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News & Updates New Setup PyMOL-open-source-windows-setup v3.1 has been released on January 20, 2025. More information under Windows Install. New Plugin PySSA aims to combine PyMOL and ColabFold to enable the prediction and analysis of 3D protein structures for the scientific end-user. v1.0 has been released on July 10, 2024. Official Release PyMOL v3.0 has been released on March 12, 2024. New Plugin CavitOmiX calculate Catalophore™ cavities, predict protein structures with OpenFold by NVIDIA-BioNeMo, ESMFold and retrieve Alphafold models Official Release PyMOL v2.5 has been released on May 10, 2021. Python 3 New Python 3 compatibility guide for scripts and plugins POSF New PyMOL fellowship announced for 2022-2023 Tutorial Plugins Tutorial updated for PyQt5 New Plugin PICv is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe Selection keywords New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll! Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons Older News See Older News.

Did you know... Save save writes selected atoms to a file. Details The file format is autodetected if the extension is .pdb, .pqr, .mol, .sdf, .pkl, .pkla, .mmd, .out, .dat, .mmod, .pmo, .pov, .png, .pse, .psw, .aln, .fasta, .obj, .mtl, .wrl, .idtf, .dae, or .mol2. If the file extension is ".pse" (PyMOL Session), the complete PyMOL state is always saved to the file (the selection and state parameters are thus ignored). CLUSTALW formatted alignments can be written by PyMOL as well. Once you perform an alignment like the following, align proteinA, proteinB, object=A_on_B the alignment can be written using: save A_aligned_with_B.aln, A_on_B USAGE save file [,(selection) [,state [,format]] ] EXAMPLES # save only the alpha carbons save onlyCAs.pdb, n. CA # save my MD trajectory file to disk save myTraj.pdb, myMDTrajectory, state=0 # save a PyMOL session save thisSession.pse ===PYMOL ..→

A Random PyMOL-generated Cover. See Covers.