puerto Rico
> 00936-5067
> 
> t. 787-758-2525 x1603
> f. 787-274-8724
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