pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Did not recieve Email

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

Hello Alga,

I'll reach out to you.

Best,
Jarrett J

On Thu, Jun 23, 2022 at 3:11 AM Alga Manggara <alg...@gm...>
wrote:

>  Hello I am Algafari Manggara from Indonesia
> I am a lecture of Pharmacy department Institut Ilmu Kesehatan Bhakti
> Wiyata Kediri
>  I have already registered my email to download PyMOL software for free
> lisence via registration for education. But I didn't get a reply email.
> Thank you.
>
> Best regards,
> Alga Manggara
>
>
> _______________________________________________
> 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] Did not recieve Email

[Alga M. <alg...@gm...>]

 Hello I am Algafari Manggara from Indonesia
I am a lecture of Pharmacy department Institut Ilmu Kesehatan Bhakti Wiyata
Kediri
 I have already registered my email to download PyMOL software for free
lisence via registration for education. But I didn't get a reply email.
Thank you.

Best regards,
Alga Manggara

[PyMOL] adding ego objects to an existing object/state

[Randy Z. <rz...@sj...>]

Hi, 

I am trying to add custom graphics to each frame of a trajectory. 

I use split_states to divide the trajectory (multi-pdb file)  into one state per frame, then attempt to load graphics objects into a specific frame:

cmd.load_cgo( obj, name, frame#) 

However, this simply appends the objects into their own states at the end - they are all visible.

I can find no example of attaching graphics to a specific existing state - is it possible?

It seems it must be, as graphics objects like ribbons are associated with a specific molecule ?

Thanks!

Randy

Re: [PyMOL] "PyMOL-users" mailing list

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

Hello,

Yes. If you have any questions about how to use PyMOL or best practices,
users of this mailing list can help.Otherwise if you have personal issues
regarding your account or license, then contact he...@sc... .
There is also our github tracker for open-source related questions/queries
( https://github.com/schrodinger/pymol-open-source/issues ).

Best,

Jarrett J

On Tue, Jun 21, 2022 at 9:40 PM Jiaqiao ZHOU <
zhou-jiaqiao1998@g.ecc.u-tokyo.ac.jp> wrote:

> To whom it may concern,
>
> I am sorry, but I wonder if this is the address I should write to
> if I have questions about PyMOL.
>
> Kind regards,
> _______________________________________________
> 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] EduPymol Not sending Liscene

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

Hi Sophie,

I will email you.

Jarrett J.

On Tue, Jun 21, 2022 at 8:11 PM Sophie Hurwitz <hur...@uw...> wrote:

> Hello,
>
> I'm a PhD biochemistry student and I've tried to sign for the educational
> version of PyMol multiple times, but have still not received an email with
> the licensing code.  Is there a way to work around this problem and get the
> license to activate PyMol?
>
> -
> Sophie
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] "PyMOL-users" mailing list

[Jiaqiao Z. <zhou-jiaqiao1998@g.ecc.u-tokyo.ac.jp>]

To whom it may concern,

I am sorry, but I wonder if this is the address I should write to
if I have questions about PyMOL.

Kind regards,

[PyMOL] EduPymol Not sending Liscene

[Sophie H. <hur...@uw...>]

Hello,

I'm a PhD biochemistry student and I've tried to sign for the educational
version of PyMol multiple times, but have still not received an email with
the licensing code.  Is there a way to work around this problem and get the
license to activate PyMol?

-
Sophie

Re: [PyMOL] [EXTERNAL] How to get hydrophobic colors??

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Joaodejota,

The shortcut "yrb" will color the molecular surface to highlight hydrophobicity using the method of Hagemans et al. 2015.
The shortcut is part of a collection of shortcuts found here https://github.com/MooersLab/pymolshortcuts/blob/master/README.md

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________
From: JJ Oliveira <joa...@gm...>
Sent: Saturday, June 18, 2022 9:27 AM
To: PyM...@li... <PyM...@li...>
Subject: [EXTERNAL] [PyMOL] How to get hydrophobic colors??

Hi guys
Is there a method to detect superficial hydrophobic regions?
Thank you!

[PyMOL] How to get hydrophobic colors??

[JJ O. <joa...@gm...>]

Hi guys
Is there a method to detect superficial hydrophobic regions?
Thank you!

Re: [PyMOL] pymol education license

[Xiang Z. <zx...@ma...>]

Wow, good to hear your advice. Thank you!


-----Original Messages-----
From:"EDUARDO JOSÉ AZEVEDO CORREA" <ed...@ep...>
Sent Time:2022-06-18 03:29:37 (Saturday)
To: "Jarrett Johnson" <jar...@sc...>
Cc: "Xiang Zhang" <zx...@ma...>, "Pymol User list" <pym...@li...>
Subject: Re: [PyMOL] pymol education license


Well I got the educational license for one year.
however, I can get the revalidation.
So I bought the professional license for one year. I negotiate with Schrodinger and Get a reduction in price.
Suggest you to talk with Evan Stoll <eva...@sc...>


Good Luck for you


Em sex., 17 de jun. de 2022 às 15:34, Jarrett Johnson <jar...@sc...> escreveu:

Hello Xiang,


I believe this is an issue being currently worked on. Please send a query to he...@sc...

Best,

Jarrett J


On Fri, Jun 17, 2022 at 12:31 AM Xiang Zhang <zx...@ma...> wrote:




-----Original Messages-----
From:"Xiang Zhang" <zx...@ma...>
Sent Time:2022-06-17 12:13:07 (Friday)
To:pym...@li...
Cc:
Subject: pymol education license

Hi 
I can't receive pymol education license in my mail box even though I tried 2 mail address.


Best,
Xiang Zhang
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Archives: http://www.mail-archive.com/pym...@li...
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--

|

Jarrett Johnson | Senior Developer, PyMOL

|
|
|
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--



| |

Eduardo José Azevedo Corrêa

Biólogo| Professor e Pesquisador




|
|

(37)9997-5771

(37)3271-4673

www.epamig.br

| |

EPAMIG Pitangui
Rodovia BR - MG352 Km35 Zona Rural


Caixa Postal 43

CEP 35650-000 - Pitangui - MG

|

Re: [PyMOL] pymol education license

[EDUARDO J. A. C. <ed...@ep...>]

Well I got the educational license for one year.
however, I can get the revalidation.
So I bought the professional license for one year. I negotiate with
Schrodinger and Get a reduction in price.
Suggest you to talk with Evan Stoll <eva...@sc...>

Good Luck for you

Em sex., 17 de jun. de 2022 às 15:34, Jarrett Johnson <
jar...@sc...> escreveu:

> Hello Xiang,
>
> I believe this is an issue being currently worked on. Please send a query
> to he...@sc...
>
> Best,
>
> Jarrett J
>
> On Fri, Jun 17, 2022 at 12:31 AM Xiang Zhang <zx...@ma...>
> wrote:
>
>>
>>
>>
>> -----Original Messages-----
>> *From:*"Xiang Zhang" <zx...@ma...>
>> *Sent Time:*2022-06-17 12:13:07 (Friday)
>> *To:* pym...@li...
>> *Cc:*
>> *Subject:* pymol education license
>>
>> Hi
>> I can't receive pymol education license in my mail box even though I
>> tried 2 mail address.
>>
>> Best,
>> Xiang Zhang
>>
>> _______________________________________________
>> 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-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Eduardo José Azevedo Corrêa*

Biólogo| Professor e Pesquisador


(37)9997-5771

(37)3271-4673

*www.epamig.br <http://www.epamig.br/>*

*EPAMIG Pitangui*
Rodovia BR - MG352 Km35 Zona Rural

Caixa Postal 43

CEP 35650-000 - Pitangui - MG

Re: [PyMOL] pymol education license

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

Hello Xiang,

I believe this is an issue being currently worked on. Please send a query
to he...@sc...

Best,

Jarrett J

On Fri, Jun 17, 2022 at 12:31 AM Xiang Zhang <zx...@ma...>
wrote:

>
>
>
> -----Original Messages-----
> *From:*"Xiang Zhang" <zx...@ma...>
> *Sent Time:*2022-06-17 12:13:07 (Friday)
> *To:* pym...@li...
> *Cc:*
> *Subject:* pymol education license
>
> Hi
> I can't receive pymol education license in my mail box even though I tried
> 2 mail address.
>
> Best,
> Xiang Zhang
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Re: [PyMOL] pymol education license

[Xiang Z. <zx...@ma...>]

-----Original Messages-----
From:"Xiang Zhang" <zx...@ma...>
Sent Time:2022-06-17 12:13:07 (Friday)
To: pym...@li...
Cc:
Subject: pymol education license

Hi 
I can't receive pymol education license in my mail box even though I tried 2 mail address.


Best,
Xiang Zhang

[PyMOL] Default altloc selection

[Ioannis R. <riz...@eb...>]

Hello,

Is there a way to set a default altloc to be selected, if the residue/atom is disordered? I can do this manually with a notation like ‘select foo, obj//chain/resid/atom and alt A’ but if the residue/atom is not disordered, the selection will be empty (I call this through a script for a set of structures so I cannot know if there is disorder beforehand). 

If the ‘and alt A’ conditional is omitted, all the alternative residues/atoms are selected, but I don’t want that. It would be very handy to be able to select a default altloc for these kinds of selections.

Cheers,

--
Ioannis G. Riziotis
PhD Fellow - Thornton Group
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

Re: [PyMOL] apbs: program locations

[Matic K. <Mat...@ki...>]

Hi Michael,

if you haven't figured it out yet, this thread might help you:
https://sourceforge.net/p/pymol/mailman/pymol-users/thread/EAA6862A-4914-483F-A12F-92B5A1E81233%40schrodinger.com/

It can be done in the configuration file of the plugin.

Best regards!
Matic


On 1. 06. 22 05:26, mic...@gm...<mailto:mic...@gm...> wrote:
Dear all,

Can I save the “program locations” information in APBS plugin? Once I exit the plugin and open it again, the previous input disappears.
I am using windows version pymol.

Thank you very much.

Michael


[cid:par...@ki...]




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[PyMOL] morphing problem

[Criss H. <cri...@gm...>]

I have two objects of the same protein in different conformational states
and I want to show the conformational change using morph.
Each object is a homopentamer, chains A-E.
However, one object has the chains arranged in a clockwise direction and
the second object has them arranged in a counterclockwise direction. When I
morph them, I get a wierd twisty thing as a result of chains swapping with
one another.
I tried to fix this by changing the names of the chains (alter PDB1 and
chain B, chain="E" ...and so on) so that now chain names A-E of both PDBs
are clockwise. Although I succeed in renaming the chains, this has has no
effect on the morphing. SO, I wondered if the segment identifer was the
problem. Each chain also has a corresponding segment identifier (for
example, originally PDB1/B/B which has now been changed to PDB1/B/E). I
tried changing the segment identifier using the same syntax (alter PDB1 and
segment B, segment="E"). Although the output message shows "modified 2667
atoms" the segment identifier in the sequencce window does not change and
selection of segment E yields nothing and the morphing is unchanged.
Sorry for the long narrative, but the main question is: what can I do to
make this morphing work? Thanks.

Re: [PyMOL] [EXTERNAL] PyMOL scripting issues

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

 Hi Martin,

Which version of PyMOL are you using?
How did you install PyMOL?
These details matter because there are several paths for installing PyMOL on Linux.
Some paths use the system python and some do not.
The incentive PyMOL has Anaconda Python bundled inside.

You could install Ancaonda3 and then create a conda env called pymolconda.
Then you can activate this env, install pymol with conda, and then call pymol as module with the Anaconda Python.

Best regards,

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________
From: Martin Urban <mar...@st...>
Sent: Saturday, June 11, 2022 2:34 AM
To: pym...@li... <pym...@li...>
Subject: [EXTERNAL] [PyMOL] PyMOL scripting issues

Hello,

I have a problem with PyMOL. I am writing a more complex automation
script, and I want to import pymol's cmd module. The problem is that the
python interpreter on my linux system doesn't recognize pymol and it
throws an ModuleNotFound Error. I have a Ubuntu system and I installed
pymol with the apt package manager. Does anyone know how the systems
python3 interpreter can find the cmd module from PyMOL?

Greetings from Germany,

Martin

--

Martin Urban

Westfälische Hochschule / Westphalian University of Applied Sciences
Fachbereich Ingenieur- und Naturwissenschaften (FB 8) / Department of
Engineering and Natural Sciences
August-Schmidt-Ring 10
D-45665 Recklinghausen, Germany


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[PyMOL] PyMOL scripting issues

[Martin U. <mar...@st...>]

Hello,

I have a problem with PyMOL. I am writing a more complex automation 
script, and I want to import pymol's cmd module. The problem is that the 
python interpreter on my linux system doesn't recognize pymol and it 
throws an ModuleNotFound Error. I have a Ubuntu system and I installed 
pymol with the apt package manager. Does anyone know how the systems 
python3 interpreter can find the cmd module from PyMOL?

Greetings from Germany,

Martin

--

Martin Urban

Westfälische Hochschule / Westphalian University of Applied Sciences
Fachbereich Ingenieur- und Naturwissenschaften (FB 8) / Department of 
Engineering and Natural Sciences
August-Schmidt-Ring 10
D-45665 Recklinghausen, Germany

[PyMOL] black shadows on povray mesh2

[Suzuki, R. <rs...@af...>]

Hello,

Do you have any idea to calculate nice normal vectors that can be
rendered cleanly?

When I draw with povray using include files created by pymol, sometimes
black shadows appear on the secondary structures, especially in the
planes near perpendicular to the picture.

I removed the normal vectors and these shadows disappeared. But the
smoothing process between the triangles that make up the mesh2 objects
was also not performed.

I calculated the average of the unit normal vectors of the triangles
that contain each vertex and compose the same plane and set in place of
the original normal vectors, and the black shadows disappeared.
Smoothing also took place, but was less smooth than in the original
file. Also, some edges was emphasized compared to the original.

Thanks,

Rintarou

[PyMOL] apbs: program locations

[<mic...@gm...>]

Dear all,

 

Can I save the "program locations" information in APBS plugin? Once I exit
the plugin and open it again, the previous input disappears. 

I am using windows version pymol.

 

Thank you very much.

 

Michael

 

 

[PyMOL] setting specific state in no-gui mode

[Enrico M. <jms...@gm...>]

Dear Pymol Users!
I am using pymol in batch mode to select specific state from the
multi-state object and then save screen-shoot and the pse session for
it.

cmd.set('state','5','my_object*')
cmd.png('image.png',dpi=50,ray=1)
cmd.save('session.pse')

The problem is that in the pse session I may see only the selected
state. I've tried to change the states using arrows in the GUI but it
always frozen to the state selected before saving the pse session. Is
it possible via some command to reset to the default (1) state before
saving the pymol session ?
Cheers,
Enrico

[PyMOL] ImportError when launching open-source pymol

[Ioannis R. <riz...@eb...>]

Hello,

Anyone any idea how to tackle this error when launching pymol after compiling from source?

ImportError: /hps/software/users/xx/xx/miniconda3/envs/py3/lib/python3.8/site-packages/pymol/_cmd.cpython-38-x86_64-linux-gnu.so: undefined symbol: _Z15MapSetupExpressP7MapType

Trial version works fine though.

Cheers,
Yannis

--
Ioannis G. Riziotis
PhD Fellow - Thornton Group
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

[PyMOL] Help superimposing protein and sugar

[Savannah S. <sav...@gm...>]

Hello all,

TLDR; What’s the best way to place one molecule over a geometrically similar but unrelated second molecule?

I’m a scientist studying the docking of glycans to antibodies. I’m trying to use pymol to position my glycan, a 10-mer called gxm, close to its putative binding site. My glycan has a protein mimetic, p1, an 11-mer, that I already have docked to my antibody. 

Since p1 and gxm have similar structures, I’d like to align gxm as close as possible to where p1 goes on my p1-antibody co-crystal structure. However, since my glycan and my protein have no sequence alignment, I haven’t been able to use align, super, fit, etc. I tried using pair fit and pymol kept crashing when I called it. Cealign sounded like a good option, but, because I’m using a 10-mer and an 11-mer, I got an error that the sequences were too short.

The best I’ve been able to do is translate gxm to p1’s center of mass, then manually adjust gxm with my mouse. However, that’s obviously imprecise. Does anyone have any ideas for how I could overlap my glycan more closely to my protein?

Thanks!

Savannah Speir

Post Baccalaureate Fellow
Rosetta Commons
Johns Hopkins University

[PyMOL] Problem to get RMSD between crystal ligand and docked ligand

[Maximiliano J. G. t. <max...@co...>]

Hello everyone, I am trying to obtain the RMSD value between a docked
ligand I got with Autodock Vina (PDBQT file) and a crystal ligand structure
i downloaded from rcsb.org (PDB file).

The thing is when I open the crystal ligand file on PyMOL this error
appears:

Warning: Invalid characters in 'MLN_Cristalizado_PDB' have been
replaced or stripped
 ObjectMolecule: Read crystal symmetry information.
 CmdLoad: "" loaded as "MLN_Cristalizado_PDB".


And when I try to run the rms command this error appears:


PyMOL>rms MLN_Cristalizado_PDB (crystal ligand), MLN_H-4760_prueba21R4L
(docked ligand)
ExecutiveRMS-Error: No atoms selected.


Previously running the rms command, I run these commands:


alter all, segi=""

alter all, chain=""


How can I get an easier way of solving this problem? Can I get an
approximate RMSD value with another command?


I attach the two files for you to try for yourselves if you want to.


I want to add that when i open the two files on the notepad the identifiers
of the atoms are different, I have also gotten the error of mismatched
identifiers before too.


Thanks in advance to anyone who replies, good luck!

[PyMOL] why does coordinates not overlap with map

[sunyeping <sun...@al...>]

Dear pymol users,

I have a coordinate file (pdb) and a map file (mtz), and I want to make a image that shows both the coordinate and the map. I generate a .map.ccp4 file using fft in CCP4 program. However, when I open the pdb file and the .map.ccp4 in pymol, I find the coordinates are out of the map. Please see the image at the following link:
       https://drive.google.com/file/d/1TmH-mFCnsCNghcq4RQJ9mNOBlTfCRsHW/view?usp=sharing
Could anyone tell me how to map them overlap?

Thank you in advance.

Best regards