pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] open source installation on Windows broken?

[Thomas H. <th...@th...>]

Hi Bob,

Looks like Christoph Gohlke has moved his wheels to Github:
https://github.com/cgohlke/pymol-open-source-wheels/

Another option would be the conda-forge channel:
https://anaconda.org/conda-forge/pymol-open-source

Cheers,
  Thomas

On Mon, Jul 22, 2024 at 4:46 AM Robert Hanson via PyMOL-users
<pym...@li...> wrote:
>
> At
> https://pymolwiki.org/index.php/Windows_Install
> the process fails for
>
> 3. Download the appropriate wheel files,
>
> which is a dead link.
>
> Does anyone know how to run open source PyMOL on Windows OS?
>
> Bob Hanson
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Create command with ranges of states

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

Hi Istvan,

I have not yet come across a better way to do this (perhaps someone has a
clever way to approach this), but I do think that adding a range of states
to the create function is reasonable. The other idea that came to mind was
to do a full copy with `create` and just delete states, but it seems
deleting states is not yet implemented (although I have seen a few requests
for this before). I'll see if I can address this for PyMOL 3.1. The
Timeline programs select a range to view in the movie, but doesn't actually
alter the structure data.

Jarrett J.

On Fri, Jul 19, 2024 at 6:46 PM Istvan Kolossvary <iko...@gm...>
wrote:

> Hi,
>
> It seems that the Create command can only copy either a single state or
> all states but no ranges. The range option would be very useful in
> stitching together a trajectory from parts of other trajectories. This
> functionality is readily available in the Timeline, but AFAIK not available
> in Create. Right now the only solution seems to use a hugely inefficient
> loop copying a whole range state by state. Does anyone know a better
> solution?
>
> Thanks,
>
>    Istvan
> _______________________________________________
> 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] open source installation on Windows broken?

[Robert H. <ha...@st...>]

At
https://pymolwiki.org/index.php/Windows_Install
the process fails for

3. Download the appropriate wheel files
<http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol-open-source>,

which is a dead link.

Does anyone know how to run open source PyMOL on Windows OS?

Bob Hanson

Re: [PyMOL] Pymol 3 Timeline issues

[Lei S. <le...@gm...>]

Hi Jarrett,

I feel it is easy enough for you to test in the scripting mode that whether
"cmd.movie.produce(moviename,mode='ray',quality=85,quiet=0)" would produce
the same with pymol3 and pymol2 after you load a 1000-frame dcd file to an
object with load_traj. If not, do you have any suggestions how to let
pymol3 behave like pymol2? Of course, I can always switch back to use
pymol2, like I am doing now.

Thanks,
Lei

On Sat, Jul 20, 2024 at 9:47 PM Jarrett Johnson <
jar...@sc...> wrote:

> Hi Lei,
>
> I may need more details on how you're producing your movies. I would note
> that the File menu will only produce a movie based on the movie that's in
> the timeline *not* the one from PyMOL 2. So if you're using the old movie
> API to export out a movie in PyMOL 3, your results won't be as expected
> unless you use the legacy export menu. The `load_traj` command, I believe,
> was unchanged moving to PyMOL3, if you can provide more details on what has
> changed for you, that'd be great. While the interface is improved in
> PyMOL3, I've also made sure to accommodate for most use cases of the
> Timeline to be configured via scripting. The Python API for it is located
> here: https://pymolwiki.org/index.php/Timeline_Python_API.
>
> Jarrett J
>
> On Sat, Jul 20, 2024 at 12:26 PM Lei Shi <le...@gm...> wrote:
>
>> Hi Istvan,
>>
>> I have related but not the same problems with pymol3 when making the
>> movies. Using the pymol script that works for pymol 2.5, pymol3 could only
>> produce a movie for the first 240(?) frames and I could not find the
>> setting to fix this issue. In addition, I believe they also changed the
>> default options of load_traj in pymol3. Overall, it appears pymol3 counts
>> on you using the interface but this is not always ideal for heavy duty
>> work, e.g., requiring running "pymol -c" (text mode) on a linux server to
>> finish the job.
>>
>> Lei
>>
>>
>>
>> On Fri, Jul 19, 2024 at 6:12 PM Istvan Kolossvary <iko...@gm...>
>> wrote:
>>
>>> Hi,
>>>
>>> I have had these issues with the new timeline. It works fine with scenes
>>> and short multi-state objects (like those showcased in the Pymol 3 online
>>> visualization course) but when it comes to real life MD trajectories I
>>> found two "dealbreaker" issues.
>>>
>>> 1) With complex movies based on MD trajectories and not scenes, the Draw
>>> mode is not working. If I select Draw to generate a movie file quickly for
>>> testing then (a) it takes almost as long as Ray Tracing and (b) the movie
>>> is complete garbage, showing only random parts of the system.
>>>
>>> 2) The Ray Tracing mode works fine, but processing time is prohibitively
>>> slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5
>>> automatically uses all the available cores for ray tracing. The way Pymol 3
>>> is right now, it takes 24-48 hours to produce a 3000 frame movie, which is
>>> only 100 seconds.
>>>
>>> Has anyone encountered similar issues?
>>>
>>> Thanks,
>>>
>>>    Istvan
>>> _______________________________________________
>>> 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
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>

Re: [PyMOL] Pymol 3 Timeline issues

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

Hi Lei,

I may need more details on how you're producing your movies. I would note
that the File menu will only produce a movie based on the movie that's in
the timeline *not* the one from PyMOL 2. So if you're using the old movie
API to export out a movie in PyMOL 3, your results won't be as expected
unless you use the legacy export menu. The `load_traj` command, I believe,
was unchanged moving to PyMOL3, if you can provide more details on what has
changed for you, that'd be great. While the interface is improved in
PyMOL3, I've also made sure to accommodate for most use cases of the
Timeline to be configured via scripting. The Python API for it is located
here: https://pymolwiki.org/index.php/Timeline_Python_API.

Jarrett J

On Sat, Jul 20, 2024 at 12:26 PM Lei Shi <le...@gm...> wrote:

> Hi Istvan,
>
> I have related but not the same problems with pymol3 when making the
> movies. Using the pymol script that works for pymol 2.5, pymol3 could only
> produce a movie for the first 240(?) frames and I could not find the
> setting to fix this issue. In addition, I believe they also changed the
> default options of load_traj in pymol3. Overall, it appears pymol3 counts
> on you using the interface but this is not always ideal for heavy duty
> work, e.g., requiring running "pymol -c" (text mode) on a linux server to
> finish the job.
>
> Lei
>
>
>
> On Fri, Jul 19, 2024 at 6:12 PM Istvan Kolossvary <iko...@gm...>
> wrote:
>
>> Hi,
>>
>> I have had these issues with the new timeline. It works fine with scenes
>> and short multi-state objects (like those showcased in the Pymol 3 online
>> visualization course) but when it comes to real life MD trajectories I
>> found two "dealbreaker" issues.
>>
>> 1) With complex movies based on MD trajectories and not scenes, the Draw
>> mode is not working. If I select Draw to generate a movie file quickly for
>> testing then (a) it takes almost as long as Ray Tracing and (b) the movie
>> is complete garbage, showing only random parts of the system.
>>
>> 2) The Ray Tracing mode works fine, but processing time is prohibitively
>> slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5
>> automatically uses all the available cores for ray tracing. The way Pymol 3
>> is right now, it takes 24-48 hours to produce a 3000 frame movie, which is
>> only 100 seconds.
>>
>> Has anyone encountered similar issues?
>>
>> Thanks,
>>
>>    Istvan
>> _______________________________________________
>> 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



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Re: [PyMOL] Pymol 3 Timeline issues

[Lei S. <le...@gm...>]

Hi Istvan,

I have related but not the same problems with pymol3 when making the
movies. Using the pymol script that works for pymol 2.5, pymol3 could only
produce a movie for the first 240(?) frames and I could not find the
setting to fix this issue. In addition, I believe they also changed the
default options of load_traj in pymol3. Overall, it appears pymol3 counts
on you using the interface but this is not always ideal for heavy duty
work, e.g., requiring running "pymol -c" (text mode) on a linux server to
finish the job.

Lei



On Fri, Jul 19, 2024 at 6:12 PM Istvan Kolossvary <iko...@gm...>
wrote:

> Hi,
>
> I have had these issues with the new timeline. It works fine with scenes
> and short multi-state objects (like those showcased in the Pymol 3 online
> visualization course) but when it comes to real life MD trajectories I
> found two "dealbreaker" issues.
>
> 1) With complex movies based on MD trajectories and not scenes, the Draw
> mode is not working. If I select Draw to generate a movie file quickly for
> testing then (a) it takes almost as long as Ray Tracing and (b) the movie
> is complete garbage, showing only random parts of the system.
>
> 2) The Ray Tracing mode works fine, but processing time is prohibitively
> slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5
> automatically uses all the available cores for ray tracing. The way Pymol 3
> is right now, it takes 24-48 hours to produce a 3000 frame movie, which is
> only 100 seconds.
>
> Has anyone encountered similar issues?
>
> Thanks,
>
>    Istvan
> _______________________________________________
> 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 3 Timeline issues

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

Hi Istvan,

With regards to CPU ray tracing only running on a single core, that sounds
like a major regression; we haven't changed anything in regards to that so
I'll investigate. As for your first issue, do you have any examples that I
can inspect myself to see what the issue is?

Jarrett J.

On Fri, Jul 19, 2024 at 6:11 PM Istvan Kolossvary <iko...@gm...>
wrote:

> Hi,
>
> I have had these issues with the new timeline. It works fine with scenes
> and short multi-state objects (like those showcased in the Pymol 3 online
> visualization course) but when it comes to real life MD trajectories I
> found two "dealbreaker" issues.
>
> 1) With complex movies based on MD trajectories and not scenes, the Draw
> mode is not working. If I select Draw to generate a movie file quickly for
> testing then (a) it takes almost as long as Ray Tracing and (b) the movie
> is complete garbage, showing only random parts of the system.
>
> 2) The Ray Tracing mode works fine, but processing time is prohibitively
> slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5
> automatically uses all the available cores for ray tracing. The way Pymol 3
> is right now, it takes 24-48 hours to produce a 3000 frame movie, which is
> only 100 seconds.
>
> Has anyone encountered similar issues?
>
> Thanks,
>
>    Istvan
> _______________________________________________
> 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 command with ranges of states

[Istvan K. <iko...@gm...>]

Hi,

It seems that the Create command can only copy either a single state or all
states but no ranges. The range option would be very useful in stitching
together a trajectory from parts of other trajectories. This functionality
is readily available in the Timeline, but AFAIK not available in Create.
Right now the only solution seems to use a hugely inefficient loop copying
a whole range state by state. Does anyone know a better solution?

Thanks,

   Istvan

Re: [PyMOL] Pymol 3 Timeline issues

[Istvan K. <iko...@gm...>]

Hi Jarrett,

Thanks for the quick reply. I am using version 3.03 on Linux and Mac. No
conda package is yet available, so these are the Schrödinger provided
binaries. Ray Tracing definitely uses only a single CPU.

Regarding the Draw problem, I have the example that I used in my
coursework. Can you point me to a place where I can upload it to? I have
the Pymol session and the Draw/Ray videos. The total size is ~440 MB.

BTW, I thought that saving a session with an active Timeline would save the
Timeline as well, but that doesn't seem to be the case as you can see when
you open the session file.

Many thanks,

   Istvan


On Fri, Jul 19, 2024 at 6:19 PM Jarrett Johnson <
jar...@sc...> wrote:

> Hi Istvan,
>
> With regards to CPU ray tracing only running on a single core, that sounds
> like a major regression; we haven't changed anything in regards to that so
> I'll investigate. As for your first issue, do you have any examples that I
> can inspect myself to see what the issue is?
>
> Jarrett J.
>
> On Fri, Jul 19, 2024 at 6:11 PM Istvan Kolossvary <iko...@gm...>
> wrote:
>
>> Hi,
>>
>> I have had these issues with the new timeline. It works fine with scenes
>> and short multi-state objects (like those showcased in the Pymol 3 online
>> visualization course) but when it comes to real life MD trajectories I
>> found two "dealbreaker" issues.
>>
>> 1) With complex movies based on MD trajectories and not scenes, the Draw
>> mode is not working. If I select Draw to generate a movie file quickly for
>> testing then (a) it takes almost as long as Ray Tracing and (b) the movie
>> is complete garbage, showing only random parts of the system.
>>
>> 2) The Ray Tracing mode works fine, but processing time is prohibitively
>> slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5
>> automatically uses all the available cores for ray tracing. The way Pymol 3
>> is right now, it takes 24-48 hours to produce a 3000 frame movie, which is
>> only 100 seconds.
>>
>> Has anyone encountered similar issues?
>>
>> Thanks,
>>
>>    Istvan
>> _______________________________________________
>> 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] Pymol 3 Timeline issues

[Istvan K. <iko...@gm...>]

 Hi,

I have had these issues with the new timeline. It works fine with scenes
and short multi-state objects (like those showcased in the Pymol 3 online
visualization course) but when it comes to real life MD trajectories I
found two "dealbreaker" issues.

1) With complex movies based on MD trajectories and not scenes, the Draw
mode is not working. If I select Draw to generate a movie file quickly for
testing then (a) it takes almost as long as Ray Tracing and (b) the movie
is complete garbage, showing only random parts of the system.

2) The Ray Tracing mode works fine, but processing time is prohibitively
slow because Pymol 3 only uses a single CPU core for ray tracing. Pymol 2.5
automatically uses all the available cores for ray tracing. The way Pymol 3
is right now, it takes 24-48 hours to produce a 3000 frame movie, which is
only 100 seconds.

Has anyone encountered similar issues?

Thanks,

   Istvan

Re: [PyMOL] BCIF

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

Hi Robert,

BinaryCIF is already available in PyMOL open-source master
<https://github.com/schrodinger/pymol-open-source/pull/353>. This is
expected to be shipped with a patched PyMOL 2.6 LTS next week and PyMOL 3.1
when that version is shipped.

Best,
Jarrett J.

On Wed, Jul 17, 2024 at 1:23 PM Robert Hanson via PyMOL-users <
pym...@li...> wrote:

> Seeing as MMTF is being deprecated, I am wondering if efforts are underway
> to allow PyMOL to read the BinaryCIF format?
>
> Bob Hanson
>
> From July 2024 the PDB file archive will not be offered in the compressed
>> MMTF format anymore. Users are strongly encouraged to switch to the BinaryCIF
>> format <https://github.com/molstar/BinaryCIF>, which has been available
>> since 2020. Details on how to access BinaryCIF (BCIF) data files for the
>> entire PDB archive are available here
>> <https://www.rcsb.org/docs/programmatic-access/file-download-services#pdb-entry-files>
>> .
>
>
>> RCSB PDB support is ready to assist with any issues or questions at
> in...@rc....
>
>
>
> ---
> Jose Duarte
> RCSB Protein Data Bank
> San Diego Supercomputer Center
> UC San Diego
> La Jolla CA, USA
>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry, Emeritus
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
> *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We
> honor with gratitude the people who have stewarded the land throughout the
> generations and their ongoing contributions to this region. We acknowledge
> the ongoing injustices that we have committed against the Dakota Nation,
> and we wish to interrupt this legacy, beginning with acts of healing and
> honest storytelling about this place.*
> _______________________________________________
> 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] BCIF

[Robert H. <ha...@st...>]

Seeing as MMTF is being deprecated, I am wondering if efforts are underway
to allow PyMOL to read the BinaryCIF format?

Bob Hanson

>From July 2024 the PDB file archive will not be offered in the compressed
> MMTF format anymore. Users are strongly encouraged to switch to the BinaryCIF
> format <https://github.com/molstar/BinaryCIF>, which has been available
> since 2020. Details on how to access BinaryCIF (BCIF) data files for the
> entire PDB archive are available here
> <https://www.rcsb.org/docs/programmatic-access/file-download-services#pdb-entry-files>
> .


> RCSB PDB support is ready to assist with any issues or questions at
in...@rc....



---
Jose Duarte
RCSB Protein Data Bank
San Diego Supercomputer Center
UC San Diego
La Jolla CA, USA




-- 
Robert M. Hanson
Professor of Chemistry, Emeritus
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

*We stand on the homelands of the Wahpekute Band of the Dakota Nation. We
honor with gratitude the people who have stewarded the land throughout the
generations and their ongoing contributions to this region. We acknowledge
the ongoing injustices that we have committed against the Dakota Nation,
and we wish to interrupt this legacy, beginning with acts of healing and
honest storytelling about this place.*

[PyMOL] Flipping a Waters Coordinates to the other Side of a Ligand Inquiry

[Joel S. <mjs...@al...>]

Hello Pymol Community, I hope you're well:).

Towards the above-topic, my trajectory files .inp File´s water coordinates
need to be flipped to the other side of the ligand C5´s interaction-site to
preclude inappropriate interactions with the adjacent C-atom and to
moreover bring the final .xyz trajectory file distance to less than 5.0 A
(see screenshots attached labeled .inp and .xyz, first and last coordinates
of the trajectory file, dashed lines exhibit water H-bonds to C5).  How
would I flip these Cartesian Coordinates to the other side of C5?

Thanks if you know:),
Joel 🚀

[PyMOL] Example of embedding the main viewer window as a widget in a wxPython application

[Jorge M. <jor...@gm...>]

I am wondering if anyone has an example of embedding the main pymol window
inside a wxPython application as a widget. Since in the wx toolkit, both
the C++ layer (wxWidgets) and the python layer (wxPython) support having a
custom widget rendered by OpenGL, this should be possible (
https://wiki.wxwidgets.org/WxGLCanvas and
https://docs.wxpython.org/wx.glcanvas.GLCanvas.html either at the C++ level
or the python level.

My goal is to create an open source project containing such a widget if it
doesn't already exist. I am not familiar with pymol but I am a regular
contributor to wxPython and I have in particular contributed to the
embedding of matplotlib figures inside wxPython (See
https://github.com/matplotlib/matplotlib/pull/26710) Any help getting
started on this would be greatly appreciated. Thank you,

Jorge

[PyMOL] help

[<724...@qq...>]

I want to ask for your help.
The circumstances is I want to download a license file, but when I click it, it appears a error,just like the picture shows.So how can I solve that?

Re: [PyMOL] [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US

[Xu, Q. <qx...@an...>]

This is a reminder that we are still accepting applications for the upcoming CCP4@APS workshop below. Potential students, esp those from outside the US, are encouraged to submit their applications asap.

This Message Is From an External Sender
This message came from outside your organization.


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:
https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-2024/index.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RU9QBjAs8$. 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
https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-school/publications.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUPTfq2LA$). 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://urldefense.us/v3/__https://www.ccp4.ac.uk/schools/APS-2024/application.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUhRwAcxE$

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

########################################################################

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________________________________
From: CCP4 bulletin board <CC...@JI...> on behalf of Qingping Xu <000...@JI...>
Sent: Monday, April 8, 2024 1:26 PM
To: CC...@JI... <CC...@JI...>
Subject: [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US

This Message Is From an External Sender
This message came from outside your organization.


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:
https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-2024/index.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RU9QBjAs8$. 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
https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-school/publications.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUPTfq2LA$). 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://urldefense.us/v3/__https://www.ccp4.ac.uk/schools/APS-2024/application.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUhRwAcxE$

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

########################################################################

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[PyMOL] Add a docked ligand to each state of a trajectory object

[Istvan K. <iko...@gm...>]

Hi,

I want to do the following. I have a trajectory file with numerous frames
that I load to Pymol as a multi-state object called traj and I have a
single state object with a ligand molecule called lig. I have a simple
align command (with a particular selection of some residues) that allows me
to (approximately) dock the ligand to each state in traj. I would like to
create a new traj object where in every state the ligand is docked.

I was hoping that the following code would do the job.
python
align lig, traj, target_state=1  # omitted align selection details
create docked_traj, lig or traj, source_state=1, target_state=1
for i in range (2,num_traj_states+1):
    align lig, traj, target_state=i
    create docked_traj, lig or traj, source_state=i, target_state=i
python end

However, the docked_traj coordinates are garbled. I figured this could be
attributed to merging a multi-state object and a single state object and
"source_state" might be ill-defined in this case. So, I tried using
split_states to avoid this ambiguity. The modified code is.
python
split_states traj, 1, 1, tmp
align lig, tmp0001  # omitted align selection details
create docked_traj, lig or tmp0001, target_state=1
for i in range (2,num_traj_states+1):
    split_states traj, i, i, tmp
    align lig, tmp0001
    create docked_traj, lig or tmp0001, target_state=i
python end

Unfortunately, the end result is exactly the same. I attached two
screenshots, one with the correct coordinates and one with the garbled
ones. (The overlap between green and blue atoms is not a problem in this
context.)

Can anyone suggest a solution?

Many thanks,

   Istvan

[image: image.png]
[image: image.png]

Re: [PyMOL] How to obtain a PyMOL selection within Python

[Zhou, Y. <yin...@no...>]

Here is the solution. Wonder if someone can help explain why the line below gives an error about print is not defined:
out=x.cmd.do("iterate mysel and name CA, print(resi)")

Thanks!
~~~~

import pymol2
x=pymol2.PyMOL()
x.start()
x.cmd.do("fetch 1crn; select mysel, /1crn//A/10-20")
out=[]
def f(chain, resi): out.append((chain,resi))
myspace={'f':f}
x.cmd.iterate("mysel and name CA", "f(chain, resi)", space=myspace)
print(out)

From: Zhou, Yingyao
Sent: Tuesday, May 28, 2024 3:57 PM
To: pym...@li...
Subject: How to obtain a PyMOL selection within Python

Hi,

In the example code below, there is a selection object "myself" within PyMOL, I try to obtain the selected residues within Python.
The "out=x.cmd.do" prints the selection to stdout, but the variable out remains None. What would be a good way to get the selection without going through disk I/O?

import pymol2
x=pymol2.PyMOL()
x.start()
x.cmd.do("fetch 1crn; select mysel, /1crn//A/10-20")
out=x.cmd.do("iterate mysel and name CA, (resi)")
print(out)

A separate question, when I run the following line of Python, I got an error (however the command works using PyMOL's command interface):

out=x.cmd.do("iterate mysel and name CA, print(resi)")

I got an error:
return _cmd.alter(_self._COb, selection, expression, True,
  File "", line 1, in <module>
NameError: name 'print' is not defined

What's the syntax error in this line?

Thank you,
Yingyao

[PyMOL] How to obtain a PyMOL selection within Python

[Zhou, Y. <yin...@no...>]

Hi,

In the example code below, there is a selection object "myself" within PyMOL, I try to obtain the selected residues within Python.
The "out=x.cmd.do" prints the selection to stdout, but the variable out remains None. What would be a good way to get the selection without going through disk I/O?

import pymol2
x=pymol2.PyMOL()
x.start()
x.cmd.do("fetch 1crn; select mysel, /1crn//A/10-20")
out=x.cmd.do("iterate mysel and name CA, (resi)")
print(out)

A separate question, when I run the following line of Python, I got an error (however the command works using PyMOL's command interface):

out=x.cmd.do("iterate mysel and name CA, print(resi)")

I got an error:
return _cmd.alter(_self._COb, selection, expression, True,
  File "", line 1, in <module>
NameError: name 'print' is not defined

What's the syntax error in this line?

Thank you,
Yingyao

Re: [PyMOL] `set grid_mode, 1` not working on a pml script?

[Francisco M. P. <fra...@ib...>]

Dear Jarrett and everybody else.


Running the minimal example in the linux terminal, it works ok (with
pymol-os-3.0, not with pymol-os-2.5).

Trying with my pml.
I get a 4x3 grid (again, pymol-os-3.0).
I get a 1x1 grid (or no grid?) (with pymol-os-2.5)

It works (I get a 4x4 grid) with either version If I copy/paste lines from
the script into the pymol console.

Thanks for your help. I appreciate it.


El lun, 20 may 2024 a la(s) 4:55 p.m., Jarrett Johnson (
jar...@sc...) escribió:

> Hi Francisco,
>
> This issue seems to be fixed between 2.5 and 3.0. I recommend finding a
> PyMOL 3.0+ open-source build. The release was in the past month, so I
> assume it may take some time for package managers to come up. I believe
> conda-forge has a 3.0 open-source build ready to go if you use conda.
>
> In the meantime, if that's not immediately suitable, the workaround for
> that issue was to dispatch the following command in your pml script before
> using `png`:
>
> *cmd._cmd._draw(cmd._COb)*
>
> Best,
> Jarrett J.
>
> On Mon, May 20, 2024 at 5:45 PM Francisco Murphy Pérez <
> fra...@ib...> wrote:
>
>> Hi.. I am using the open source version.
>> PyMOL 2.5.0 Open-Source, 2024-01-25
>> Installed in Fedora with `sudo dnf install pymol`
>>
>>
>> Thanks for your help!!
>>
>> PS Tried, several times, to buy the new 3.x version but paypal would not
>> let me...or something.
>>
>>
>> El lun, 20 may 2024 a la(s) 12:36 p.m., Jarrett Johnson (
>> jar...@sc...) escribió:
>>
>>> Hi Francisco,
>>>
>>> Which version of PyMOL are you using?
>>>
>>> Jarrett J.
>>>
>>> On Mon, May 20, 2024 at 2:30 PM Francisco Murphy Pérez <
>>> fra...@ib...> wrote:
>>>
>>>> Dear all
>>>> Got this script
>>>>
>>>> ```
>>>> load ./1ema.pdb
>>>> load ./1emg.pdb
>>>> set grid_mode, 1
>>>> png picture.png, dpi=300, width=1920, ray=1
>>>> ```
>>>>
>>>> When I try to run in a linux terminal `pymol script.pml` I get no grid.
>>>> When I try the same lines with pymol opened, I get a grid.
>>>>
>>>> What's going on?
>>>>
>>>> Thanks a lot!!
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>

Re: [PyMOL] `set grid_mode, 1` not working on a pml script?

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

Hi Francisco,

This issue seems to be fixed between 2.5 and 3.0. I recommend finding a
PyMOL 3.0+ open-source build. The release was in the past month, so I
assume it may take some time for package managers to come up. I believe
conda-forge has a 3.0 open-source build ready to go if you use conda.

In the meantime, if that's not immediately suitable, the workaround for
that issue was to dispatch the following command in your pml script before
using `png`:

*cmd._cmd._draw(cmd._COb)*

Best,
Jarrett J.

On Mon, May 20, 2024 at 5:45 PM Francisco Murphy Pérez <
fra...@ib...> wrote:

> Hi.. I am using the open source version.
> PyMOL 2.5.0 Open-Source, 2024-01-25
> Installed in Fedora with `sudo dnf install pymol`
>
>
> Thanks for your help!!
>
> PS Tried, several times, to buy the new 3.x version but paypal would not
> let me...or something.
>
>
> El lun, 20 may 2024 a la(s) 12:36 p.m., Jarrett Johnson (
> jar...@sc...) escribió:
>
>> Hi Francisco,
>>
>> Which version of PyMOL are you using?
>>
>> Jarrett J.
>>
>> On Mon, May 20, 2024 at 2:30 PM Francisco Murphy Pérez <
>> fra...@ib...> wrote:
>>
>>> Dear all
>>> Got this script
>>>
>>> ```
>>> load ./1ema.pdb
>>> load ./1emg.pdb
>>> set grid_mode, 1
>>> png picture.png, dpi=300, width=1920, ray=1
>>> ```
>>>
>>> When I try to run in a linux terminal `pymol script.pml` I get no grid.
>>> When I try the same lines with pymol opened, I get a grid.
>>>
>>> What's going on?
>>>
>>> Thanks a lot!!
>>>
>>>
>>> _______________________________________________
>>> 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
>>
>>

-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Re: [PyMOL] `set grid_mode, 1` not working on a pml script?

[Francisco M. P. <fra...@ib...>]

Hi.. I am using the open source version.
PyMOL 2.5.0 Open-Source, 2024-01-25
Installed in Fedora with `sudo dnf install pymol`


Thanks for your help!!

PS Tried, several times, to buy the new 3.x version but paypal would not
let me...or something.


El lun, 20 may 2024 a la(s) 12:36 p.m., Jarrett Johnson (
jar...@sc...) escribió:

> Hi Francisco,
>
> Which version of PyMOL are you using?
>
> Jarrett J.
>
> On Mon, May 20, 2024 at 2:30 PM Francisco Murphy Pérez <
> fra...@ib...> wrote:
>
>> Dear all
>> Got this script
>>
>> ```
>> load ./1ema.pdb
>> load ./1emg.pdb
>> set grid_mode, 1
>> png picture.png, dpi=300, width=1920, ray=1
>> ```
>>
>> When I try to run in a linux terminal `pymol script.pml` I get no grid.
>> When I try the same lines with pymol opened, I get a grid.
>>
>> What's going on?
>>
>> Thanks a lot!!
>>
>>
>> _______________________________________________
>> 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
>
>

Re: [PyMOL] `set grid_mode, 1` not working on a pml script?

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

Hi Francisco,

Which version of PyMOL are you using?

Jarrett J.

On Mon, May 20, 2024 at 2:30 PM Francisco Murphy Pérez <
fra...@ib...> wrote:

> Dear all
> Got this script
>
> ```
> load ./1ema.pdb
> load ./1emg.pdb
> set grid_mode, 1
> png picture.png, dpi=300, width=1920, ray=1
> ```
>
> When I try to run in a linux terminal `pymol script.pml` I get no grid.
> When I try the same lines with pymol opened, I get a grid.
>
> What's going on?
>
> Thanks a lot!!
>
>
> _______________________________________________
> 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] `set grid_mode, 1` not working on a pml script?

[Francisco M. P. <fra...@ib...>]

Dear all
Got this script

```
load ./1ema.pdb
load ./1emg.pdb
set grid_mode, 1
png picture.png, dpi=300, width=1920, ray=1
```

When I try to run in a linux terminal `pymol script.pml` I get no grid.
When I try the same lines with pymol opened, I get a grid.

What's going on?

Thanks a lot!!

[PyMOL] You're invited to Educator's Week 2024

[Teaching w. S. <tea...@sc...>]

Hi,

The Schrödinger Education team is hosting a free event from May 28-31
called Educator's Week 2024 <https://events.bizzabo.com/educators_week_2024>,
connecting educators from all over the world to discuss the growing role of
educational technology in the classroom and integrating computational
molecular modeling into modern science curricula.

*May 28-30, 2024*
12:00 to 2:00 PM ET
Virtual conference with live presentations

*May 31, 2024*
10:00 AM to 2:00 PM ET
In-person, hands-on workshops at the Schrödinger New York City Headquarters

*Register for the free event.
<https://events.bizzabo.com/educators_week_2024>*

We're very excited that* Thomas Stewart, PyMOL Developer, from
Schrödinger *will
be hosting a workshop on *PyMOL 3* and will discuss the new movie-making
features. We'll also be hosting several teachers and professors who will
highlight how molecular modeling is revolutionizing elementary school
science, among other chemistry and biology teachers and college-level
professors.

Hope to see you there!

Best,

Schrödinger Education Team | Teaching