pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] PyMOL 3 Webinar Recording and Online Course

[Thomas S. <tho...@sc...>]

Hello everyone,

I recently covered many of the new features of PyMOL 3.0 during a webinar
hosted by Schrödinger, the recording of which can be found here: Webinar
Recording
<https://www.schrodinger.com/life-science/learn/webinar/introducing-pymol-3-bring-your-biochemistry-to-life-with-3d-molecular-visualization-and-movie-making/>

In this webinar, I'll show you the following:

   -

   Basics of the new interface and motivation behind its design
   -

   New Scenes Panel and power of scenes as a tool
   -

   New Timeline and how easy it is to make basic movies
   -

   Introduction to advanced movie making using subtracks
   -

   Animating objects in the workspace using the new Gizmo
   -

   Q&A with the developers regarding PyMOL 3 and future plans


For those of you interested in exploring PyMOL 3
<https://www.schrodinger.com/platform/products/pymol/>, I hope this serves
as a solid starting point and inspires you to delve deeper into the
possibilities of all the new features. For anyone still not convinced to
give it a try, I would encourage you to skim the recording to see the
improvements in action.

Additionally, we are offering a free online course to anyone with a valid
PyMOL license (including educational licenses for students). This course is
titled “Visualizing Science with PyMOL 3” and will provide a far more
comprehensive overview of what is possible with PyMOL 3. Click this link to
learn more and join the waitlist: Visualizing Science with PyMOL 3
<https://www.schrodinger.com/life-science/learn/education/courses/pymol/>

Excited to see what you create,

- The PyMOL Team at Schrödinger
-- 

Thomas Stewart | Developer II | Product Manager, PyMOL

[image: Schrödinger, Inc.] <https://schrodinger.com/>

Re: [PyMOL] Exporting movie as PNG frames produces only single frame

[Jarrett J. <jar...@sc...>]

Hi Christoph,

Thanks for trying out the new Timeline panel. I received reports this issue
but forgot to track and add for yesterday's patch; I'll make sure that the
PNG frame export is consistent with the timeline for the next patch release.

As for the 30 global frames vs 60 composition frames you see, this is
another difference from PyMOL2's movie maker, which perhaps could be made a
little bit more clear in the documentation. In the previous movie maker
version, the number of frames exported from a movie was intimately tied to
molecular state whereas in PyMOL 3, each composition's length is set
independent of multistate objects. The composition FPS is currently locked
at 60fps for now, but this will eventually be customizable per composition
soon.

Best,
Jarrett J.

On Thu, May 2, 2024 at 1:13 PM Christoph Parthier via PyMOL-users <
pym...@li...> wrote:

> Hi,
>
> I'm currently trying out the improved movie functions of PyMOL 3.03
> (timeline, scenes) which I think are a great improvement.  However, I
> noticed when I want to write out a composition as single frames (PNG) using
> the 'Export movie' function only one frame gets written (the first one).
> When exporting as MPEG1 movie the composition is exported normally (all
> frames). I also noticed creating a composition does not trigger the display
> of the 'global frames panel', while in PyMOL 2.x adding a movie program
> (e.g. scene loop) would display (and update) the number of frames the movie
> contains.
>
> In contrast, creating a morph (e.g. over 30 states) will trigger the
> 'global frames' panel showing 30 frames. When creating a 'state sweep'
> movie from the morph using the movie commands the corresponding 60 frames
> are shown (and played) in the timeline, but the 'global frames' panel still
> shows only 30 frames. Also exporting the frames as PNGs will only export
> the first 30 frames representing the different states, while the
> MPEG1-export function will export the full state sweep movie.
>
> I tried this with PyMOL 3.03 running under Linux and also Windows 10. The
> observed behavior is the same.
>
> Is there anything that's wrong in my approach?
>
> Christoph
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] Exporting movie as PNG frames produces only single frame

[Christoph P. <cpa...@go...>]

Hi,

I'm currently trying out the improved movie functions of PyMOL 3.03
(timeline, scenes) which I think are a great improvement.  However, I
noticed when I want to write out a composition as single frames (PNG) using
the 'Export movie' function only one frame gets written (the first one).
When exporting as MPEG1 movie the composition is exported normally (all
frames). I also noticed creating a composition does not trigger the display
of the 'global frames panel', while in PyMOL 2.x adding a movie program
(e.g. scene loop) would display (and update) the number of frames the movie
contains.

In contrast, creating a morph (e.g. over 30 states) will trigger the
'global frames' panel showing 30 frames. When creating a 'state sweep'
movie from the morph using the movie commands the corresponding 60 frames
are shown (and played) in the timeline, but the 'global frames' panel still
shows only 30 frames. Also exporting the frames as PNGs will only export
the first 30 frames representing the different states, while the
MPEG1-export function will export the full state sweep movie.

I tried this with PyMOL 3.03 running under Linux and also Windows 10. The
observed behavior is the same.

Is there anything that's wrong in my approach?

Christoph

Re: [PyMOL] ordering objects in the Object Control Panel in PyMOL 3

[Thomas S. <tho...@sc...>]

Hello Engin,

This is something I'm actively working on and should be improved in the
near future. I unfortunately had to disable reordering for/within groups
until the feature can be implemented properly (including with groups of
groups, which are also currently disabled). With regard to the Ctrl-single
click drag, this is just an oversight on my part and should be easy to
correct. I tend to always use a mouse when I'm developing/testing, so it's
easy for me to forget where the trackpad controls need special
consideration. Hopefully some or all of these concerns will be addressed in
an upcoming patch and I will go through the rest of the 3.0 changes using
only the trackpad to try to catch any similar issues.

Thanks,
Thomas Stewart

On Thu, Apr 25, 2024 at 10:57 AM Engin Özkan <eo...@uc...> wrote:

> Hi,
>
> I have been using the new PyMOL 3.0.2 for the last week. One of the
> issues I've come across is that ordering objects and selections appear
> in the Object Control Panel sometimes fails. I can two-finger drag to
> move them sometimes in 1-button-viewing mode (on a MacBook Pro, OS
> 14.4.1 using the trackpad), but I can no longer do that with
> Ctrl-single-click -> drag, which used to be possible in PyMOL 2. I
> cannot figure out why reordering sometimes fails and sometimes does not,
> but it may be that I cannot move an object or selection to a position
> above a group, but only below. Deleting all groups lets me fully order
> the list again using two-finger drag (but ctrl-drag still does not work).
>
> Also I have not managed to move groups at all using mouse actions. I
> have not tried the order command in command line.
>
> Best,
>
> Engin
>
>
> --
> Engin Özkan, Ph.D.
> Associate Professor
> Dept of Biochemistry and Molecular Biology
> University of Chicago
> http://ozkan.uchicago.edu
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

Thomas Stewart | Developer II | Product Manager, PyMOL

[image: Schrödinger, Inc.] <https://schrodinger.com/>

[PyMOL] ordering objects in the Object Control Panel in PyMOL 3

[Engin Ö. <eo...@uc...>]

Hi,

I have been using the new PyMOL 3.0.2 for the last week. One of the 
issues I've come across is that ordering objects and selections appear 
in the Object Control Panel sometimes fails. I can two-finger drag to 
move them sometimes in 1-button-viewing mode (on a MacBook Pro, OS 
14.4.1 using the trackpad), but I can no longer do that with 
Ctrl-single-click -> drag, which used to be possible in PyMOL 2. I 
cannot figure out why reordering sometimes fails and sometimes does not, 
but it may be that I cannot move an object or selection to a position 
above a group, but only below. Deleting all groups lets me fully order 
the list again using two-finger drag (but ctrl-drag still does not work).

Also I have not managed to move groups at all using mouse actions. I 
have not tried the order command in command line.

Best,

Engin


-- 
Engin Özkan, Ph.D.
Associate Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
http://ozkan.uchicago.edu

[PyMOL] Announcing PyMOL 3.0 Release

[Jarrett J. <jar...@sc...>]

Greetings,

We are happy to announce the release of PyMOL 3.0! Download ready-to-use
bundles from https://pymol.org/ or update your installation with:

conda install -c conda-forge -c schrodinger pymol


Incentive features:

   -

   Revamped User Interface:
   -

      PyMOL 3 introduces a modern, minimalist interface, blending
      innovation and nostalgia. This refreshed design seamlessly integrates
      frequently used features and provides a fresh yet familiar user
experience.
      -

   New Scenes Panel:
   -

      Effortlessly organize work with the Scenes panel, featuring
      thumbnails for easy visualization and storyboarding. Manage scenes with
      ease, streamlining workflow and enhancing productivity.
      -

   New Movie Maker (Timeline) Panel:
   -

      Craft professional-quality movies and animations with the new
      Timeline. Drag and drop keyframes to adjust camera views and molecular
      structures, enabling seamless transitions and dynamic storytelling.
      -

   New Presets Panel:
   -

      Personalize presentation style with the Presets panel, enabling the
      import, editing, and export of style presets and scripts. Customize PyMOL
      to suit unique needs, empowering users to tailor settings to their
      preferences.
      -

   New Gizmo:
   -

      A new 3D tool to facilitate seamless movement and rotation of
      independent molecular objects within the workspace.


Open-source features migrated from Incentive:

   -

   APBS electrostatics plugin:
   -

      This plugin allows users to run macromolecular electrostatics
      calculations and display the results as a color gradient on the
surface of
      a given molecule.
      -

   Nucleic acid builder:
   -

      Expands the functionality of the builder panel to include nucleic
      acids. Create or extend nucleic acid chains with single residues or base
      pairs. This feature can also be accessed through the fnab command.


We remain committed to improving open-source PyMOL and will continue to
migrate over certain incentive features in addition to the standard bug
fixes.

Fellowship:

   -

   Announcements regarding the 2024-2025 Warren L. DeLano Memorial PyMOL
   Fellowship will be announced within the next several weeks.
   -

   Learn more information about the fellowship and see previous fellows at
   https://pymol.org/fellowship/


Other relevant links:

   -

   Find the complete release notes at: https://pymol.org/d/media:new
   <https://pymol.org/d/media:new30>30
   -

   Check out the Schrödinger Product Page for PyMOL:
   https://www.schrodinger.com/platform/products/pymol/


We welcome any feedback and bug reports.

Cheers,

- The PyMOL Team at Schrödinger


-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] 16th Annual CCP4/APS Crystallographic School (2024) in the US

[Qingping Xu <qx...@an...>]

Dear Colleagues,

We are pleased to announce the 16th annual CCP4/APS crystallographic 
school “From data collection to structure refinement and beyond” will be 
held on Oct 28th to Nov 4th, 2024 at the Advanced Photon Source (APS), 
Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All 
details can be found at the school website: 
http://www.ccp4.ac.uk/schools/APS-2024/index.php. This will be our first 
work post the APS-U upgrade.


Dates: October 28 through November 4, 2024

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near

Chicago), Illinois, USA

The school comprises two parts: data collection (provisional pending APS 
availability) workshop and crystallographic computing workshop. Data 
collection workshop includes beamline training, data collection on 
GM/CA@APS beamlines, and data processing, using only the participants' 
crystals. Crystallographic computation workshop will feature many modern 
crystallographic software packages taught by authors and other experts. 
This workshop will also introduce elements of CryoEM. The daily schedule 
will be organized in three sections – lectures, tutorials, and hands-on 
(interactive trouble-shooting of the technical difficulties the 
participants face in their projects). We have had considerable success 
resolving these problems in past years, attested by resulting 
publications (see 
http://www.ccp4.ac.uk/schools/APS-school/publications.php). A draft 
program can be found at the School website.

Applicants: The workshop strongly encourages students who need expert 
help with difficulties/challenges in their own projects. Graduate 
students, postdoctoral researchers and early-career faculty, along with 
commercial/industrial researchers are encouraged to apply. Only about 20 
applicants will be selected for participation.

Application: Application deadline is  August 31st, 2024. To apply, 
visit  https://www.ccp4.ac.uk/schools/APS-2024/application.php

Fees: There is a $500 participation fee for the selected academic 
students and $1500 for industrial researchers. No credit card will be 
required for registration, students who are selected to participate will 
be contacted to pay. The students will be responsible for their 
transportation and lodging. The workshop organizers can assist in making 
lodging reservations at the Argonne Guest House. The workshop will cover 
all other expenses (including meals).


We hope to see you at the school.

Charles, Andrey, Garib and Qingping

Re: [PyMOL] labels on nucleic acids

[Jarrett J. <jar...@sc...>]

Hi Joel,

Unless I'm misunderstanding, the label command, label menu, and the label
wizard all support proteins and nucleic acids. Do you have an example where
that's not the case?

Best,
Jarrett J.

On Wed, Apr 3, 2024 at 4:16 AM Joel Mackay via PyMOL-users <
pym...@li...> wrote:

> Hi
>
> Am using pymol 3. Am I correct in thinking that you can’t use the ‘label’
> dialogues to label nucleotides in a nucleic acid? Only proteins?
>
> Thanks
> Joel
>
>
>
>
>
>
> -----------------------------------------------------------------------------------------------------------------------------
>
> *Professor Joel Mackay*
>
> School of Life and Environmental Sciences
>
> THE UNIVERSITY OF SYDNEY
>
>
>
> A: School of Life and Environmental Sciences | Rm 674, Building G08 |
> Butlin Ave
>
> The University of Sydney | NSW | 2006 | Australia
>
> T: +61 2 9351 3906
>
> E: joe...@sy...  | W: www.mackaymatthewslab.org
> <https://url.au.m.mimecastprotect.com/s/0-PhCE8wmrt130Xr6Sp2TTu?domain=mackaymatthewslab.org>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] labels on nucleic acids

[Joel M. <joe...@sy...>]

Hi
Am using pymol 3. Am I correct in thinking that you can't use the 'label' dialogues to label nucleotides in a nucleic acid? Only proteins?
Thanks
Joel


-----------------------------------------------------------------------------------------------------------------------------
Professor Joel Mackay
School of Life and Environmental Sciences
THE UNIVERSITY OF SYDNEY

A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave
The University of Sydney | NSW | 2006 | Australia
T: +61 2 9351 3906
E: joe...@sy...<mailto:joe...@sy...>  | W: www.mackaymatthewslab.org<https://url.au.m.mimecastprotect.com/s/0-PhCE8wmrt130Xr6Sp2TTu?domain=mackaymatthewslab.org>

Re: [PyMOL] create new object from selection - version 3.0

[Joel M. <joe...@sy...>]

Thanks very much for the response Jarrett – great to know it’s been ID-ed and is in the process of being mended.
J


-----------------------------------------------------------------------------------------------------------------------------
Professor Joel Mackay
School of Life and Environmental Sciences
THE UNIVERSITY OF SYDNEY

A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave
The University of Sydney | NSW | 2006 | Australia
T: +61 2 9351 3906
E: joe...@sy...<mailto:joe...@sy...>  | W: www.mackaymatthewslab.org<https://url.au.m.mimecastprotect.com/s/0-PhCE8wmrt130Xr6Sp2TTu?domain=mackaymatthewslab.org>

From: Jarrett Johnson <jar...@sc...>
Sent: Tuesday, April 2, 2024 2:57 PM
To: Joel Mackay <joe...@sy...>
Cc: pym...@li...
Subject: Re: [PyMOL] create new object from selection - version 3.0

Hi Joel,

Thanks for your feedback. You're correct in both assessments. I can reproduce the first issue (the `copy to object` menu should produce a submenu), and should be able to get a fix for that very soon. There are some submenu quirks that are still being ironed out; some of which, at least for linux, are also being addressed this week--but all still ongoing.

Best,
Jarrett J.

On Mon, Apr 1, 2024 at 10:16 PM Joel Mackay via PyMOL-users <pym...@li...<mailto:pym...@li...>> wrote:
Hi
I’ve always found the command allowing you to create a ‘cloned’ object from a selection to be extremely useful. That is, select a chain (for example) and then use:

Action > copy to object > new

This seems to be disabled in version 3. You can extract a chain that you’ve selected, but not make a fresh copy. Am I just missing something?

[It also seems a bit strange that submenus now don’t disappear as you scroll down the list of possible actions, until you reach the next command that has a submenu – it’s a bit disconcerting]

Thanks
Joel


[cid:image001.png@01DA8513.C8E14410]
-----------------------------------------------------------------------------------------------------------------------------
Professor Joel Mackay
School of Life and Environmental Sciences
THE UNIVERSITY OF SYDNEY

A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave
The University of Sydney | NSW | 2006 | Australia
T: +61 2 9351 3906
E: joe...@sy...<mailto:joe...@sy...>  | W: www.mackaymatthewslab.org<https://url.au.m.mimecastprotect.com/s/N7OGCROND2unrxr95T91Df2?domain=mackaymatthewslab.org>

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Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://url.au.m.mimecastprotect.com/s/RukhCWLVXkUzjVj7DSKq6AH?domain=sourceforge.net>


--

Jarrett Johnson | Senior Developer, PyMOL
[Image removed by sender.]

Re: [PyMOL] create new object from selection - version 3.0

[Jarrett J. <jar...@sc...>]

Hi Joel,

Thanks for your feedback. You're correct in both assessments. I can
reproduce the first issue (the `copy to object` menu should produce a
submenu), and should be able to get a fix for that very soon. There are
some submenu quirks that are still being ironed out; some of which, at
least for linux, are also being addressed this week--but all still ongoing.

Best,
Jarrett J.

On Mon, Apr 1, 2024 at 10:16 PM Joel Mackay via PyMOL-users <
pym...@li...> wrote:

> Hi
>
> I’ve always found the command allowing you to create a ‘cloned’ object
> from a selection to be extremely useful. That is, select a chain (for
> example) and then use:
>
>
>
> Action > copy to object > new
>
>
>
> This seems to be disabled in version 3. You can extract a chain that
> you’ve selected, but not make a fresh copy. Am I just missing something?
>
>
>
> [It also seems a bit strange that submenus now don’t disappear as you
> scroll down the list of possible actions, until you reach the next command
> that has a submenu – it’s a bit disconcerting]
>
>
>
> Thanks
> Joel
>
>
>
>
>
>
> -----------------------------------------------------------------------------------------------------------------------------
>
> *Professor Joel Mackay*
>
> School of Life and Environmental Sciences
>
> THE UNIVERSITY OF SYDNEY
>
>
>
> A: School of Life and Environmental Sciences | Rm 674, Building G08 |
> Butlin Ave
>
> The University of Sydney | NSW | 2006 | Australia
>
> T: +61 2 9351 3906
>
> E: joe...@sy...  | W: www.mackaymatthewslab.org
> <https://url.au.m.mimecastprotect.com/s/0-PhCE8wmrt130Xr6Sp2TTu?domain=mackaymatthewslab.org>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] create new object from selection - version 3.0

[Joel M. <joe...@sy...>]

Hi
I've always found the command allowing you to create a 'cloned' object from a selection to be extremely useful. That is, select a chain (for example) and then use:

Action > copy to object > new

This seems to be disabled in version 3. You can extract a chain that you've selected, but not make a fresh copy. Am I just missing something?

[It also seems a bit strange that submenus now don't disappear as you scroll down the list of possible actions, until you reach the next command that has a submenu - it's a bit disconcerting]

Thanks
Joel


[cid:image001.png@01DA84FA.CEE5D470]
-----------------------------------------------------------------------------------------------------------------------------
Professor Joel Mackay
School of Life and Environmental Sciences
THE UNIVERSITY OF SYDNEY

A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave
The University of Sydney | NSW | 2006 | Australia
T: +61 2 9351 3906
E: joe...@sy...<mailto:joe...@sy...>  | W: www.mackaymatthewslab.org<https://url.au.m.mimecastprotect.com/s/0-PhCE8wmrt130Xr6Sp2TTu?domain=mackaymatthewslab.org>

Re: [PyMOL] where can I ask questions? Is there any forum?

[Elizabeth T. <tsa...@ho...>]

Thank you very much for your reply.
I will work some things that are seemingly working
for the moment
and if I see this does not lead anywhere, I ll come back to you.

Greetings,
Elizabeth

Sent from Outlook<http://aka.ms/weboutlook>

________________________________
From: Dr. Vijay Masand <vij...@gm...>
Sent: Monday, April 1, 2024 5:02 PM
To: Elizabeth Tsakelidou <tsa...@ho...>
Cc: pymol-users <pym...@li...>
Subject: Re: [PyMOL] where can I ask questions? Is there any forum?

Dear Elizabeth
A simple solution is to use DockingApp in Windows. Downliad it from following site:
http://www.computationalbiology.it/software.html
It is very easy to use it. Contact if you need any help.
From
Dr. Vijay H. Masand


On Mon, 1 Apr, 2024, 8:55 pm Elizabeth Tsakelidou, <tsa...@ho...<mailto:tsa...@ho...>> wrote:

Hey

I would like to know what is the best way to install and work protein-ligand docking.
I have Windows 11 and I tried Anaconda PyMOL but I think this way
you cannot have all plugins available.
So, what if I tried ubuntu with all is available on GitHub?
Can I do this?
The query arises because it is said that if you want to install linux in windows
you better use cygwin.
What do you think?
Thanks

Elizabeth

Sent from Outlook<http://aka.ms/weboutlook>

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Archives: http://www.mail-archive.com/pym...@li...
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Re: [PyMOL] where can I ask questions? Is there any forum?

[Dr. V. M. <vij...@gm...>]

Dear Elizabeth
A simple solution is to use DockingApp in Windows. Downliad it from
following site:
http://www.computationalbiology.it/software.html
It is very easy to use it. Contact if you need any help.
From
Dr. Vijay H. Masand


On Mon, 1 Apr, 2024, 8:55 pm Elizabeth Tsakelidou, <tsa...@ho...>
wrote:

>
> Hey
>
> I would like to know what is the best way to install and work
> protein-ligand docking.
> I have Windows 11 and I tried Anaconda PyMOL but I think this way
> you cannot have all plugins available.
> So, what if I tried ubuntu with all is available on GitHub?
> Can I do this?
> The query arises because it is said that if you want to install linux in
> windows
> you better use cygwin.
> What do you think?
> Thanks
>
> Elizabeth
>
> Sent from Outlook <http://aka.ms/weboutlook>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] where can I ask questions? Is there any forum?

[Tamas H. <bio...@gm...>]

Hi,

I think that you have two issues:

#1 pymol autodock/vina plugin; it should work on windows, since it is written in python. The issue u might encounter: it may have written in an older python version than the pymol install

#2 you have to perform the docking with autodock or autodock vina. I think that these will not run on win.
You also have to prepare the prot and small molecule w autodocktools. Some gui apps might have preparation wizard.

Bests



⁣Az Android BlueMail letöltése ​

2024. ápr. 1. 17:23-n, 17:23-kor, Elizabeth Tsakelidou <tsa...@ho...> ezt írta:
>
>Hey
>
>I would like to know what is the best way to install and work
>protein-ligand docking.
>I have Windows 11 and I tried Anaconda PyMOL but I think this way
>you cannot have all plugins available.
>So, what if I tried ubuntu with all is available on GitHub?
>Can I do this?
>The query arises because it is said that if you want to install linux
>in windows
>you better use cygwin.
>What do you think?
>Thanks
>
>Elizabeth
>
>Sent from Outlook<http://aka.ms/weboutlook>
>
>
>------------------------------------------------------------------------
>
>
>
>------------------------------------------------------------------------
>
>_______________________________________________
>PyMOL-users mailing list
>Archives: http://www.mail-archive.com/pym...@li...
>Unsubscribe:
>https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] where can I ask questions? Is there any forum?

[Elizabeth T. <tsa...@ho...>]

Hey

I would like to know what is the best way to install and work protein-ligand docking.
I have Windows 11 and I tried Anaconda PyMOL but I think this way
you cannot have all plugins available.
So, what if I tried ubuntu with all is available on GitHub?
Can I do this?
The query arises because it is said that if you want to install linux in windows
you better use cygwin.
What do you think?
Thanks

Elizabeth

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[PyMOL] parameters for cation-pi identification

[Julien B. <jul...@ki...>]

Dear All,
I am wondering what parameters (cutoff distance, angles, side chains relative orientations) are used by the functions implemented in pymol (distance (mode =7 and A>find>pi-cation))to define cation-pi interaction. I didn’t find it in the documentation. Is there any way to eventually tune these parameters?

Thank you for your responses,
Best,
Julien




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Re: [PyMOL] Pymol not opening files

[Petro <sub...@kh...>]

Thanks.
I will try that.

On Sun, 25 Feb 2024, 07:08 Jared Sampson, <jar...@co...>
wrote:

> Hi Shivani -
>
> PyMOL's defer_builds_mode
> <https://pymolwiki.org/index.php/Defer_builds_mode> setting can improve
> performance when loading large trajectories.
>
> You can type `set defer_builds_mode, 3` on the PyMOL command line or
> adjust it via the Settings > Edit All menu.
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
>
> On Fri, Feb 23, 2024 at 4:15 PM shivani godbole <shi...@gm...>
> wrote:
>
>> Hello,
>>
>> This is Shivani Godbole. I use Pymol for the movie files generated using
>> MD simulations. I am trying to use Pymol to visualize one of the movie
>> files which is around 2 GB in size, but Pymol keeps crashing every time I
>> open it. I was hoping you could assist me with the same. My computer
>> uses 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz   2.42 GHz processor
>> and has 8 GB RAM and a 64-bit OS.
>>
>> Thank you!
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Pymol not opening files

[Jared S. <jar...@co...>]

Hi Shivani -

PyMOL's defer_builds_mode
<https://pymolwiki.org/index.php/Defer_builds_mode> setting can improve
performance when loading large trajectories.

You can type `set defer_builds_mode, 3` on the PyMOL command line or adjust
it via the Settings > Edit All menu.

Hope that helps.

Cheers,
Jared



On Fri, Feb 23, 2024 at 4:15 PM shivani godbole <shi...@gm...> wrote:

> Hello,
>
> This is Shivani Godbole. I use Pymol for the movie files generated using
> MD simulations. I am trying to use Pymol to visualize one of the movie
> files which is around 2 GB in size, but Pymol keeps crashing every time I
> open it. I was hoping you could assist me with the same. My computer
> uses 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz   2.42 GHz processor
> and has 8 GB RAM and a 64-bit OS.
>
> Thank you!
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] [Help]About indentifying interaction between residues

[Jared S. <jar...@co...>]

Hi Nikita -

To me this looks like the cartoon representation for missing residues,
which is controlled by the cartoon_gap_cutoff
<https://pymolwiki.org/index.php/Cartoon_gap_cutoff> setting.  If you
either `hide cartoon` or `set cartoon_gap_cutoff, 0`, does it go away?

Usually the dashed line would be somewhat curved for a normal gap to mimic
an unmodeled flexible loop, but I can reproduce something similar to your
image by creating a new object containing only with two non-contiguous
residues and showing the cartoon for that object:

```
fetch 1shv
as cartoon

create gap_res, polymer.protein and resi 237+243

show sticks, gap_res

```


Hope that helps.

Cheers,
Jared


On Sat, Feb 17, 2024 at 3:36 AM Maisnam Nikita Chanu <mni...@gm...>
wrote:

> Dear All,
>
> My name is Nikita, I am a graduate student at Academia Sinica, Taiwan.
> This e-mail aims to ask for help in identifying the bond/interaction
> between two residues.
>
> I am currently learning about PyMol to utilize in my project. I used PyMol
> to visualize potential H-bond interactions in specific amino acid residues.
> However, I have just discovered that Arg465 and Ser461 show a distinct
> interaction, as shown in the file.
> Please help identify this interaction.
> I would be grateful for any help or suggestions.
>
> Please don't hesitate to contact me if you have any questions.
> I look forward to hearing from you.
>
> Best regards,
> Nikita Chanu
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Pymol not opening files

[Petro <sub...@kh...>]

I would not use pymol for big trajectory analysis.



On Fri, 23 Feb 2024 at 22:13, shivani godbole <shi...@gm...> wrote:

> Hello,
>
> This is Shivani Godbole. I use Pymol for the movie files generated using
> MD simulations. I am trying to use Pymol to visualize one of the movie
> files which is around 2 GB in size, but Pymol keeps crashing every time I
> open it. I was hoping you could assist me with the same. My computer
> uses 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz   2.42 GHz processor
> and has 8 GB RAM and a 64-bit OS.
>
> Thank you!
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Pymol not opening files

[Roy, K. R. <kr...@Co...>]

Hi Shivani,

To avoid PyMOL crashes when handling large movie files, try reducing the file size, increasing virtual memory, minimizing memory usage by adjusting PyMOL settings, loading only specific frames, upgrading RAM or CPU, preprocessing the movie file with external tools, and closing other memory-intensive apps.



Regards,

[University of Houston logo]            Kushal Raj Roy (he/him)
MS | BS
Research Assistant
Department of Biology & Biochemistry
University of Houston
kr...@uh...<mailto:kr...@uh...>
https://uh.edu<https://uh.edu/>

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________________________________
From: shivani godbole <shi...@gm...>
Sent: Friday, February 23, 2024 3:12:31 PM
To: pym...@li... <pym...@li...>
Subject: [PyMOL] Pymol not opening files


Hello,

This is Shivani Godbole. I use Pymol for the movie files generated using MD simulations. I am trying to use Pymol to visualize one of the movie files which is around 2 GB in size, but Pymol keeps crashing every time I open it. I was hoping you could assist me with the same. My computer uses 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz   2.42 GHz processor and has 8 GB RAM and a 64-bit OS.

Thank you!

[PyMOL] Pymol not opening files

[shivani g. <shi...@gm...>]

Hello,

This is Shivani Godbole. I use Pymol for the movie files generated using MD
simulations. I am trying to use Pymol to visualize one of the movie files
which is around 2 GB in size, but Pymol keeps crashing every time I open
it. I was hoping you could assist me with the same. My computer uses 11th
Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz   2.42 GHz processor and has 8 GB
RAM and a 64-bit OS.

Thank you!

[PyMOL] Align command and alternate residue conformations

[João C. M. R. <ra...@mb...>]

Dear all,

I would like to compare two crystal structures of the same protein, one obtained by X-ray diffraction and the other by neutron diffraction. I used the Align command in PyMOL with zero cycles of refinement to align these structures and obtain a rmsd between all non-H/D protein atoms. However, I would like to understand how Align calculates the rmsd, specifically how does it handle alternate residue conformations. Does it pair side-chain conformations based on their name (e.g. A, B, C..) or on their spatial proximity (i.e., conformations are paired regarding their position). I can imagine 2 scenarios that might be problematic: 1) where the side-chain conformations closer in space have different names; 2) where one structure has a double side-chain conformation, and the other has a single conformation.

Best regards,
Joao Ramos

[PyMOL] [Help]About indentifying interaction between residues

[Maisnam N. C. <mni...@gm...>]

Dear All,

My name is Nikita, I am a graduate student at Academia Sinica, Taiwan.
This e-mail aims to ask for help in identifying the bond/interaction
between two residues.

I am currently learning about PyMol to utilize in my project. I used PyMol
to visualize potential H-bond interactions in specific amino acid residues.
However, I have just discovered that Arg465 and Ser461 show a distinct
interaction, as shown in the file.
Please help identify this interaction.
I would be grateful for any help or suggestions.

Please don't hesitate to contact me if you have any questions.
I look forward to hearing from you.

Best regards,
Nikita Chanu