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
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>>
>
>
> --
>
> *Jarrett Johnson* | Staff Developer, PyMOL
>
>

-- 

*Jarrett Johnson* | Staff Developer, PyMOL