pymol-users — Collaborative support and tips for PyMOL users

[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

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

To unsubscribe from the CCP4BB list, click the following link:
https://urldefense.us/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUtJdGhk8$

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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

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

To unsubscribe from the CCP4BB list, click the following link:
https://urldefense.us/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUtJdGhk8$

This message was issued to members of https://urldefense.us/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUIlqrIeo$, a mailing list hosted by https://urldefense.us/v3/__http://www.jiscmail.ac.uk__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUyfFpMcY$, terms & conditions are available at https://urldefense.us/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUuFJW2bU$

[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

[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>