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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