pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] 'Extent' representation in PyMOL

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

Hi Dani,

The extent should simply be the bounding box that contains all of the map
density data in cartesian space.

Best,
Jarrett J

On Sat, Apr 12, 2025 at 7:27 AM Daniel Martinez <mar...@ho...>
wrote:

> Dear PyMOL user community,
> I’ve been trying to understand exactly what the *'extent'* representation
> refers to in PyMOL.
> It’s listed as a type of *Map representation* in the following reference:
> https://pymol.org/dokuwiki/doku.php?id=representation
> However, I haven’t been able to find any further documentation or
> explanation about it.
> Could anyone provide some insight or point me to where it might be
> described?
> Thank you in advance!
> Best regards,
> Dani.
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 

*Jarrett Johnson* | Staff Developer, PyMOL

[PyMOL] 'Extent' representation in PyMOL

[Daniel M. <mar...@ho...>]

Dear PyMOL user community,
I’ve been trying to understand exactly what the 'extent' representation refers to in PyMOL.
It’s listed as a type of Map representation in the following reference:
https://pymol.org/dokuwiki/doku.php?id=representation
However, I haven’t been able to find any further documentation or explanation about it.
Could anyone provide some insight or point me to where it might be described?
Thank you in advance!
Best regards,
Dani.

Re: [PyMOL] [ccp4bb] Announcement: The 17th CCP4/APS Crystallographic School, June 23rd-30th, 2025, APS

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

Dear friends,

This is a reminder of that registration is still open for the upcoming 2025 CCP4/APS workshop. If you have any questions, please let us know.

Charles, Andrey, Garib and Qingping

________________________________
From: CCP4 bulletin board <CC...@JI...> on behalf of Xu, Qingping <000...@JI...>
Sent: Monday, January 27, 2025 8:36 AM
To: CC...@JI... <CC...@JI...>
Subject: [ccp4bb] Announcement: The 17th CCP4/APS Crystallographic School, June 23rd-30th, 2025, APS

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

Dear Colleagues,

We are pleased to announce that the 17th annual CCP4/APS Crystallographic School, "From Data Collection to Structure Refinement and Beyond," will be held from June 23rd to 30th, 2025, at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found on the school website: http://www.ccp4.ac.uk/schools/APS-2025/index.php<https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-2025/index.php__;!!G_uCfscf7eWS!efj1mSIiPgk0NgZMHmGe4hJPfYd2OQDHTAN3c3Vrem3MB2NKtbVF54Rrswt012yfTyeTDwQiLmscAeDYLd-jpEoeFbg6-D4$>.

Dates: June 23rd through 30th, 2025 (on-site), June 2nd and 16th (virtual)
Location: Advanced Photon Source, Argonne National Laboratory, Argonne (near
Chicago), Illinois, USA

The school comprises two parts: a data collection workshop and a crystallographic computing workshop. The data collection workshop includes beamline training, data collection at GM/CA@APS beamlines, and data processing, using only the participants' crystals. The crystallographic computation workshop will feature many modern crystallographic software packages (including CCP4, PHENIX, XDS, HKL, and DIALS) taught by authors and other experts. This workshop will also introduce elements of CryoEM, such as model building and refinement. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive troubleshooting of the technical difficulties participants face in their projects). Two additional virtual days (June 2nd and 16th, 2025) will cover sample preparation (cryo-cooling), bioinformatics, and introductory crystallography lectures. We have had considerable success resolving these problems in past years, as attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php<https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-school/publications.php__;!!G_uCfscf7eWS!efj1mSIiPgk0NgZMHmGe4hJPfYd2OQDHTAN3c3Vrem3MB2NKtbVF54Rrswt012yfTyeTDwQiLmscAeDYLd-jpEoeWp70wu8$>). A draft program can be found on 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: The application deadline is May 15th, 2025, we strongly encourage interested participants to apply as soon as possible. To apply, visit https://www.ccp4.ac.uk/schools/APS-2025/application.php<https://urldefense.us/v3/__https://www.ccp4.ac.uk/schools/APS-2025/application.php__;!!G_uCfscf7eWS!efj1mSIiPgk0NgZMHmGe4hJPfYd2OQDHTAN3c3Vrem3MB2NKtbVF54Rrswt012yfTyeTDwQiLmscAeDYLd-jpEoePiMMUbg$>

Fees: There is a $500 participation fee for selected academic students and $1,500 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:
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Re: [PyMOL] 3.1.3.1 no viewport sizing with the movie timeline panel toggled on?

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

Hi Rachelle,

This is a known issue and something we plan to address hopefully in the
near future!

Jarrett J.

On Wed, Apr 2, 2025 at 2:55 PM Gaudet, Rachelle <ga...@mc...>
wrote:

> Hello,
>
>
>
> I’m getting a weird behavior with PyMOL 3.1.3.1: When I toggle on the
> movie timeline panel (clicking on the camera icon), the PyMOL window
> changes, such that the aspect ratio of the display window is now very wide
> and not what I’d like it to be. I also cannot decrease the PyMOL window
> width with the timeline on. It seems to be locked at a minimal width,
> perhaps to fit all the buttons at the bottom of the movie timeline panel?
>
>
>
> The one “fix” I’ve found is to change the width of the Contents Panel
> (increasing it to decrease the width of the display window). But I do this
> manually, so I don’t really have precision like I did in PyMOL 2 with the
> “viewport” command. (The “viewport” command still works with the movie
> panel toggled off, but doesn’t work properly with the movie panel toggled
> on.)
>
>
>
> I realize I can change the aspect ratio of the movie when I’m saving it.
> But it is useful to plan and build the movie with the intended aspect ratio
> in view.
>
>
>
> Any tips?
>
>
>
> Best,
>
> Rachelle
>
>
>
> ___________________________________________________________________
>
>  Rachelle Gaudet, Ph.D.
>
>  Professor and Chair
>
>  Department of Molecular and Cellular Biology
> <https://www.mcb.harvard.edu/>
>
>  Co-Director of Graduate Studies, Biophysics
> <https://biophysics.fas.harvard.edu/>
>  Harvard University
>  52 Oxford Street, Northwest Labs room 311.13
>
>  Cambridge, MA 02138
>  Voice: (617) 495-5616    e-mail: ga...@mc...
>
>  https://projects.iq.harvard.edu/gaudetlab/home
>
> ___________________________________________________________________
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 

*Jarrett Johnson* | Staff Developer, PyMOL

[PyMOL] 3.1.3.1 no viewport sizing with the movie timeline panel toggled on?

[Gaudet, R. <ga...@mc...>]

Hello,

I'm getting a weird behavior with PyMOL 3.1.3.1: When I toggle on the movie timeline panel (clicking on the camera icon), the PyMOL window changes, such that the aspect ratio of the display window is now very wide and not what I'd like it to be. I also cannot decrease the PyMOL window width with the timeline on. It seems to be locked at a minimal width, perhaps to fit all the buttons at the bottom of the movie timeline panel?

The one "fix" I've found is to change the width of the Contents Panel (increasing it to decrease the width of the display window). But I do this manually, so I don't really have precision like I did in PyMOL 2 with the "viewport" command. (The "viewport" command still works with the movie panel toggled off, but doesn't work properly with the movie panel toggled on.)

I realize I can change the aspect ratio of the movie when I'm saving it. But it is useful to plan and build the movie with the intended aspect ratio in view.

Any tips?

Best,
Rachelle

___________________________________________________________________
 Rachelle Gaudet, Ph.D.
 Professor and Chair
 Department of Molecular and Cellular Biology<https://www.mcb.harvard.edu/>
 Co-Director of Graduate Studies, Biophysics<https://biophysics.fas.harvard.edu/>
 Harvard University
 52 Oxford Street, Northwest Labs room 311.13
 Cambridge, MA 02138
 Voice: (617) 495-5616    e-mail: ga...@mc...<mailto:ga...@mc...>
 https://projects.iq.harvard.edu/gaudetlab/home
___________________________________________________________________

Re: [PyMOL] Thermal ellipsoids with principal axes

[Takanori N. <tna...@os...>]

Hi,

I ended up implementing this myself, drawing three ellipses
by CGO over PyMOL's native ellipsoids.
My current style is like the one in
https://www.chem.gla.ac.uk/~louis/software/ortep/index.html.

At the moment my code does not support object's TTT matrix
and per-atom colors. Once I fix these limitations,
I will put my script to my GitHub or PyMOL wiki.

I also want to implement the "cutting out one octant" feature
like ORTEP but that would require completely hiding
PyMOL's native ellipsoids and drawing everything from scratch.

Best regards,

Takanori Nakane

On 3/25/25 22:30, Takanori Nakane wrote:
> Dear PyMOL users,
> 
> I am preparing figures for small molecular crystallography.
> I know I can plot thermal ellipsoids in PyMOL but can I add
> principal axes on the surface (or cut out one octant)?
> 
> I would like to draw something like ORTEP:
> https://www.chem.gla.ac.uk/~louis/software/ortep/fig2.gif.
> 
> Do I have to code CGO objects?
> 
> Best regards,
> 
> Takanori Nakane
> 
> 
> _______________________________________________
> 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 3.1.4

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

Hello Everyone,

We have just released PyMOL 3.1.4.1 (which is still a digit of pi so the pi
mole remains!) to fix the issues discussed in this thread.

Please give this version a try if you haven't updated recently since many
other small issues have also been fixed in recent patches.

You can download this version from the website (
https://www.pymol.org/#download) and please check back later if 3.1.4.1
isn't showing up for you yet.

Release Notes:

   - Selection names are now properly shown within parentheses again (i.e.
   “(sele)”)
   - Fix for selections using the incorrect “Action” menu
   - Wizards that require keyboard input now focus properly
   - Fix for timeline extending off the edge of smaller Mac screens
   - Fix for issues toggling objects after reordering
   - Fix for group members not showing following an empty group


Thank you for your patience and happy PyMOL-ing,
Thomas

Thomas Stewart | Senior Developer I | Product Manager, PyMOL

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


On Thu, Mar 20, 2025 at 8:42 PM Engin Özkan <eo...@uc...> wrote:

> Dear Thomas,
>
> Thank you for getting back quickly and on your work on PyMOL. Looking
> forward to testing the patched version.
>
> Best,
>
> Engin
>
>
> On 3/20/25 9:44 AM, Thomas Stewart wrote:
>
> Hello Engin and Vaheh,
>
> Both of these are simply oversights on my part and will be fixed in the
> next patch (3.1.4.1). For this update, I completely rewrote the code for
> the Contents Panel and there appears to be certain ASHLC menus that are not
> pulling the correct set of menu options for their object type.
>
> I will also add the parentheses back to the selections! I'm honestly
> surprised I didn't immediately notice this in my testing but it should be a
> quick fix.
>
> Thank you for reporting these issues and let me know if you find anything
> else.
>
> Thanks again,
> Thomas
>
> Thomas Stewart | Senior Developer I | Product Manager, PyMOL
>
> [image: Schrödinger, Inc.] <https://schrodinger.com/>
>
>
> On Thu, Mar 20, 2025 at 9:08 AM Oganesyan, Vaheh <
> vah...@as...> wrote:
>
>> To add a bit to Engin’s message: under A when selecting “extract” I’m
>> getting “copy” instead. I think it is a bug in 3.1.4.
>>
>>
>>
>> Thank you.
>>
>>
>>
>> Vaheh
>>
>>
>>
>> *From:* Engin Özkan <eo...@uc...>
>> *Sent:* Wednesday, March 19, 2025 8:02 PM
>> *To:* pym...@li...
>> *Subject:* [PyMOL] PyMOL 3.1.4
>>
>>
>>
>> Hi,
>>
>> In the latest version of PyMOL, 3.1.4, I cannot see if an item in the
>> list on the right-hand column is a selection or an object. The
>> parantheses were really useful before. Is this intentional or an
>> oversight?
>>
>> But more urgently, for a selection I made, I no longer see the options
>> under "A" many options I use every session, such as copy to object,
>> extract object, rename selection, align, etc. I am sure I can do these
>> actions via command-line just fine, but not nearly with the same ease of
>> use.
>>
>> Also delete selection has been replaced by delete selections. Why
>> plural? I am scared to click on it, especially now that I don't know
>> which items are selections and which are objects. I'll downgrade for now
>> to be able to use selections effectively in PyMOL; I assume many users
>> also depend on their ability to modify, align and rename selections
>> easily.
>>
>> (And thanks for fixing some of the selection group bugs that popped up
>> with v. 3 early on.)
>>
>> Best,
>>
>> Engin
>>
>> --
>> Engin Özkan, Ph.D.
>> Associate Professor
>> Dept of Biochemistry and Molecular Biology
>> University of Chicago
>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>> ------------------------------
>>
>> *Confidentiality Notice: *This message is private and may contain
>> confidential and proprietary information. If you have received this message
>> in error, please notify us and remove it from your system and note that you
>> must not copy, distribute or take any action in reliance on it. Any
>> unauthorized use or disclosure of the contents of this message is not
>> permitted and may be unlawful.
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
> --
> Engin Özkan, Ph.D.
> Associate Professor
> Dept of Biochemistry and Molecular Biology
> University of Chicago
> Phone: (773) 834-5498http://ozkan.uchicago.edu
>
>

[PyMOL] Thermal ellipsoids with principal axes

[Takanori N. <tna...@os...>]

Dear PyMOL users,

I am preparing figures for small molecular crystallography.
I know I can plot thermal ellipsoids in PyMOL but can I add
principal axes on the surface (or cut out one octant)?

I would like to draw something like ORTEP:
https://www.chem.gla.ac.uk/~louis/software/ortep/fig2.gif.

Do I have to code CGO objects?

Best regards,

Takanori Nakane

Re: [PyMOL] PyMOL 3.1.4

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

Hi Thomas, Engin,

Thanks for looking into this. Another thing with Select is that in this Pi
version there is a "delete everything" option, which is very dangerous (it
does delete every single object). It used to be "remove atoms" to remove
only the atoms in the selection.

Best regards,

   Istvan

On Thu, Mar 20, 2025 at 8:59 PM Engin Özkan <eo...@uc...> wrote:

> Dear Thomas,
>
> Thank you for getting back quickly and on your work on PyMOL. Looking
> forward to testing the patched version.
>
> Best,
>
> Engin
>
>
> On 3/20/25 9:44 AM, Thomas Stewart wrote:
>
> Hello Engin and Vaheh,
>
> Both of these are simply oversights on my part and will be fixed in the
> next patch (3.1.4.1). For this update, I completely rewrote the code for
> the Contents Panel and there appears to be certain ASHLC menus that are not
> pulling the correct set of menu options for their object type.
>
> I will also add the parentheses back to the selections! I'm honestly
> surprised I didn't immediately notice this in my testing but it should be a
> quick fix.
>
> Thank you for reporting these issues and let me know if you find anything
> else.
>
> Thanks again,
> Thomas
>
> Thomas Stewart | Senior Developer I | Product Manager, PyMOL
>
> [image: Schrödinger, Inc.] <https://schrodinger.com/>
>
>
> On Thu, Mar 20, 2025 at 9:08 AM Oganesyan, Vaheh <
> vah...@as...> wrote:
>
>> To add a bit to Engin’s message: under A when selecting “extract” I’m
>> getting “copy” instead. I think it is a bug in 3.1.4.
>>
>>
>>
>> Thank you.
>>
>>
>>
>> Vaheh
>>
>>
>>
>> *From:* Engin Özkan <eo...@uc...>
>> *Sent:* Wednesday, March 19, 2025 8:02 PM
>> *To:* pym...@li...
>> *Subject:* [PyMOL] PyMOL 3.1.4
>>
>>
>>
>> Hi,
>>
>> In the latest version of PyMOL, 3.1.4, I cannot see if an item in the
>> list on the right-hand column is a selection or an object. The
>> parantheses were really useful before. Is this intentional or an
>> oversight?
>>
>> But more urgently, for a selection I made, I no longer see the options
>> under "A" many options I use every session, such as copy to object,
>> extract object, rename selection, align, etc. I am sure I can do these
>> actions via command-line just fine, but not nearly with the same ease of
>> use.
>>
>> Also delete selection has been replaced by delete selections. Why
>> plural? I am scared to click on it, especially now that I don't know
>> which items are selections and which are objects. I'll downgrade for now
>> to be able to use selections effectively in PyMOL; I assume many users
>> also depend on their ability to modify, align and rename selections
>> easily.
>>
>> (And thanks for fixing some of the selection group bugs that popped up
>> with v. 3 early on.)
>>
>> Best,
>>
>> Engin
>>
>> --
>> Engin Özkan, Ph.D.
>> Associate Professor
>> Dept of Biochemistry and Molecular Biology
>> University of Chicago
>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>> ------------------------------
>>
>> *Confidentiality Notice: *This message is private and may contain
>> confidential and proprietary information. If you have received this message
>> in error, please notify us and remove it from your system and note that you
>> must not copy, distribute or take any action in reliance on it. Any
>> unauthorized use or disclosure of the contents of this message is not
>> permitted and may be unlawful.
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
> --
> Engin Özkan, Ph.D.
> Associate Professor
> Dept of Biochemistry and Molecular Biology
> University of Chicago
> Phone: (773) 834-5498http://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

Re: [PyMOL] PyMOL 3.1.4

[Engin Ö. <eo...@uc...>]

Dear Thomas,

Thank you for getting back quickly and on your work on PyMOL. Looking 
forward to testing the patched version.

Best,

Engin


On 3/20/25 9:44 AM, Thomas Stewart wrote:
> Hello Engin and Vaheh,
>
> Both of these are simply oversights on my part and will be fixed in 
> the next patch (3.1.4.1). For this update, I completely rewrote the 
> code for the Contents Panel and there appears to be certain ASHLC 
> menus that are not pulling the correct set of menu options for their 
> object type.
>
> I will also add the parentheses back to the selections! I'm honestly 
> surprised I didn't immediately notice this in my testing but it 
> should be a quick fix.
>
> Thank you for reporting these issues and let me know if you find 
> anything else.
>
> Thanks again,
> Thomas
>
> Thomas Stewart | Senior Developer I | Product Manager, PyMOL
>
> Schrödinger, Inc. <https://schrodinger.com/>
>
>
>
> On Thu, Mar 20, 2025 at 9:08 AM Oganesyan, Vaheh 
> <vah...@as...> wrote:
>
>     To add a bit to Engin’s message: under A when selecting “extract”
>     I’m getting “copy” instead. I think it is a bug in 3.1.4.
>
>     Thank you.
>
>     Vaheh
>
>     *From:*Engin Özkan <eo...@uc...>
>     *Sent:* Wednesday, March 19, 2025 8:02 PM
>     *To:* pym...@li...
>     *Subject:* [PyMOL] PyMOL 3.1.4
>
>     Hi,
>
>     In the latest version of PyMOL, 3.1.4, I cannot see if an item in the
>     list on the right-hand column is a selection or an object. The
>     parantheses were really useful before. Is this intentional or an
>     oversight?
>
>     But more urgently, for a selection I made, I no longer see the
>     options
>     under "A" many options I use every session, such as copy to object,
>     extract object, rename selection, align, etc. I am sure I can do
>     these
>     actions via command-line just fine, but not nearly with the same
>     ease of
>     use.
>
>     Also delete selection has been replaced by delete selections. Why
>     plural? I am scared to click on it, especially now that I don't know
>     which items are selections and which are objects. I'll downgrade
>     for now
>     to be able to use selections effectively in PyMOL; I assume many
>     users
>     also depend on their ability to modify, align and rename
>     selections easily.
>
>     (And thanks for fixing some of the selection group bugs that
>     popped up
>     with v. 3 early on.)
>
>     Best,
>
>     Engin
>
>     -- 
>     Engin Özkan, Ph.D.
>     Associate Professor
>     Dept of Biochemistry and Molecular Biology
>     University of Chicago
>
>
>
>     _______________________________________________
>     PyMOL-users mailing list
>     Archives:
>     http://www.mail-archive.com/pym...@li...
>     Unsubscribe:
>     https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>     ------------------------------------------------------------------------
>
>     *Confidentiality Notice: *This message is private and may contain
>     confidential and proprietary information. If you have received
>     this message in error, please notify us and remove it from your
>     system and note that you must not copy, distribute or take any
>     action in reliance on it. Any unauthorized use or disclosure of
>     the contents of this message is not permitted and may be unlawful.
>
>     _______________________________________________
>     PyMOL-users mailing list
>     Archives:
>     http://www.mail-archive.com/pym...@li...
>     Unsubscribe:
>     https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
-- 
Engin Özkan, Ph.D.
Associate Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
Phone: (773) 834-5498
http://ozkan.uchicago.edu

Re: [PyMOL] PyMOL 3.1.4

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

Hello Engin and Vaheh,

Both of these are simply oversights on my part and will be fixed in the
next patch (3.1.4.1). For this update, I completely rewrote the code for
the Contents Panel and there appears to be certain ASHLC menus that are not
pulling the correct set of menu options for their object type.

I will also add the parentheses back to the selections! I'm honestly
surprised I didn't immediately notice this in my testing but it should be a
quick fix.

Thank you for reporting these issues and let me know if you find anything
else.

Thanks again,
Thomas

Thomas Stewart | Senior Developer I | Product Manager, PyMOL

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


On Thu, Mar 20, 2025 at 9:08 AM Oganesyan, Vaheh <
vah...@as...> wrote:

> To add a bit to Engin’s message: under A when selecting “extract” I’m
> getting “copy” instead. I think it is a bug in 3.1.4.
>
>
>
> Thank you.
>
>
>
> Vaheh
>
>
>
> *From:* Engin Özkan <eo...@uc...>
> *Sent:* Wednesday, March 19, 2025 8:02 PM
> *To:* pym...@li...
> *Subject:* [PyMOL] PyMOL 3.1.4
>
>
>
> Hi,
>
> In the latest version of PyMOL, 3.1.4, I cannot see if an item in the
> list on the right-hand column is a selection or an object. The
> parantheses were really useful before. Is this intentional or an oversight?
>
> But more urgently, for a selection I made, I no longer see the options
> under "A" many options I use every session, such as copy to object,
> extract object, rename selection, align, etc. I am sure I can do these
> actions via command-line just fine, but not nearly with the same ease of
> use.
>
> Also delete selection has been replaced by delete selections. Why
> plural? I am scared to click on it, especially now that I don't know
> which items are selections and which are objects. I'll downgrade for now
> to be able to use selections effectively in PyMOL; I assume many users
> also depend on their ability to modify, align and rename selections easily.
>
> (And thanks for fixing some of the selection group bugs that popped up
> with v. 3 early on.)
>
> Best,
>
> Engin
>
> --
> Engin Özkan, Ph.D.
> Associate Professor
> Dept of Biochemistry and Molecular Biology
> University of Chicago
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> ------------------------------
>
> *Confidentiality Notice: *This message is private and may contain
> confidential and proprietary information. If you have received this message
> in error, please notify us and remove it from your system and note that you
> must not copy, distribute or take any action in reliance on it. Any
> unauthorized use or disclosure of the contents of this message is not
> permitted and may be unlawful.
>
> _______________________________________________
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> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

Re: [PyMOL] PyMOL 3.1.4

[Oganesyan, V. <vah...@as...>]

To add a bit to Engin’s message: under A when selecting “extract” I’m getting “copy” instead. I think it is a bug in 3.1.4.

Thank you.

Vaheh

From: Engin Özkan <eo...@uc...>
Sent: Wednesday, March 19, 2025 8:02 PM
To: pym...@li...
Subject: [PyMOL] PyMOL 3.1.4

Hi,

In the latest version of PyMOL, 3.1.4, I cannot see if an item in the
list on the right-hand column is a selection or an object. The
parantheses were really useful before. Is this intentional or an oversight?

But more urgently, for a selection I made, I no longer see the options
under "A" many options I use every session, such as copy to object,
extract object, rename selection, align, etc. I am sure I can do these
actions via command-line just fine, but not nearly with the same ease of
use.

Also delete selection has been replaced by delete selections. Why
plural? I am scared to click on it, especially now that I don't know
which items are selections and which are objects. I'll downgrade for now
to be able to use selections effectively in PyMOL; I assume many users
also depend on their ability to modify, align and rename selections easily.

(And thanks for fixing some of the selection group bugs that popped up
with v. 3 early on.)

Best,

Engin

--
Engin Özkan, Ph.D.
Associate Professor
Dept of Biochemistry and Molecular Biology
University of Chicago



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________________________________

Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.

[PyMOL] PyMOL 3.1.4

[Engin Ö. <eo...@uc...>]

Hi,

In the latest version of PyMOL, 3.1.4, I cannot see if an item in the 
list on the right-hand column is a selection or an object. The 
parantheses were really useful before. Is this intentional or an oversight?

But more urgently, for a selection I made, I no longer see the options 
under "A" many options I use every session, such as copy to object, 
extract object, rename selection, align, etc. I am sure I can do these 
actions via command-line just fine, but not nearly with the same ease of 
use.

Also delete selection has been replaced by delete selections. Why 
plural? I am scared to click on it, especially now that I don't know 
which items are selections and which are objects. I'll downgrade for now 
to be able to use selections effectively in PyMOL; I assume many users 
also depend on their ability to modify, align and rename selections easily.

(And thanks for fixing some of the selection group bugs that popped up 
with v. 3 early on.)

Best,

Engin

-- 
Engin Özkan, Ph.D.
Associate Professor
Dept of Biochemistry and Molecular Biology
University of Chicago

Re: [PyMOL] Neat feature seems to have discontinued in v3.x

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

Hello Istvan,

I actually wasn't even aware of this behavior when I was creating the new
Contents Panel! I couldn't add it in time for this release (3.1.4) but I'll
hopefully have something ready in the near future. There are many small
"features" like this in older versions of PyMOL that are difficult to
discover if you've never seen them used before.

If anyone else has any Contents Panel related features that are now
missing, please feel free to send me an email directly and I will do my
best to restore them in future updates. This PyMOL 3.1.4 update includes a
full reimplementation of the Contents Panel based on a request to improve
performance and stability when a large number of objects are loaded in.
Give this version a try before emailing me with a feature request because
it may already be added!

Thanks,
Thomas

Thomas Stewart | Senior Developer I | Product Manager, PyMOL

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


On Sun, Mar 9, 2025 at 6:31 PM Istvan Kolossvary <iko...@gm...>
wrote:

> Hi,
>
> Pymol v2.x has a great feature, which seems not to exist in v3.x any more.
> On Linux, I could hold down the Ctrl key and then hover the cursor
> vertically over the object list to flip through the objects. Moving the
> cursor away from an object turned it off automatically while the next
> object under the cursor was automatically turned on in the display area.
> This feature is extremely useful for example to flip through multiple
> docking poses. (I think it also worked on the Mac using the Cmd key.) Is it
> still available in v3.x, perhaps with other key combinations?
>
> Thanks for any suggestions,
>
>    Istvan
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Neat feature seems to have discontinued in v3.x

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

Hi,

Pymol v2.x has a great feature, which seems not to exist in v3.x any more.
On Linux, I could hold down the Ctrl key and then hover the cursor
vertically over the object list to flip through the objects. Moving the
cursor away from an object turned it off automatically while the next
object under the cursor was automatically turned on in the display area.
This feature is extremely useful for example to flip through multiple
docking poses. (I think it also worked on the Mac using the Cmd key.) Is it
still available in v3.x, perhaps with other key combinations?

Thanks for any suggestions,

   Istvan

Re: [PyMOL] Caver3 plugin failure to initialise

[Irwin S. <irw...@db...>]

Hi Jarrett,


The issue was I downloaded the "master" zip linked in the instructions subsection of the github page. Using the "pyqt" zip linked from the code button worked.


Cheers,


Irwin

________________________________
From: Jarrett Johnson <jar...@sc...>
Sent: 27 February 2025 11:20:43
To: Irwin Selvam
Cc: pym...@li...
Subject: Re: [PyMOL] Caver3 plugin failure to initialise

Hi Irwin,

I'll ask others to double check on their setups too, but this one should have all imports of tkinter removed. Are you using the specific `pyqt` branch there and not `master`, and is the old one uninstalled first?

Best,
Jarrett J.

On Thu, Feb 27, 2025 at 6:44 PM Irwin Selvam <irw...@db...<mailto:irw...@db...>> wrote:

Hi,


Unfortunately, I'm still getting the same error ("no module named tkinter") and a failure to initialise. Any ideas?


Cheers,


Irwin

________________________________
From: Jarrett Johnson <jar...@sc...<mailto:jar...@sc...>>
Sent: 17 February 2025 00:33:26
To: Irwin Selvam
Cc: pym...@li...<mailto:pym...@li...>
Subject: Re: [PyMOL] Caver3 plugin failure to initialise

Hi Irwin,

A few months ago I worked on converting Caver 3 to use PyQt, I'm unsure if it's in a complete state, but within the next couple of months I'll be sure to finish it up and update the Caver PyMOLWiki page.

https://github.com/JarrettSJohnson/caver-pymol-plugin/tree/pyqt . Should just be able to press the Code button and Download Zip.

Best,
Jarrett J.


On Wed, Feb 12, 2025 at 5:03 AM Irwin Selvam via PyMOL-users <pym...@li...<mailto:pym...@li...>> wrote:

Hi all,


I'm trying to run the Caver3 plugin on PyMOL 2.5.7 on an M2 mac (Sequoia 15.3) but it's failing to initialise due to the "tkinter" module being missing. I've updated python to 3.13.2, which should come with tkinter 8.6. Does anyone have a solution?


Cheers,


Irwin

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PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...
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--

Jarrett Johnson | Staff Developer, PyMOL


[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]



--

Jarrett Johnson | Staff Developer, PyMOL


[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]

Re: [PyMOL] Caver3 plugin failure to initialise

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

Hi Irwin,

I'll ask others to double check on their setups too, but this one should
have all imports of tkinter removed. Are you using the specific `pyqt`
branch there and not `master`, and is the old one uninstalled first?

Best,
Jarrett J.

On Thu, Feb 27, 2025 at 6:44 PM Irwin Selvam <irw...@db...> wrote:

> Hi,
>
>
> Unfortunately, I'm still getting the same error ("no module named
> tkinter") and a failure to initialise. Any ideas?
>
>
> Cheers,
>
>
> Irwin
> ------------------------------
> *From:* Jarrett Johnson <jar...@sc...>
> *Sent:* 17 February 2025 00:33:26
> *To:* Irwin Selvam
> *Cc:* pym...@li...
> *Subject:* Re: [PyMOL] Caver3 plugin failure to initialise
>
> Hi Irwin,
>
> A few months ago I worked on converting Caver 3 to use PyQt, I'm unsure if
> it's in a complete state, but within the next couple of months I'll be sure
> to finish it up and update the Caver PyMOLWiki page.
>
> https://github.com/JarrettSJohnson/caver-pymol-plugin/tree/pyqt . Should
> just be able to press the Code button and Download Zip.
>
> Best,
> Jarrett J.
>
>
> On Wed, Feb 12, 2025 at 5:03 AM Irwin Selvam via PyMOL-users <
> pym...@li...> wrote:
>
>> Hi all,
>>
>>
>> I'm trying to run the Caver3 plugin on PyMOL 2.5.7 on an M2 mac (Sequoia
>> 15.3) but it's failing to initialise due to the "tkinter" module being
>> missing. I've updated python to 3.13.2, which should come with tkinter 8.6.
>> Does anyone have a solution?
>>
>>
>> Cheers,
>>
>>
>> Irwin
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>
>
> --
>
> *Jarrett Johnson* | Staff Developer, PyMOL
>
>

-- 

*Jarrett Johnson* | Staff Developer, PyMOL

Re: [PyMOL] Caver3 plugin failure to initialise

[Irwin S. <irw...@db...>]

Hi,


Unfortunately, I'm still getting the same error ("no module named tkinter") and a failure to initialise. Any ideas?


Cheers,


Irwin

________________________________
From: Jarrett Johnson <jar...@sc...>
Sent: 17 February 2025 00:33:26
To: Irwin Selvam
Cc: pym...@li...
Subject: Re: [PyMOL] Caver3 plugin failure to initialise

Hi Irwin,

A few months ago I worked on converting Caver 3 to use PyQt, I'm unsure if it's in a complete state, but within the next couple of months I'll be sure to finish it up and update the Caver PyMOLWiki page.

https://github.com/JarrettSJohnson/caver-pymol-plugin/tree/pyqt . Should just be able to press the Code button and Download Zip.

Best,
Jarrett J.


On Wed, Feb 12, 2025 at 5:03 AM Irwin Selvam via PyMOL-users <pym...@li...<mailto:pym...@li...>> wrote:

Hi all,


I'm trying to run the Caver3 plugin on PyMOL 2.5.7 on an M2 mac (Sequoia 15.3) but it's failing to initialise due to the "tkinter" module being missing. I've updated python to 3.13.2, which should come with tkinter 8.6. Does anyone have a solution?


Cheers,


Irwin

_______________________________________________
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Archives: http://www.mail-archive.com/pym...@li...
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


--

Jarrett Johnson | Staff Developer, PyMOL


[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]

[PyMOL] 3D/Stereoscopic hardware options in 2025?

[Blankenfeldt, W. <wul...@he...>]

Dear all,

I have just been shocked by our IT department that they will force us into migration to Win11 very soon. I know I am a dinosaur, but I still use and love my old nvidia Quadro/Asus/shutter glasses combi (over 10 years old) for hardware stereo viewing of protein structures under Win10. I am afraid that this will simply not work anymore once I have been upgraded, since nvdia has disabled hardware stereo in its drivers long time ago.

Personally, I cannot understand how modern structural biology can live without it and I would love to still be able view structures in 3D.

I know that the PyMol community is graphics- and tech-savvy, I am therefore asking if you know of any modern day hardware solution for 3D viewing in our favorite programs (PyMol, Coot ...).


Thank you in advance for your advice,


Wulf





Prof. Wulf Blankenfeldt
Struktur und Funktion der Proteine (SFPR)

HZI - Helmholtz-Zentrum f?r Infektionsforschung GmbH

SCIENCE CAMPUS Braunschweig-S?d
Inhoffenstra?e 7, 38124 Braunschweig
Tel. +49 5316181-7000
wul...@he...
www.helmholtz-hzi.de


[cid:Helmholtz_HZI_Logo_RGB_DE_nebeneinander_beschnitt2_1acc279d-0673-4590-b45d-24938b462e30.jpg]




________________________________

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Handelsregister: Amtsgericht Braunschweig, HRB 477

Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/

Re: [PyMOL] Caver3 plugin failure to initialise

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

Hi Irwin,

A few months ago I worked on converting Caver 3 to use PyQt, I'm unsure if
it's in a complete state, but within the next couple of months I'll be sure
to finish it up and update the Caver PyMOLWiki page.

https://github.com/JarrettSJohnson/caver-pymol-plugin/tree/pyqt . Should
just be able to press the Code button and Download Zip.

Best,
Jarrett J.


On Wed, Feb 12, 2025 at 5:03 AM Irwin Selvam via PyMOL-users <
pym...@li...> wrote:

> Hi all,
>
>
> I'm trying to run the Caver3 plugin on PyMOL 2.5.7 on an M2 mac (Sequoia
> 15.3) but it's failing to initialise due to the "tkinter" module being
> missing. I've updated python to 3.13.2, which should come with tkinter 8.6.
> Does anyone have a solution?
>
>
> Cheers,
>
>
> Irwin
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 

*Jarrett Johnson* | Staff Developer, PyMOL

[PyMOL] Caver3 plugin failure to initialise

[Irwin S. <irw...@db...>]

Hi all,


I'm trying to run the Caver3 plugin on PyMOL 2.5.7 on an M2 mac (Sequoia 15.3) but it's failing to initialise due to the "tkinter" module being missing. I've updated python to 3.13.2, which should come with tkinter 8.6. Does anyone have a solution?


Cheers,


Irwin

Re: [PyMOL] Question on geometry option in replace command

[Norbert S. <st...@bb...>]

Dear Lei,


the best way to build a new molecule is via the builder in the GUI.


The commands "replace" or "attach" are not well documented. I could 
reproduce your problem and I think PyMOL runs some kind of check routine 
after you issue a replace or attach command and it will reset the atomic 
valence and geometry to sensible values based on the atom environment.


For example, if you construct aniline using the builder the nitrogen has 
geometry=3 and valence=3. If you try to convert it to a sp3-hybridized 
nitrogen via "replace N, 4, 3" it keeps geometry=3 and valence=3. You 
can query the geometry and valence by selecting one or several atoms and 
use the command:

cmd.iterate("sele", "print(name, geom, valence)").

Next you convert the N-conjugated "double bond" of the aromatic system 
to a single bond using the builder. The nitrogen stays planar and the 
geometry ist still 3. Now the command "replace N, 4, 3" works as the 
nitrogen is no longer next to an aromatic system.


Best wishes,


Norbert



Am 06.02.2025 um 17:54 schrieb Lei Qian:
> Dear users,
> Could I ask a question on geometry option in replace command?
> I tried to use Build/Fragment/XXX to replace an atom to a new one, and 
> pymol GUI shows the corresponding replace command.
> However, I found the geometry option always equals to 4.
> For example,
> PyMOL>replace O, 4, 2
> PyMOL>replace N, 4, 3
> PyMOL>replace C, 4, 4
> I tried to replace the atom in different types of bonds: 
> single/double/triple bonds, but the geometry value is always 4.
> Could you please help me figure it out? Thank you very much!
> Best,
> Lei
>
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives:http://www.mail-archive.com/pym...@li...
> Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Question on geometry option in replace command

[Lei Q. <lei...@ou...>]

Dear users,
Could I ask a question on geometry option in replace command?
I tried to use Build/Fragment/XXX to replace an atom to a new one, and pymol GUI shows the corresponding replace command.
However, I found the geometry option always equals to 4.
For example,
PyMOL>replace O, 4, 2
PyMOL>replace N, 4, 3
PyMOL>replace C, 4, 4
I tried to replace the atom in different types of bonds: single/double/triple bonds, but the geometry value is always 4.
Could you please help me figure it out? Thank you very much!
Best,
Lei

[PyMOL] Announcement: The 17th CCP4/APS Crystallographic School, June 23rd-30th, 2025, APS

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

Dear Colleagues,

We are pleased to announce that the 17th annual CCP4/APS Crystallographic School, "From Data Collection to Structure Refinement and Beyond," will be held from June 23rd to 30th, 2025, at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found on the school website: http://www.ccp4.ac.uk/schools/APS-2025/index.php.

Dates: June 23rd through 30th, 2025 (on-site), June 2nd and 16th (virtual)
Location: Advanced Photon Source, Argonne National Laboratory, Argonne (near
Chicago), Illinois, USA

The school comprises two parts: a data collection workshop and a crystallographic computing workshop. The data collection workshop includes beamline training, data collection at GM/CA@APS beamlines, and data processing, using only the participants' crystals. The crystallographic computation workshop will feature many modern crystallographic software packages (including CCP4, PHENIX, XDS, HKL, and DIALS) taught by authors and other experts. This workshop will also introduce elements of CryoEM, such as model building and refinement. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive troubleshooting of the technical difficulties participants face in their projects). Two additional virtual days (June 2nd and 16th, 2025) will cover sample preparation (cryo-cooling), bioinformatics, and introductory crystallography lectures. We have had considerable success resolving these problems in past years, as attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A draft program can be found on 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: The application deadline is May 15th, 2025, we strongly encourage interested participants to apply as soon as possible. To apply, visit https://www.ccp4.ac.uk/schools/APS-2025/application.php

Fees: There is a $500 participation fee for selected academic students and $1,500 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] How to iterate over a distance object?

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

Please, google "pymol iterate objects"
3rd in the hit list: [PyMOL] iterating over list of objects
for i in *cmd.get_object_list()*: cmd.align( i, reference )


On Mon, Jan 27, 2025 at 9:56 AM Csongor MATYAS via PyMOL-users <
pym...@li...> wrote:

> I am trying to iterate over lots of distances that I can generate with
> cmd.distance(name = 'distA_B', selection1 = 'selA', selection2 = 'selB',
> cutoff = 3.6, mode = 2) for example. My only problem is that I don't know
> how to iterate over them. How can one iterate over objects that are not
> selection of atoms?
> (I'm doing this from python using the pymol-bundle, but even in pymol I
> can't find a way to save these into a file or print them or save them in a
> variable somehow)
>
> Kind regards,
> Csongor
>
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