September 2024 - ChimeraX-users - RBVI Mailing Lists

ChimeraX 1.8 release
by Elaine Meng 13 Oct '24

13 Oct '24

UCSF ChimeraX version 1.8 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html Updates since version 1.7 (Dec 2023) include: - show worm depictions of attribute values (B-factor, conservation, etc.) using Render by Attribute tool or "cartoon byattribute" command - show attribute values with atomic radii using Render by Attribute or "size byattribute" - Select by Attribute graphical interface - Join Models generalized to any covalent bond (not just peptide) - show multiple alternate locations simultaneously with "altlocs show" - "pbond" command to create arbitrary pseudobonds - "measure contactarea" to report the area of one surface within a cutoff distance of another - Segmentations tool for interactive manual segmentation in 2D slice views, 3D (desktop), or 3D (VR) can be applied to any volume data, not just medical images; several fixes and ergonomic improvements including icons to assign/deassign mouse and VR hand-controller modes with a single click - set up and analyze batch AlphaFold predictions to search for protein-protein interactions (commands for advanced users who can run ColabFold directly on Linux) support for: - reading predicted aligned error (PAE) data from AlphaFold 3 - reading docking results from MOE - fetching atomic structures and maps from PDB-REDO - fetching/display of PDB NMR-STAR restraints For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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Support for _ma_qa_metric_local_pairwise to display PAE matrices stored in ModelArchive
by Gerardo Tauriello 11 Oct '24

11 Oct '24

Dear ChimeraX developers, Following up on discussions in https://github.com/chaidiscovery/chai-lab/issues/52 and the large amounts of models which have been deposited in ModelArchive (MA; https://modelarchive.org/) in the meantime, I would propose to support loading PAE (or other local-pairwise scores) values from ModelCIF files as used by MA. Here I link some examples which should capture most use cases: 1. ma-bak-cepc-0944<https://www.modelarchive.org/doi/10.5452/ma-bak-cepc-0944> includes 2 local-pairwise scores (PAE and "contact probability") and only stores scores for inter-chain residue-pairs. 2. ma-dm-hisrep-003<https://www.modelarchive.org/doi/10.5452/ma-dm-hisrep-003> includes a full PAE matrix. 3. In all cases in MA, entries contain a single accompanying zip file which also contains the local pairwise scores which are extracted into a separate file to keep the main ModelCIF file at a manageable size. The linked modelcif_examples_for_chimerax.zip<https://sibcloud-my.sharepoint.com/:u:/g/personal/gerardo_tauriello_sib_swi…> package includes pae_associated_file where the pairwise scores are directly in a separate file instead of being in a zip file and pae_in_main_file which includes the pairwise scores directly in the main ModelCIF file. Already now ChimeraX is able to parse the ma_qa_metric_local category in ModelCIF to do per-residue coloring for pLDDT etc which is awesome. To make sense of ma_qa_metric_local_pairwise one needs the following (I try to be detailed to simplify the implementation): 1. Parse ma_qa_metric and keep the IDs (_ma_qa_metric.id) for rows with ma_qa_metric.mode == "local-pairwise". If we want to restrict this to PAE matrices, one would additionally check that _ma_qa_metric.type == "PAE". 2. Look for the _ma_qa_metric_local_pairwise category. There are 3 options on where to find it: * Directly in the main ModelCIF file (as in pae_in_main_file/003-Spombe_H3-H4_tetramer_DPB3.cif). * In a separate file via _ma_entry_associated_files (as in pae_associated_file/003-Spombe_H3-H4_tetramer_DPB3.cif). You can find the file via _ma_entry_associated_files.file_url for the _ma_entry_associated_files row with file_content == "local pairwise QA scores". * In a separate file via _ma_associated_archive_file_details (as in all MA entries such as ma-bak-cepc-0944 and ma-dm-hisrep-003). Procedure to get it: * Find row in _ma_associated_archive_file_details with file_content == "local pairwise QA scores" and keep archive_file_id and file_path. * Find zip file in _ma_entry_associated_files with id == archive_file_id and download via file_url. * Fetch file named file_path from that zip file. 3. Within the _ma_qa_metric_local_pairwise extract scores for all given residue pairs for metric_id matching the desired IDs from step 1. Each residue is identified with model_id, label_asym_id, label_seq_id, and (redundantly) label_comp_id. There are no guarantees on the order of the data or completeness of the data but each referenced residue is guaranteed to exist in the atom_site category. Here is the current list of model sets in MA which include PAE matrices: ma-bak-cepc<https://modelarchive.org/doi/10.5452/ma-bak-cepc>, ma-coffe-slac<https://modelarchive.org/doi/10.5452/ma-coffe-slac>, ma-tbvar3d<https://modelarchive.org/doi/10.5452/ma-tbvar3d>, ma-ornl-sphdiv<https://modelarchive.org/doi/10.5452/ma-ornl-sphdiv>, ma-t3vr3<https://modelarchive.org/doi/10.5452/ma-t3vr3>, ma-low-csi<https://modelarchive.org/doi/10.5452/ma-low-csi>, ma-ombbaf2<https://modelarchive.org/doi/10.5452/ma-ombbaf2>, ma-rap-bacsu<https://modelarchive.org/doi/10.5452/ma-rap-bacsu>, ma-nmpfamsdb<https://modelarchive.org/doi/10.5452/ma-nmpfamsdb>, ma-jd-viral<https://modelarchive.org/doi/10.5452/ma-jd-viral>, ma-dm-prc<https://modelarchive.org/doi/10.5452/ma-dm-prc>, ma-dm-hisrep<https://modelarchive.org/doi/10.5452/ma-dm-hisrep>, ma-osf-ppp2r2a<https://modelarchive.org/doi/10.5452/ma-osf-ppp2r2a>. All together MA has over 200'000 models with PAE matrices which all supplement the AFDB in some way (e.g. protein complexes, viral proteins and other proteins not covered in UniProt). It would be great to include support for ModelArchive's ModelCIF files in ChimeraX and I am happy to provide further information and help as needed. Regards, Gerardo

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system log of ChimeraX
by Enrico Martinez 02 Oct '24

02 Oct '24

Dear ChimeraX users! I wonder if there is some system log file containing the full history of previously executed commands and scripts in Chimera-X on the linux machine ? This could be useful if I did not save something and would like to resolve the full story. All the best, Enrico

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Increasing ChimeraX speed?
by Altobelli, Chad 30 Sep '24

30 Sep '24

Hi, I love using ChimeraX to make morphs, but my protein is quite a large hexamer (500kda) and the progression through the coordset can be quite slow during playback. When I look at my Windows taskmanager, I can see that neither my CPU (12th Gen Intel i7-12700H), RAM, or GPU (NVIDIA RTX 3050 Laptop) are maxed out. Is there a way to speed up Chimera morphs? Thanks, Chad

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Molecular Dynamics in ChimeraX
by Enrico Martinez 30 Sep '24

30 Sep '24

Dear ChimeraX users! I noticed that in ChimeraX there is no built-in molecular dynamics simulation engine as opposed to the older UCSF Chimera. Is it possible to use some visualization trick to deform slightly static coordinates of atomic selection introducing (visually) the impression that they move during movie recording ? Many thanks in advance Enrico

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Software copyright consulting
by 姜恩誉 27 Sep '24

27 Sep '24

Hello, is the application of your Chimera X software for paper publication a non-commercial use？ Looking forward to your reply. Thank you 姜恩誉 2023111025(a)stu.njau.edu.cn

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info distmat command
by NUR AIDA SAKINAH 27 Sep '24

27 Sep '24

Hi ChimeraX teams, Can you guide me to use the *atoms-spec* for info distmat command. I want the output in chimerax log to list out distances between drug compound and the amino acids side chains and only display the distances below than 4 A. For now, what i have got, the output include distances between atoms in the drug itself and atoms in the amino acids itself. The command that i have try are: 1. info distmat (protein & sideonly) | :dex ::num_distance< 4 2. info distmat (protein & sideonly) | :dex 3. info distmat (protein & sideonly) & (:dex) distance < 4 Hope you could help me with this. Regards with thanks, Aida.

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Atoms command spec
by NUR AIDA SAKINAH 27 Sep '24

27 Sep '24

Hi ChimeraX teams, Can you guide me to use the *atoms-spec* for info distmat command. I want the output in the chimerax log to list out distances between *the drug compound and the amino acids side chains and only display the distances below than 4A*. For now, what I have got, the output includes distances between atoms in the drug itself and atoms in the amino acids itself and I don't want that. Only display distances between atoms of the drug and the amino acids side chains. The protein and drug details: PDBID= *4YVP* with drug compound *DEX* The drug binding site distance is below than *4A*. The command that i have try are: 1. info distmat (protein & sideonly) | :dex ::num_distance< 4 2. info distmat (protein & sideonly) | :dex 3. info distmat (protein & sideonly) & (:dex) distance < 4 Hope you could help me with this. Regards with thanks, Aida.

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How to increase the font size of pseudobond labels
by Suhas Srinivasan 26 Sep '24

26 Sep '24

Dear ChimeraX Community, I was trying to increase the default font size of the very small labels displayed on the pseudobonds that are generated from the “distance” command. Selecting the pseudobond label and then using the command “label size 512” had no effect. Your help would be appreciated and thank you for your time. UCSF ChimeraX 1.8 macOS 14.7

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ChimeraX download problem
by Sophie Scobell 26 Sep '24

26 Sep '24

Hi, I've been trying to download ChimeraX on my personal computer for the past two weeks and keep getting this error message: "Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error. More information about this error may be available in the server error log." I'm using a Mac and I've tried the MacOS download on both Safari and Chrome with the same issue. Any advice would be greatly appreciated, Thank you! Sophie

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