pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Mutagenesis rotamer states saved as scenes but appearing in movie

[Colin D. <Col...@uw...>]

PyMol 3

Am using the mutagenesis wizard to investigate rotamers for an aa change. I can save each rotamer as a scene in the Scenes sidebar and they appear there as the correct rotamer with clashes, etc as in the main window. I can also add them to the timeline but the movie just shows the original unchanged aa. Is there a way of creating a movie illustrating the various states?

Re: [PyMOL] subscription of pymol

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

Hello,

Can you please email "he...@sc..." for subscription requests?

Best,
Jarrett J.

On Sun, Oct 26, 2025 at 3:35 AM Sehrish Murtaza <blu...@gm...>
wrote:

> i need to subscribe this software for the my research work
> _______________________________________________
> 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] subscription of pymol

[Sehrish M. <blu...@gm...>]

i need to subscribe this software for the my research work

[PyMOL] PyDescriptorC* uses PyMOL for molecular descriptor calculation

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

Dear PyMOL users
We are delighted to share that PyDescriptorC*, the new version of
PyDescriptor, is available for the PyMOL community. It uses PyMOL for
molecular descriptor calculation.
Please visit: https://sites.google.com/view/pydescriptorcstar/home
*Salient features:*
1. PyDescriptorC* is developed to compute a total 1,12,194 molecular
descriptors for each molecule.
2. It calculates constitutional, topological, geometric/spatial, circular
fingerprints, quantum chemical, and chirality-specific descriptors.
3. Chirality-aware descriptors: uniquely capture stereochemistry, combining
chirality with electronic, geometric, and topological features.
4. No external dependencies beyond Python and PyMOL.
5. Output: descriptors automatically saved in CSV format.
We hope it will be useful to the broad PyMOL community.
Cheers
Vijay

*Prof. Dr. Vijay H. Masand*
Professor (Full), Department of Chemistry,
Vidya Bharati Mahavidyalaya, Amravati- 444 602
Maharashtra, India.
Phone number- +91-9403312628

Re: [PyMOL] keyboard shorcuts

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

Hello,

In 3.0, you can find your keyboard shortcuts under `Settings > Keyboard
shortcuts` from the top menu bar.

Jarrett J.

On Wed, Sep 10, 2025 at 12:35 AM Julio Coll <jul...@gm...> wrote:

> I cannot find how to use the keyboard shorcuts in PyMol version 3, while
> those same shortcuts worked on previous versions. Any hints?
>
>  *Julio M. Coll        **orcid: 0000-0001-8496-3493*
> Dr.Biología. Univ.Complutense, Madrid, SPAIN;                 PhD
> Biology.Massachusetts Institute of Technology, Boston, USA
> Profesor de Investigación. Emérito. (Dpt.Biotecnologia, Centro Nacional
> INIA). CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS, CSIC
>  *@*jul...@gm...              *@*jul...@cs...       *✆*:
> 680154451
>   La reproduccion de los genomas: http://www.jcoll.org
> <http://www.imtra-vac.unileon.es/>        Publicaciones científicas:
> http://www.jcoll.org/coll-pdfs/
>
>
> _______________________________________________
> 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] keyboard shorcuts

[Julio C. <jul...@gm...>]

I cannot find how to use the keyboard shorcuts in PyMol version 3, while
those same shortcuts worked on previous versions. Any hints?

 *Julio M. Coll        **orcid: 0000-0001-8496-3493*
Dr.Biología. Univ.Complutense, Madrid, SPAIN;                 PhD
Biology.Massachusetts Institute of Technology, Boston, USA
Profesor de Investigación. Emérito. (Dpt.Biotecnologia, Centro Nacional
INIA). CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS, CSIC
 *@*jul...@gm...              *@*jul...@cs...       *✆*:
680154451
  La reproduccion de los genomas: http://www.jcoll.org
<http://www.imtra-vac.unileon.es/>        Publicaciones científicas:
http://www.jcoll.org/coll-pdfs/

Re: [PyMOL] Fe in heme disappears

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

Works for me with PyMOL 3.1.6 and Open-Source PyMOL 3.2.0a when
deleting the bonds with the "unbond" command.

fetch 4WMZ
as licorice
zoom elem FE
unbond elem FE, *

System info:
Arch Linux
NVIDIA GeForce GTX 1070/PCIe/SSE2
4.6.0 NVIDIA 575.64.05
PyQt5 5.15.11 (Qt 5.15.15)

Cheers,
  Thomas

On Thu, Jul 31, 2025 at 8:08 AM Takanori Nakane
<tna...@os...> wrote:
>
> Hi,
>
> Indeed I could not show the iron as nb_spheres but I managed to use
> spheres instead.
>
> fetch 4WMZ
> as spheres, elem FE
> set sphere_scale, 0.4, elem FE
>
> (I am using the open-source version of PyMOL 3.1.0 installed using brew)
>
> Best regards,
>
> Takanori Nakane
>
> On 2025/07/31 12:47, Joel Tyndall via PyMOL-users wrote:
> > Hi All,
> >
> > I’m trying to make a pretty picture of a protein containing  a heme and
> > ligand. Previously I could delete the bonds (using builderthat pymol
> > shows for coordination as I prefer to not show them as stick form and
> > then “show nb_sphere” to show the metal ion. I can no longer do this (Fe
> > doesn’t show as nb_sphere). When I select the HEM in SEQ view, it is
> > still there but I cant . It is part of the HEM residue no a single ion.
> >
> > Using 4WMZ; PyMOL 3.1.3
> >
> > Any suggestions?
> >
> > J
> >
> > University of Otago
> >
> >
> >
> > *Professor Joel Tyndall*
> >
> > BSc(Hons) PhD
> >
> > School of Pharmacy | He Rau Kawakawa
> > University of Otago | Ōtākou Whakaihu Waka
> > Mobile//Waea pūkoro/ +64 21 051 0940
> >
> > Dunedin| Ōtepoti
> > PO Box 56, Dunedin 9054
> > New Zealand | Aotearoa
> >
> >
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Fe in heme disappears

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

Hi,

Indeed I could not show the iron as nb_spheres but I managed to use
spheres instead.

fetch 4WMZ
as spheres, elem FE
set sphere_scale, 0.4, elem FE

(I am using the open-source version of PyMOL 3.1.0 installed using brew)

Best regards,

Takanori Nakane

On 2025/07/31 12:47, Joel Tyndall via PyMOL-users wrote:
> Hi All,
> 
> I’m trying to make a pretty picture of a protein containing  a heme and 
> ligand. Previously I could delete the bonds (using builderthat pymol 
> shows for coordination as I prefer to not show them as stick form and 
> then “show nb_sphere” to show the metal ion. I can no longer do this (Fe 
> doesn’t show as nb_sphere). When I select the HEM in SEQ view, it is 
> still there but I cant . It is part of the HEM residue no a single ion.
> 
> Using 4WMZ; PyMOL 3.1.3
> 
> Any suggestions?
> 
> J
> 
> University of Otago
> 
> 	
> 
> *Professor Joel Tyndall*
> 
> BSc(Hons) PhD
> 
> School of Pharmacy | He Rau Kawakawa
> University of Otago | Ōtākou Whakaihu Waka
> Mobile//Waea pūkoro/ +64 21 051 0940
> 
> Dunedin| Ōtepoti
> PO Box 56, Dunedin 9054
> New Zealand | Aotearoa
> 
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Fe in heme disappears

[Joel T. <joe...@ot...>]

Hi All,

I’m trying to make a pretty picture of a protein containing  a heme and ligand. Previously I could delete the bonds (using builderthat pymol shows for coordination as I prefer to not show them as stick form and then “show nb_sphere” to show the metal ion. I can no longer do this (Fe doesn’t show as nb_sphere). When I select the HEM in SEQ view, it is still there but I cant . It is part of the HEM residue no a single ion.

Using 4WMZ; PyMOL 3.1.3

Any suggestions?

J

[University of Otago]
Professor Joel Tyndall
BSc(Hons) PhD

School of Pharmacy | He Rau Kawakawa
University of Otago | Ōtākou Whakaihu Waka
Mobile/Waea pūkoro +64 21 051 0940

Dunedin | Ōtepoti
PO Box 56, Dunedin 9054
New Zealand | Aotearoa

[PyMOL] Weird color conection

[alberto m. <zr...@ho...>]

i need help please We have observed that when performing superpositions, the visual aid links between corresponding atoms are sometimes displayed in yellow and, in other cases, in purple. We have been trying to understand the underlying logic that determines this color difference.
For instance, we've noticed that complex, non-local, or multi-part superpositions sometimes result in purple links, while simpler alignments often result in yellow ones, but this is not always consistent. Our working hypothesis is that the color may be related to the energetic favorability or the complexity of the alignment solution, but this is purely speculation on our part.
understanding what does this conection between atoms mean is critical for our work please help

Re: [PyMOL] Pymol license not found on cluster

[Nambiar, N. <nna...@vo...>]

Hi Jarrett,

The issue still persists with the latest PyMOL version (3.1.6.1). I made a
new conda environment and installed Pymol and also downloaded a new license
file, renamed it to license.lic and placed in the 2 locations described
earlier:
/lustre/isaac24/scratch/nnambia1/envs/pymol36env/share/pymol/license.lic
$HOME/.pymol/license.lic

I run the following code in python to generate the images:

import pymol2
import sys
import MDAnalysis as mda
import os



path = sys.argv[1] + '/'
#'/lustre/isaac/scratch/nnambia1/pex/pex_full_allatom/gromacs/'


filename = 'step9'


lipid_dict = {
    'DPPE': {
        'headgroups': ['P', 'C2'],
        'tailgroups': ['C314', 'C315', 'C316', 'C214', 'C215', 'C216'],
        'voronoicolor': 'firebrick'
    },
    'DPPG': {
        'headgroups': ['P', 'C2'],
        'tailgroups': ['C314', 'C315', 'C316', 'C214', 'C215', 'C216'],
        'voronoicolor': 'forest'
    },
    'PMCL2': {
        'headgroups': ['P1','P3','C32','C12'],
        'tailgroups':
['CA14','CA15','CA16','CB14','CB15','CB16','CC14','CC15','CC16','CD14','CD15','CD16'],
        'voronoicolor': 'marine'
    }
}

#loading universe
univ = mda.Universe(path+filename+'.tpr', path+filename+'.trr')
#Finding unique lipid names
head_group_selection = "name P*"  # Common lipid head group atoms
head_groups = univ.select_atoms(head_group_selection)
resnames = set(r.resname for r in head_groups.residues)
lipidnames = sorted(resnames)
numlipids = len(lipidnames)


#open pymol window
p1 = pymol2.PyMOL()
p1.start()

#load the pdbs
for i in range(0,numlipids):
    print('load ', lipidnames[i])
    p1.cmd.load(path+'component_trajectories/'+lipidnames[i]+'.pdb')

p1.cmd.do('hide everything')
p1.cmd.do('show sticks')

#color by element except carbon atoms
p1.cmd.do('color atomic, (not elem C)')

#color lipid tails by species
for i in range(0,numlipids):
    p1.cmd.do('color '+lipid_dict[lipidnames[i]]['voronoicolor']+' , (name
C*) and '+lipidnames[i])


#producemovie top view
# Create output directory if it doesn't exist
#os.makedirs(path+'out_topview', exist_ok=True)
#p1.cmd.mpng(path+'out_topview/out'+'{:03d}'.format(i),mode = 2, height =
1200, width = 1920, quiet = 1)


#turn to side view
p1.cmd.turn('x', 90 )
#producemovie sideview
# Create output directory if it doesn't exist
os.makedirs(path+'out_sideview1', exist_ok=True)
# Write PNG
p1.cmd.mpng(path+'out_sideview1/out'+'{:03d}'.format(i),mode = 2, height =
1200, width = 1920, quiet = 1)


Best
Nikhil

On Mon, Jun 30, 2025 at 10:49 AM Jarrett Johnson <
jar...@sc...> wrote:

> Hi Nikhil,
>
> Does the issue still persist with the latest PyMOL version (3.1.6.1)? If
> so, can you also provide the precise commands you're using to generate the
> image?
>
> Jarrett J
>
> On Mon, Jun 23, 2025 at 10:35 PM Nambiar, Nikhil via PyMOL-users <
> pym...@li...> wrote:
>
>> Hi,
>>
>> I'm working on a remote cluster and using pymol without GUI and am
>> currently getting the license not found error. I installed pymol in a
>> virtual conda environment. The version of pymol I am running is pymol
>> 3.1.4.1. I downloaded an educational license and renamed it to license.lic
>> and placed them in 2 folder after finding a similar issue from  earlier on
>> the board (
>> https://sourceforge.net/p/pymol/mailman/pymol-users/thread/694...@sc.../
>> )
>>
>> /lustre/isaac24/scratch/nnambia1/envs/pymol3env/share/pymol/license.lic
>> $HOME/.pymol/license.lic
>>
>> I amstill getting the license not found watermark on my saved images. I
>> checked the pymol path using the following code too:
>>
>> import pymol2
>> p1 = pymol2.PyMOL()
>> p1.start()
>> print(os.environ['PYMOL_PATH'])
>>
>> which printed
>> out /lustre/isaac24/scratch/nnambia1/envs/pymol3env/share/pymol
>> For reference I activate the conda env by
>> conda activate /lustre/isaac24/scratch/nnambia1/envs/pymol3env
>>
>> Is there a way to direct pymol to the license file and get rid of the
>> watermark?
>>
>> Best
>> Nikhil Nambiar
>>
>>
>>
>>
>>
>> _______________________________________________
>> 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
>
>

Re: [PyMOL] Pymol license not found on cluster

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

Hi Nikhil,

Does the issue still persist with the latest PyMOL version (3.1.6.1)? If
so, can you also provide the precise commands you're using to generate the
image?

Jarrett J

On Mon, Jun 23, 2025 at 10:35 PM Nambiar, Nikhil via PyMOL-users <
pym...@li...> wrote:

> Hi,
>
> I'm working on a remote cluster and using pymol without GUI and am
> currently getting the license not found error. I installed pymol in a
> virtual conda environment. The version of pymol I am running is pymol
> 3.1.4.1. I downloaded an educational license and renamed it to license.lic
> and placed them in 2 folder after finding a similar issue from  earlier on
> the board (
> https://sourceforge.net/p/pymol/mailman/pymol-users/thread/694...@sc.../
> )
>
> /lustre/isaac24/scratch/nnambia1/envs/pymol3env/share/pymol/license.lic
> $HOME/.pymol/license.lic
>
> I amstill getting the license not found watermark on my saved images. I
> checked the pymol path using the following code too:
>
> import pymol2
> p1 = pymol2.PyMOL()
> p1.start()
> print(os.environ['PYMOL_PATH'])
>
> which printed
> out /lustre/isaac24/scratch/nnambia1/envs/pymol3env/share/pymol
> For reference I activate the conda env by
> conda activate /lustre/isaac24/scratch/nnambia1/envs/pymol3env
>
> Is there a way to direct pymol to the license file and get rid of the
> watermark?
>
> Best
> Nikhil Nambiar
>
>
>
>
>
> _______________________________________________
> 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] Add hydrogens different with .cif files

[Joel T. <joe...@ot...>]

Hi team (and support),

I have found that when I “get a pdb” file or use a .cif file with the latest versions (3.1) and then add hydrogens, it behaves differently to previously where the amines and acids are not ionised  (should be ammonium/guanidinuim and carboxylate).

But it does it with some and not others… e.g. 7LCJ vs 1D4K

Hoping someone can confirm this and if there is a fix?

Cheers
J

[University of Otago]
Professor Joel Tyndall
BSc(Hons) PhD

School of Pharmacy | He Rau Kawakawa
University of Otago | Ōtākou Whakaihu Waka
Mobile/Waea pūkoro +64 21 051 0940

Dunedin | Ōtepoti
PO Box 56, Dunedin 9054
New Zealand | Aotearoa

[PyMOL] Compatibility Issue: Cartoon Representation Disappears After Ray Tracing When Opening Old PSE Files in New PyMOL Versions

[<cz...@fo...>]

Dear PyMOL Community,

I am encountering a version compatibility issue with PyMOL and would appreciate your insights. The problem occurs when opening legacy session files (.pse) created in older PyMOL versions in newer releases (3.1.5.1).

Observed Behavior:


In the original environment (older PyMOL):


Session contains objects with simultaneous cartoon and surface representations



Both have active transparency settings



ray command correctly renders both semi-transparent elements(ray by original version.png)




In newer PyMOL versions (3.1.5.1):



Session loads without errors



ray command execution causes cartoon representation to completely disappear(ray by new version.png)



surface and other representations (e.g., sticks) render normally



Transparency settings appear preserved in GUI but ignored during rendering



The following prompt message appears when loading the PSE file:
PyMOL(TM) 3.1.5.1 - Incentive Product
Copyright (C) Schrodinger, LLC
This Executable Build integrates and extends Open-Source PyMOL.
Detected OpenGL version 2.1. Shaders available.


 Tessellation shaders not available
 Detected GLSL version 1.20.
 OpenGL graphics engine:
  GL_VENDOR:   Apple
  GL_RENDERER: Apple M2
  GL_VERSION:  2.1 Metal - 76.3
 License Expiry date: 2025-12-01 
Appreciate any guidance on resolving this rendering discrepancy while maintaining visualization integrity across versions.

Best regards,
[eva]

[PyMOL] Pymol license not found on cluster

[Nambiar, N. <nna...@vo...>]

Hi,

I'm working on a remote cluster and using pymol without GUI and am
currently getting the license not found error. I installed pymol in a
virtual conda environment. The version of pymol I am running is pymol
3.1.4.1. I downloaded an educational license and renamed it to license.lic
and placed them in 2 folder after finding a similar issue from  earlier on
the board (
https://sourceforge.net/p/pymol/mailman/pymol-users/thread/694...@sc.../
)

/lustre/isaac24/scratch/nnambia1/envs/pymol3env/share/pymol/license.lic
$HOME/.pymol/license.lic

I amstill getting the license not found watermark on my saved images. I
checked the pymol path using the following code too:

import pymol2
p1 = pymol2.PyMOL()
p1.start()
print(os.environ['PYMOL_PATH'])

which printed
out /lustre/isaac24/scratch/nnambia1/envs/pymol3env/share/pymol
For reference I activate the conda env by
conda activate /lustre/isaac24/scratch/nnambia1/envs/pymol3env

Is there a way to direct pymol to the license file and get rid of the
watermark?

Best
Nikhil Nambiar

Re: [PyMOL] Pymol loading pdb files twice

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

Hello,

Sorry, I'm a little late to reply here, but we released 3.1.6.1 early last
week which should hopefully address the issue where files were doubly
loaded.

Jarrett J.

On Thu, May 29, 2025 at 7:45 PM Jarrett Johnson <
jar...@sc...> wrote:

> Hi Kevin,
>
> Looks like we saw this issue as well back in December but seems like it
> slipped through the cracks. We've updated the priority to fix this
> hopefully by the next release. I'll reply here with any future updates.
>
> Best,
> Jarrett J.
>
> On Tue, May 27, 2025 at 1:58 PM Kevin M Jude <kj...@st...> wrote:
>
>> Using Pymol 3.1.3 (for mac from SBgrid) I notice that when I open pymol
>> by double clicking a pdb file in finder or starting up from the command
>> line with a pdb file, it appends a second state:
>>
>>
>>
>> % pymol ~/Downloads/4kc3.pdb
>>
>> PyMOL(TM) 3.1.3 - Incentive Product
>>
>> Copyright (C) Schrodinger, LLC
>>
>>
>>
>> This Executable Build integrates and extends Open-Source PyMOL.
>>
>> License Expiry date: 2025-06-30
>>
>>
>>  Detected OpenGL version 2.1. Shaders available.
>>  Tessellation shaders not available
>>  Detected GLSL version 1.20.
>>  OpenGL graphics engine:
>>   GL_VENDOR:   Apple
>>   GL_RENDERER: Apple M1
>>   GL_VERSION:  2.1 Metal - 88.1
>> HEADER    IMMUNE SYSTEM                           24-APR-13   4KC3
>> TITLE     CYTOKINE/RECEPTOR BINARY COMPLEX
>> COMPND    MOL_ID: 1;
>> COMPND   2 MOLECULE: INTERLEUKIN-33;
>> COMPND   3 CHAIN: A;
>> COMPND   4 FRAGMENT: UNP RESIDUES 112-270;
>>
>> COMPND   5 SYNONYM: IL-33, INTERLEUKIN-1 FAMILY MEMBER 11, IL-1F11, NUCLEAR`
>> COMPND   6 FACTOR FROM HIGH ENDOTHELIAL VENULES, NF-HEV;
>> COMPND   7 ENGINEERED: YES;
>> COMPND   8 MOL_ID: 2;
>> COMPND   9 MOLECULE: INTERLEUKIN-1 RECEPTOR-LIKE 1;
>> COMPND  10 CHAIN: B;
>> COMPND  11 FRAGMENT: UNP RESIDUES 19-321;
>> COMPND  12 SYNONYM: PROTEIN ST2;
>> COMPND  13 ENGINEERED: YES
>>  ObjectMolecule: Read secondary structure assignments.
>>  ObjectMolecule: Read crystal symmetry information.
>>  CmdLoad: "" loaded as "4kc3".
>>
>>  Detected 8 CPU cores.  Enabled multithreaded rendering.
>> HEADER    IMMUNE SYSTEM                           24-APR-13   4KC3
>> TITLE     CYTOKINE/RECEPTOR BINARY COMPLEX
>> COMPND    MOL_ID: 1;
>> COMPND   2 MOLECULE: INTERLEUKIN-33;
>> COMPND   3 CHAIN: A;
>> COMPND   4 FRAGMENT: UNP RESIDUES 112-270;
>>
>> COMPND   5 SYNONYM: IL-33, INTERLEUKIN-1 FAMILY MEMBER 11, IL-1F11, NUCLEAR
>> COMPND   6 FACTOR FROM HIGH ENDOTHELIAL VENULES, NF-HEV;
>> COMPND   7 ENGINEERED: YES;
>> COMPND   8 MOL_ID: 2;
>> COMPND   9 MOLECULE: INTERLEUKIN-1 RECEPTOR-LIKE 1;
>> COMPND  10 CHAIN: B;
>> COMPND  11 FRAGMENT: UNP RESIDUES 19-321;
>> COMPND  12 SYNONYM: PROTEIN ST2;
>> COMPND  13 ENGINEERED: YES
>>  ObjectMolecule: Read secondary structure assignments.
>>  ObjectMolecule: Read crystal symmetry information.
>>  CmdLoad: "" appended into object "4kc3", state 2.
>>
>>
>>
>> While if I load a pdb file into an already running instance of pymol, by
>> drag and drop or File > Open, it behaves as I expect, just loading the file
>> once. I do not see this behavior in version 3.0.0.
>>
>>
>>
>> --
>>
>> Kevin Jude, PhD
>>
>> Structural Biology Research Specialist, Garcia Lab
>>
>> Howard Hughes Medical Institute
>>
>> Stanford University School of Medicine
>>
>> Beckman B177, 279 Campus Drive, Stanford CA 94305
>> _______________________________________________
>> 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] Two issues with the draw command with current pymol version 3.1.5.1

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

Hi Norbert

Sorry, a little late to reply here, but we released 3.1.6.1 early last
week. The second issue where the image is rendered partially from the draw
command should have been addressed.

Unfortunately, the label issue still remains. It seems this has been an
issue In PyMOL for a while. For the draw command by default, PyMOL will
render the image at a higher resolution and scale it back down to remove
jagged edges (Supersampling Antialiasing). However since we draw text at
constant font size regardless of the viewport size, the text shrinks when
we perform the downscaling for the whole image. One way to avoid this is to
set the *antialias *parameter (which is separate from the settings) to zero
(see here <https://pymolwiki.org/index.php/Draw>) which will elide SSAA
pass altogether (you should still be able to use the antialias shader
settings in conjunction with this if you want smoother edges).

Hope that helps,
Jarrett J.

On Thu, May 29, 2025 at 9:00 PM Jarrett Johnson <
jar...@sc...> wrote:

> Hi Norbert,
>
> Thanks very much for the repro steps. I could reproduce this and I believe
> I know where the issue lies (since I caused them 😅). I'll aim to have
> these ironed out by the next patch.
>
> Best,
> Jarrett J
>
> On Fri, May 23, 2025 at 5:38 PM Norbert Straeter <
> st...@bb...> wrote:
>
>> Dear all,
>>
>> I would like to report two issues with the current pymol version
>> 3.1.5.1, which were present as well already in 3.1.4. The two problems
>> were not present in my previous installation of version 3.0.2. The two
>> problems are observed on a windows 11 notebook and on a linux computer.
>> The issues appear with different images, the following is a simple test
>> case:
>>
>> reinitialize
>> viewport 800,600
>> pseudoatom my_atom, pos=[1.0, 2.0, 3.0]
>> show spheres, my_atom
>> set label_position, [0.0, 0.0, 2.0]
>> label my_atom, "my_atom"
>> set label_size, 30
>> set label_color, black
>> zoom my_atom
>>
>> (1) draw command results in smaller label size
>>
>> If you use the draw command after pasting the commands above, the label
>> is plotted much smaller. When using the ray command, the label size is
>> fine. Using pymol 3.0.2 draw and ray commands result in approximately
>> the same label size as in the interactive working window.
>>
>> (2) draw command in conjunction with "set antialias_shader, 2" renders
>> only part of the image
>>
>> If you "set antialias_shader, 2" and use the draw command, only part of
>> the image is rendered. This may seem like a special option, but it is
>> part of the Menu option "Display, Quality, Maximum Quality", which I
>> frequently use. The ray command is not affected. "set antialias_shader,
>> 0" (the default) or "set antialias_shader, 1" cause no problem.
>>
>> Best regards,
>>
>> Norbert
>>
>>
>>
>> _______________________________________________
>> 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] about image generation limitation of the EDU license

[Yonghui Li <fen...@ya...>]

Thanks Jarrett! I've updated it via conda and the water marks are gone.

Thanks for your help!

Best,

Yonghui Li

On 5/30/2025 8:32 AM, Jarrett Johnson wrote:
> Hello,
>
> This issue, I believe, should have already been addressed in our 
> latest patch (3.1.5.1). Can you upgrade and see if you still observe 
> this issue?
>
> Thanks,
> Jarrett J.
>
> On Sat, May 24, 2025 at 8:38 AM Yonghui Li <fen...@ya...> 
> wrote:
>
>     Dear pymol developer and users,
>
>     I recently ran into a problem in generating molecule structures with
>     pymol. Pymol works great in generating about 100k small molecule
>     images.
>     But the problem is the watermark. I've received a EDU license and
>     configured to pymol. But since the 6th image, the watermark begins to
>     show in every image. Is it a limitation of the software or the
>     license?
>     BTW, I am using a server without a GUI, so I did the configuration
>     with
>     CLI. Any suggestions will be appreciated.
>
>     Here is the --diagnostics prints.
>
>       PyMOL(TM) 3.1.3.1 - Incentive Product
>       Copyright (C) Schrodinger, LLC
>
>       This Executable Build integrates and extends Open-Source PyMOL.
>       Detected 12 CPU cores.  Enabled multithreaded rendering.
>     PyMOL>diagnostics
>     PyMOL 3.1.3.1
>     build date: Wed Feb  5 07:42:22 2025 -0800
>     git sha: 698d66e4c6e73b53e79c3954053b380006455f15
>     conda build: py312h2dc6bc7_0
>     https://conda.anaconda.org/schrodinger/linux-64
>
>     License Information:
>       License Expiry date: 2025-12-01
>
>     License Files:
>     /opt/Anaconda3-2024.10-mols/share/pymol/license.lic
>     /opt/schrodinger/licenses/pymol-edu-license.lic
>
>     Operating System:
>     Linux-3.10.0-957.el7.x86_64-x86_64-with-glibc2.17
>     #1 SMP Thu Nov 8 23:39:32 UTC 2018
>
>     OpenGL Driver:
>     (none)
>     (none)
>     (none)
>     PyQt5 5.15.10 (Qt 5.15.2)
>
>     Python:
>     3.12.7 | packaged by conda-forge | (main, Oct  4 2024, 16:05:46) [GCC
>     13.3.0]
>     prefix=/opt/Anaconda3-2024.10-mols
>     executable=/opt/Anaconda3-2024.10-mols/bin/python
>     filesystemencoding=utf-8
>
>     Startup Scripts:
>     (no pymolrc file found)
>
>     Qt, Python and PyMOL Environment Variables:
>     LANG=en_US.UTF-8
>     PYMOL_DATA=/opt/Anaconda3-2024.10-mols/share/pymol/data
>     PYMOL_LICENSE_FILE=/opt/Anaconda3-2024.10-mols/share/pymol/license.lic:/opt/schrodinger/licenses
>     PYMOL_PATH=/opt/Anaconda3-2024.10-mols/share/pymol
>     PYTHONEXECUTABLE=/opt/Anaconda3-2024.10-mols/bin/python
>     PYTHONPATH=/opt/intel2024.0.0/advisor/2024.0/pythonapi
>     QTDIR=/usr/lib64/qt-3.3
>     QTINC=/usr/lib64/qt-3.3/include
>     QTLIB=/usr/lib64/qt-3.3/lib
>     QT_API=pyqt5
>     QT_GRAPHICSSYSTEM_CHECKED=1
>     QT_XKB_CONFIG_ROOT=/opt/Anaconda3-2024.10-mols/lib
>
>     PATH:
>     /opt/Anaconda3-2024.10-
>     mols/bin:/opt/intel2024.0.0/vtune/2024.0/bin64:/opt/intel2024.0.0/mpi/2021.11/
>     opt/mpi/libfabric/bin:/opt/intel2024.0.0/mpi/2021.11/bin:/opt/intel2024.0.0/mk
>     l/2024.0/bin/:/opt/intel2024.0.0/itac/2022.0/bin:/opt/intel2024.0.0/inspector/
>     2024.0/bin64:/opt/intel2024.0.0/dpcpp-ct/2024.0/bin:/opt/intel2024.0.0/dev-uti
>     lities/2024.0/bin:/opt/intel2024.0.0/debugger/2024.0/opt/debugger/bin:/opt/int
>     el2024.0.0/compiler/2024.0/opt/oclfpga/bin:/opt/intel2024.0.0/compiler/2024.0/
>     bin:/opt/intel2024.0.0/advisor/2024.0/bin64:/usr/lib64/qt-
>     3.3/bin:/opt/enviroment-modules.5.0.1/bin:/usr/local/bin:/usr/bin:/usr/local/s
>     bin:/usr/sbin:/opt/ibutils/bin:/public/home/******/.local/bin:/public/home
>     /******//bin
>
>     Diagnostics collected on Sat May 24 19:46:40 2025 -0800
>
>     ---------------------------------------------------------------------------------------------------------------
>
>     The python script is a bit complicate but it basically something like:
>
>     import os
>     #os.environ["PYMOL_LICENSE_FILE"]="/opt/license/pymol-edu-license.lic"
>     import importlib
>     import pymol
>     pymol.pymol_argv = ['pymol', '-qc']
>     from pymol import cmd
>
>     ******#some pre-processing
>
>     pymol.finish_launching()
>
>     os.system("pymol --diagnostics")
>
>     for i in range(len(meta)):
>          print(meta[i]["path"])
>          filename = Path(meta[i]["path"]).stem
>          prefix,p1,p2 = re.findall(r"(.+?)_\w+(\d{3})_\w+(\d{3})",
>     Path(meta[i]["path"]).stem)[0]
>          p1,p2 = int(p1)+1, int(p2)+1
>          xyz_path = basedir / f"{filename}.xyz"
>          get_xyz(meta[i]["path"]).write_file(xyz_path)
>          #cmd.delete('all')
>          cmd.reinitialize()
>          destfile = imgdir / f"{filename}.png"
>          cmd.load(f"{xyz_path}")
>
>          cmd.show('sticks')
>          cmd.show('spheres')
>          cmd.color('gray')
>          cmd.set('stick_radius', 0.15)
>          cmd.set('sphere_scale', 0.3)
>          cmd.color('gray', 'elem C')
>          cmd.color('red', 'elem O')
>          cmd.color('blue', 'elem N')
>          cmd.color('white', 'elem H')
>
>          L, R = f"id {p1}", f"id {p2}"
>          cmd.bond(L, R)
>          cmd.set_bond("stick_color", "orange", L, R)
>          cmd.set_bond("stick_radius", 0.3, L, R)
>          cmd.png(f"{destfile}", ray=1)
>
>
>
>     _______________________________________________
>     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
>
>

Re: [PyMOL] Two issues with the draw command with current pymol version 3.1.5.1

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

Hi Norbert,

Thanks very much for the repro steps. I could reproduce this and I believe
I know where the issue lies (since I caused them 😅). I'll aim to have
these ironed out by the next patch.

Best,
Jarrett J

On Fri, May 23, 2025 at 5:38 PM Norbert Straeter <st...@bb...>
wrote:

> Dear all,
>
> I would like to report two issues with the current pymol version
> 3.1.5.1, which were present as well already in 3.1.4. The two problems
> were not present in my previous installation of version 3.0.2. The two
> problems are observed on a windows 11 notebook and on a linux computer.
> The issues appear with different images, the following is a simple test
> case:
>
> reinitialize
> viewport 800,600
> pseudoatom my_atom, pos=[1.0, 2.0, 3.0]
> show spheres, my_atom
> set label_position, [0.0, 0.0, 2.0]
> label my_atom, "my_atom"
> set label_size, 30
> set label_color, black
> zoom my_atom
>
> (1) draw command results in smaller label size
>
> If you use the draw command after pasting the commands above, the label
> is plotted much smaller. When using the ray command, the label size is
> fine. Using pymol 3.0.2 draw and ray commands result in approximately
> the same label size as in the interactive working window.
>
> (2) draw command in conjunction with "set antialias_shader, 2" renders
> only part of the image
>
> If you "set antialias_shader, 2" and use the draw command, only part of
> the image is rendered. This may seem like a special option, but it is
> part of the Menu option "Display, Quality, Maximum Quality", which I
> frequently use. The ray command is not affected. "set antialias_shader,
> 0" (the default) or "set antialias_shader, 1" cause no problem.
>
> Best regards,
>
> Norbert
>
>
>
> _______________________________________________
> 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

Re: [PyMOL] Pymol loading pdb files twice

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

Hi Kevin,

Looks like we saw this issue as well back in December but seems like it
slipped through the cracks. We've updated the priority to fix this
hopefully by the next release. I'll reply here with any future updates.

Best,
Jarrett J.

On Tue, May 27, 2025 at 1:58 PM Kevin M Jude <kj...@st...> wrote:

> Using Pymol 3.1.3 (for mac from SBgrid) I notice that when I open pymol by
> double clicking a pdb file in finder or starting up from the command line
> with a pdb file, it appends a second state:
>
>
>
> % pymol ~/Downloads/4kc3.pdb
>
> PyMOL(TM) 3.1.3 - Incentive Product
>
> Copyright (C) Schrodinger, LLC
>
>
>
> This Executable Build integrates and extends Open-Source PyMOL.
>
> License Expiry date: 2025-06-30
>
>
>  Detected OpenGL version 2.1. Shaders available.
>  Tessellation shaders not available
>  Detected GLSL version 1.20.
>  OpenGL graphics engine:
>   GL_VENDOR:   Apple
>   GL_RENDERER: Apple M1
>   GL_VERSION:  2.1 Metal - 88.1
> HEADER    IMMUNE SYSTEM                           24-APR-13   4KC3
> TITLE     CYTOKINE/RECEPTOR BINARY COMPLEX
> COMPND    MOL_ID: 1;
> COMPND   2 MOLECULE: INTERLEUKIN-33;
> COMPND   3 CHAIN: A;
> COMPND   4 FRAGMENT: UNP RESIDUES 112-270;
>
> COMPND   5 SYNONYM: IL-33, INTERLEUKIN-1 FAMILY MEMBER 11, IL-1F11, NUCLEAR`
> COMPND   6 FACTOR FROM HIGH ENDOTHELIAL VENULES, NF-HEV;
> COMPND   7 ENGINEERED: YES;
> COMPND   8 MOL_ID: 2;
> COMPND   9 MOLECULE: INTERLEUKIN-1 RECEPTOR-LIKE 1;
> COMPND  10 CHAIN: B;
> COMPND  11 FRAGMENT: UNP RESIDUES 19-321;
> COMPND  12 SYNONYM: PROTEIN ST2;
> COMPND  13 ENGINEERED: YES
>  ObjectMolecule: Read secondary structure assignments.
>  ObjectMolecule: Read crystal symmetry information.
>  CmdLoad: "" loaded as "4kc3".
>
>  Detected 8 CPU cores.  Enabled multithreaded rendering.
> HEADER    IMMUNE SYSTEM                           24-APR-13   4KC3
> TITLE     CYTOKINE/RECEPTOR BINARY COMPLEX
> COMPND    MOL_ID: 1;
> COMPND   2 MOLECULE: INTERLEUKIN-33;
> COMPND   3 CHAIN: A;
> COMPND   4 FRAGMENT: UNP RESIDUES 112-270;
> COMPND   5 SYNONYM: IL-33, INTERLEUKIN-1 FAMILY MEMBER 11, IL-1F11, NUCLEAR
> COMPND   6 FACTOR FROM HIGH ENDOTHELIAL VENULES, NF-HEV;
> COMPND   7 ENGINEERED: YES;
> COMPND   8 MOL_ID: 2;
> COMPND   9 MOLECULE: INTERLEUKIN-1 RECEPTOR-LIKE 1;
> COMPND  10 CHAIN: B;
> COMPND  11 FRAGMENT: UNP RESIDUES 19-321;
> COMPND  12 SYNONYM: PROTEIN ST2;
> COMPND  13 ENGINEERED: YES
>  ObjectMolecule: Read secondary structure assignments.
>  ObjectMolecule: Read crystal symmetry information.
>  CmdLoad: "" appended into object "4kc3", state 2.
>
>
>
> While if I load a pdb file into an already running instance of pymol, by
> drag and drop or File > Open, it behaves as I expect, just loading the file
> once. I do not see this behavior in version 3.0.0.
>
>
>
> --
>
> Kevin Jude, PhD
>
> Structural Biology Research Specialist, Garcia Lab
>
> Howard Hughes Medical Institute
>
> Stanford University School of Medicine
>
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> _______________________________________________
> 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

Re: [PyMOL] Plugins with newer PyMOL versions

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

Hi Nikolas,

Welcome to the mailing list! For PyVOL specifically, your best bet might be
to reach out to the authors of the PyVOL plugin via Github issue (seems
like there's been various ones submitted recently)
https://github.com/schlessinger-lab/pyvol . However, it doesn't seem like
it's been updated for quite some time. It may be something we could
possibly consider adopting eventually in the PyMOL Scripts community Github
repo down the road. I'll respond here if we make any progress with that.
For now, I've created
https://github.com/Pymol-Scripts/Pymol-script-repo/issues/160 to track it
and any additions/improvements we can make to it.

Best,
Jarrett J.

On Wed, May 21, 2025 at 4:05 PM Capra, Nikolas via PyMOL-users <
pym...@li...> wrote:

> Hi everyone,
>
> just got here. I’ll break the ice with what may be a bit of a trivial
> question: is anyone experiencing issues with not-so-old plugins and newer
> versions of PyMOL?
>
> My very useful plugins, among which my dearest “PyVOL”, stopped working
> after I have upgraded from PyMOL 2.5.4. I’ve got error messages related to
> the .ini files when trying to run them, so I’m guessing it may have to do
> with the changes in the software’s API (but I’m not sure and neither I’m an
> expert).
>
>
>
> I thank you in advance for your answers and insights.
>
> Cheers,
>
> Nikolas
>
>
>
> ---
>
> Nikolas Capra, PhD
>
> Postdoctoral Research Associate – Single Crystal Diffraction
>
> Neutron Scattering Division
>
> Oak Ridge National Laboratory
>
> Bldg. 8600, K-218-A
>
>
> _______________________________________________
> 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

Re: [PyMOL] about image generation limitation of the EDU license

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

Hello,

This issue, I believe, should have already been addressed in our latest
patch (3.1.5.1). Can you upgrade and see if you still observe this issue?

Thanks,
Jarrett J.

On Sat, May 24, 2025 at 8:38 AM Yonghui Li <fen...@ya...> wrote:

> Dear pymol developer and users,
>
> I recently ran into a problem in generating molecule structures with
> pymol. Pymol works great in generating about 100k small molecule images.
> But the problem is the watermark. I've received a EDU license and
> configured to pymol. But since the 6th image, the watermark begins to
> show in every image. Is it a limitation of the software or the license?
> BTW, I am using a server without a GUI, so I did the configuration with
> CLI. Any suggestions will be appreciated.
>
> Here is the --diagnostics prints.
>
>   PyMOL(TM) 3.1.3.1 - Incentive Product
>   Copyright (C) Schrodinger, LLC
>
>   This Executable Build integrates and extends Open-Source PyMOL.
>   Detected 12 CPU cores.  Enabled multithreaded rendering.
> PyMOL>diagnostics
> PyMOL 3.1.3.1
> build date: Wed Feb  5 07:42:22 2025 -0800
> git sha: 698d66e4c6e73b53e79c3954053b380006455f15
> conda build: py312h2dc6bc7_0
> https://conda.anaconda.org/schrodinger/linux-64
>
> License Information:
>   License Expiry date: 2025-12-01
>
> License Files:
> /opt/Anaconda3-2024.10-mols/share/pymol/license.lic
> /opt/schrodinger/licenses/pymol-edu-license.lic
>
> Operating System:
> Linux-3.10.0-957.el7.x86_64-x86_64-with-glibc2.17
> #1 SMP Thu Nov 8 23:39:32 UTC 2018
>
> OpenGL Driver:
> (none)
> (none)
> (none)
> PyQt5 5.15.10 (Qt 5.15.2)
>
> Python:
> 3.12.7 | packaged by conda-forge | (main, Oct  4 2024, 16:05:46) [GCC
> 13.3.0]
> prefix=/opt/Anaconda3-2024.10-mols
> executable=/opt/Anaconda3-2024.10-mols/bin/python
> filesystemencoding=utf-8
>
> Startup Scripts:
> (no pymolrc file found)
>
> Qt, Python and PyMOL Environment Variables:
> LANG=en_US.UTF-8
> PYMOL_DATA=/opt/Anaconda3-2024.10-mols/share/pymol/data
>
> PYMOL_LICENSE_FILE=/opt/Anaconda3-2024.10-mols/share/pymol/license.lic:/opt/schrodinger/licenses
> PYMOL_PATH=/opt/Anaconda3-2024.10-mols/share/pymol
> PYTHONEXECUTABLE=/opt/Anaconda3-2024.10-mols/bin/python
> PYTHONPATH=/opt/intel2024.0.0/advisor/2024.0/pythonapi
> QTDIR=/usr/lib64/qt-3.3
> QTINC=/usr/lib64/qt-3.3/include
> QTLIB=/usr/lib64/qt-3.3/lib
> QT_API=pyqt5
> QT_GRAPHICSSYSTEM_CHECKED=1
> QT_XKB_CONFIG_ROOT=/opt/Anaconda3-2024.10-mols/lib
>
> PATH:
> /opt/Anaconda3-2024.10-
>
> mols/bin:/opt/intel2024.0.0/vtune/2024.0/bin64:/opt/intel2024.0.0/mpi/2021.11/
>
> opt/mpi/libfabric/bin:/opt/intel2024.0.0/mpi/2021.11/bin:/opt/intel2024.0.0/mk
>
> l/2024.0/bin/:/opt/intel2024.0.0/itac/2022.0/bin:/opt/intel2024.0.0/inspector/
>
> 2024.0/bin64:/opt/intel2024.0.0/dpcpp-ct/2024.0/bin:/opt/intel2024.0.0/dev-uti
>
> lities/2024.0/bin:/opt/intel2024.0.0/debugger/2024.0/opt/debugger/bin:/opt/int
>
> el2024.0.0/compiler/2024.0/opt/oclfpga/bin:/opt/intel2024.0.0/compiler/2024.0/
> bin:/opt/intel2024.0.0/advisor/2024.0/bin64:/usr/lib64/qt-
>
> 3.3/bin:/opt/enviroment-modules.5.0.1/bin:/usr/local/bin:/usr/bin:/usr/local/s
> bin:/usr/sbin:/opt/ibutils/bin:/public/home/******/.local/bin:/public/home
> /******//bin
>
> Diagnostics collected on Sat May 24 19:46:40 2025 -0800
>
>
> ---------------------------------------------------------------------------------------------------------------
>
> The python script is a bit complicate but it basically something like:
>
> import os
> #os.environ["PYMOL_LICENSE_FILE"]="/opt/license/pymol-edu-license.lic"
> import importlib
> import pymol
> pymol.pymol_argv = ['pymol', '-qc']
> from pymol import cmd
>
> ******#some pre-processing
>
> pymol.finish_launching()
>
> os.system("pymol --diagnostics")
>
> for i in range(len(meta)):
>      print(meta[i]["path"])
>      filename = Path(meta[i]["path"]).stem
>      prefix,p1,p2 = re.findall(r"(.+?)_\w+(\d{3})_\w+(\d{3})",
> Path(meta[i]["path"]).stem)[0]
>      p1,p2 = int(p1)+1, int(p2)+1
>      xyz_path = basedir / f"{filename}.xyz"
>      get_xyz(meta[i]["path"]).write_file(xyz_path)
>      #cmd.delete('all')
>      cmd.reinitialize()
>      destfile = imgdir / f"{filename}.png"
>      cmd.load(f"{xyz_path}")
>
>      cmd.show('sticks')
>      cmd.show('spheres')
>      cmd.color('gray')
>      cmd.set('stick_radius', 0.15)
>      cmd.set('sphere_scale', 0.3)
>      cmd.color('gray', 'elem C')
>      cmd.color('red', 'elem O')
>      cmd.color('blue', 'elem N')
>      cmd.color('white', 'elem H')
>
>      L, R = f"id {p1}", f"id {p2}"
>      cmd.bond(L, R)
>      cmd.set_bond("stick_color", "orange", L, R)
>      cmd.set_bond("stick_radius", 0.3, L, R)
>      cmd.png(f"{destfile}", ray=1)
>
>
>
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> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
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-- 

*Jarrett Johnson* | Staff Developer, PyMOL

[PyMOL] Pymol loading pdb files twice

[Kevin M J. <kj...@st...>]

Using Pymol 3.1.3 (for mac from SBgrid) I notice that when I open pymol by double clicking a pdb file in finder or starting up from the command line with a pdb file, it appends a second state:

% pymol ~/Downloads/4kc3.pdb
PyMOL(TM) 3.1.3 - Incentive Product
Copyright (C) Schrodinger, LLC

This Executable Build integrates and extends Open-Source PyMOL.
License Expiry date: 2025-06-30

 Detected OpenGL version 2.1. Shaders available.
 Tessellation shaders not available
 Detected GLSL version 1.20.
 OpenGL graphics engine:
  GL_VENDOR:   Apple
  GL_RENDERER: Apple M1
  GL_VERSION:  2.1 Metal - 88.1
HEADER    IMMUNE SYSTEM                           24-APR-13   4KC3
TITLE     CYTOKINE/RECEPTOR BINARY COMPLEX
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: INTERLEUKIN-33;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: UNP RESIDUES 112-270;
COMPND   5 SYNONYM: IL-33, INTERLEUKIN-1 FAMILY MEMBER 11, IL-1F11, NUCLEAR`
COMPND   6 FACTOR FROM HIGH ENDOTHELIAL VENULES, NF-HEV;
COMPND   7 ENGINEERED: YES;
COMPND   8 MOL_ID: 2;
COMPND   9 MOLECULE: INTERLEUKIN-1 RECEPTOR-LIKE 1;
COMPND  10 CHAIN: B;
COMPND  11 FRAGMENT: UNP RESIDUES 19-321;
COMPND  12 SYNONYM: PROTEIN ST2;
COMPND  13 ENGINEERED: YES
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 CmdLoad: "" loaded as "4kc3".
 Detected 8 CPU cores.  Enabled multithreaded rendering.
HEADER    IMMUNE SYSTEM                           24-APR-13   4KC3
TITLE     CYTOKINE/RECEPTOR BINARY COMPLEX
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: INTERLEUKIN-33;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: UNP RESIDUES 112-270;
COMPND   5 SYNONYM: IL-33, INTERLEUKIN-1 FAMILY MEMBER 11, IL-1F11, NUCLEAR
COMPND   6 FACTOR FROM HIGH ENDOTHELIAL VENULES, NF-HEV;
COMPND   7 ENGINEERED: YES;
COMPND   8 MOL_ID: 2;
COMPND   9 MOLECULE: INTERLEUKIN-1 RECEPTOR-LIKE 1;
COMPND  10 CHAIN: B;
COMPND  11 FRAGMENT: UNP RESIDUES 19-321;
COMPND  12 SYNONYM: PROTEIN ST2;
COMPND  13 ENGINEERED: YES
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 CmdLoad: "" appended into object "4kc3", state 2.

While if I load a pdb file into an already running instance of pymol, by drag and drop or File > Open, it behaves as I expect, just loading the file once. I do not see this behavior in version 3.0.0.

--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305

[PyMOL] about image generation limitation of the EDU license

[Yonghui Li <fen...@ya...>]

Dear pymol developer and users,

I recently ran into a problem in generating molecule structures with 
pymol. Pymol works great in generating about 100k small molecule images. 
But the problem is the watermark. I've received a EDU license and 
configured to pymol. But since the 6th image, the watermark begins to 
show in every image. Is it a limitation of the software or the license? 
BTW, I am using a server without a GUI, so I did the configuration with 
CLI. Any suggestions will be appreciated.

Here is the --diagnostics prints.

  PyMOL(TM) 3.1.3.1 - Incentive Product
  Copyright (C) Schrodinger, LLC

  This Executable Build integrates and extends Open-Source PyMOL.
  Detected 12 CPU cores.  Enabled multithreaded rendering.
PyMOL>diagnostics
PyMOL 3.1.3.1
build date: Wed Feb  5 07:42:22 2025 -0800
git sha: 698d66e4c6e73b53e79c3954053b380006455f15
conda build: py312h2dc6bc7_0 https://conda.anaconda.org/schrodinger/linux-64

License Information:
  License Expiry date: 2025-12-01

License Files:
/opt/Anaconda3-2024.10-mols/share/pymol/license.lic
/opt/schrodinger/licenses/pymol-edu-license.lic

Operating System:
Linux-3.10.0-957.el7.x86_64-x86_64-with-glibc2.17
#1 SMP Thu Nov 8 23:39:32 UTC 2018

OpenGL Driver:
(none)
(none)
(none)
PyQt5 5.15.10 (Qt 5.15.2)

Python:
3.12.7 | packaged by conda-forge | (main, Oct  4 2024, 16:05:46) [GCC 
13.3.0]
prefix=/opt/Anaconda3-2024.10-mols
executable=/opt/Anaconda3-2024.10-mols/bin/python
filesystemencoding=utf-8

Startup Scripts:
(no pymolrc file found)

Qt, Python and PyMOL Environment Variables:
LANG=en_US.UTF-8
PYMOL_DATA=/opt/Anaconda3-2024.10-mols/share/pymol/data
PYMOL_LICENSE_FILE=/opt/Anaconda3-2024.10-mols/share/pymol/license.lic:/opt/schrodinger/licenses
PYMOL_PATH=/opt/Anaconda3-2024.10-mols/share/pymol
PYTHONEXECUTABLE=/opt/Anaconda3-2024.10-mols/bin/python
PYTHONPATH=/opt/intel2024.0.0/advisor/2024.0/pythonapi
QTDIR=/usr/lib64/qt-3.3
QTINC=/usr/lib64/qt-3.3/include
QTLIB=/usr/lib64/qt-3.3/lib
QT_API=pyqt5
QT_GRAPHICSSYSTEM_CHECKED=1
QT_XKB_CONFIG_ROOT=/opt/Anaconda3-2024.10-mols/lib

PATH:
/opt/Anaconda3-2024.10-
mols/bin:/opt/intel2024.0.0/vtune/2024.0/bin64:/opt/intel2024.0.0/mpi/2021.11/
opt/mpi/libfabric/bin:/opt/intel2024.0.0/mpi/2021.11/bin:/opt/intel2024.0.0/mk
l/2024.0/bin/:/opt/intel2024.0.0/itac/2022.0/bin:/opt/intel2024.0.0/inspector/
2024.0/bin64:/opt/intel2024.0.0/dpcpp-ct/2024.0/bin:/opt/intel2024.0.0/dev-uti
lities/2024.0/bin:/opt/intel2024.0.0/debugger/2024.0/opt/debugger/bin:/opt/int
el2024.0.0/compiler/2024.0/opt/oclfpga/bin:/opt/intel2024.0.0/compiler/2024.0/
bin:/opt/intel2024.0.0/advisor/2024.0/bin64:/usr/lib64/qt-
3.3/bin:/opt/enviroment-modules.5.0.1/bin:/usr/local/bin:/usr/bin:/usr/local/s
bin:/usr/sbin:/opt/ibutils/bin:/public/home/******/.local/bin:/public/home
/******//bin

Diagnostics collected on Sat May 24 19:46:40 2025 -0800

---------------------------------------------------------------------------------------------------------------

The python script is a bit complicate but it basically something like:

import os
#os.environ["PYMOL_LICENSE_FILE"]="/opt/license/pymol-edu-license.lic"
import importlib
import pymol
pymol.pymol_argv = ['pymol', '-qc']
from pymol import cmd

******#some pre-processing

pymol.finish_launching()

os.system("pymol --diagnostics")

for i in range(len(meta)):
     print(meta[i]["path"])
     filename = Path(meta[i]["path"]).stem
     prefix,p1,p2 = re.findall(r"(.+?)_\w+(\d{3})_\w+(\d{3})", 
Path(meta[i]["path"]).stem)[0]
     p1,p2 = int(p1)+1, int(p2)+1
     xyz_path = basedir / f"{filename}.xyz"
     get_xyz(meta[i]["path"]).write_file(xyz_path)
     #cmd.delete('all')
     cmd.reinitialize()
     destfile = imgdir / f"{filename}.png"
     cmd.load(f"{xyz_path}")

     cmd.show('sticks')
     cmd.show('spheres')
     cmd.color('gray')
     cmd.set('stick_radius', 0.15)
     cmd.set('sphere_scale', 0.3)
     cmd.color('gray', 'elem C')
     cmd.color('red', 'elem O')
     cmd.color('blue', 'elem N')
     cmd.color('white', 'elem H')

     L, R = f"id {p1}", f"id {p2}"
     cmd.bond(L, R)
     cmd.set_bond("stick_color", "orange", L, R)
     cmd.set_bond("stick_radius", 0.3, L, R)
     cmd.png(f"{destfile}", ray=1)

[PyMOL] header intact

[<487...@qq...>]

header intact