- Chimera-users - RBVI Mailing Lists

Chimera
by Kotin, Robert 13 Aug '24

13 Aug '24

Good afternoon – I’d appreciate advise for virus capsid viewing. Adeno-associated viruse structures, e.g., 1lp3, consist of the asymmetric unit repeated 60x to form the icosahedral capsid (T=1). I’d like to highlight the equivalent residue in each of the 60 subunits but haven’t figured out how to do that (except by manually going through each of the 60 chains). Please let me know if there are commands that can specify the residue in chains 1, 2, 3,…60. Thank you Robert Kotin

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.crd file not opening
by safi ch 05 Aug '24

05 Aug '24

Greetings, hope you are doing well. I want your guidance on how can I open a .crd file on UCSF Chimera. I am working on a protein and its mutants and performed their docking via Swiss Dock, it gave results in form of .crd file that I cannot open. My supervisor also has no idea how to open it, so please help me in this regard, I need to open it to work further on my research. Waiting for your kind response please.

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August 1 Chimera(X) website downtime
by Elaine Meng 01 Aug '24

01 Aug '24

Planned downtime for server maintenance: The Chimera and ChimeraX websites, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable August 1, 3-6 pm PDT. Apologies for any inconvenience, 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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column selection: chimera vs chimeraX
by 7mkf 23 Jul '24

23 Jul '24

Hi there, I'm an avid user of chimera and have begun transitioning to chimeraX. A feature I find very useful in chimera is expand selection to columns within the multialignviewer. Is there a way to do this in ucsf chimeraX? Many thanks, Mike

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molmap onGrid option
by Hernando J Sosa 18 Jul '24

18 Jul '24

Dear Chimera I am using the molmap command with the option onGrid but the results are not what I would have expected. With a loaded map (#0) and an atomic model(#1) The command: molmap #1 6.0 onGrid #0 generates a map with a voxel size of 6.768 even though the loaded map #0 has a voxel size of 0.846 Trying to force the voxel size with molmap #1 6.0 onGrid #0 gridSpacing 0.846 produces the same result as the onGrid option overrides the gridSpacing option. How can I produce a map using molmap that has exactly the same dimensions and voxel size of map #0? Thanks H. _

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Internal Server Error. Can Not Download chimera 1.18
by Setyanto Md 18 Jul '24

18 Jul '24

Dear Chimera User and Development Team, I tried to download ucsf-chimera version 1.18. However, the message 500 Internal Server Error appears. Is this error from our internet network, or is it from the chimera server? Thank you ------- Setyanto Tri Wahyudi ------- Computational Biophysics Group, Department of Physics, IPB University - Indonesia Gedung Fisika Wing-S Lt.2 Jl. Meranti Kampus IPB Darmaga Bogor - 16680 Indonesia

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Docking with auto dock fails for a ligand containing a Boron atom
by Patrone Marco 15 Jul '24

15 Jul '24

Dear All, I’m trying to dock a ligand containing a boronate substituent using Auto Dock Vina within Chimera v. 1.13.1 The process fails as the B in the pdb instance is not recognized for Boron and the following syntax error is printed “Parse error on line 27 in file "ligand.pdbqt": ATOM syntax incorrect: "B" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive” Is there any way to overcome this? Are there newer/different libraries that inlcude also Boron element I can update my ADV with? Many thanks for your time and best regards, marco -- Marco Patrone – PhD Biocrystallography Unit Division of Immunology, Transplantation, and Infectious Disease (DITID) DIBIT – San Raffaele Scientific Institute Via Olgettina, 58 20132 Milano Italy phone: +39 0226434921 fax: +39 0226434153 http://www.hsr.it/research/organzation/massimo-degano [https://p.hsr.it/5xmille/b2024.jpg]<https://www.5xmille.org/?utm_source=firmamail&utm_medium=email&utm_campaign…> CODICE FISCALE 07636600962 Scopri di più su www.5xmille.org<https://www.5xmille.org/?utm_source=firmamail&utm_medium=email&utm_campaign…> Rispetta l’ambiente: non stampare questa mail se non è necessario. Respect the environment: print this email only if necessary.

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Covalent substrate modeling and minimization
by wh-kelvin.chung＠polyu.edu.hk 15 Jul '24

15 Jul '24

Good day I am a researcher studying antibiotic interaction and trying to make a model with a substrate covalently bound to the active site. There is a homolog with a crystal structure (PDB: 4KQO), and I am going to add the bound substrate in this pdb file to my target protein where the mode was generated by alphafold server. Although the workflow shall be simple, I still have some problems, could you kindly help? 1. Firstly, I would like to check whether the model of 4KQO is good enough for modeling, by examining the electron density map (open 4KQO, open 4KQO from eds). However, I found that it is a bit different from the tutorial (https://www.cgl.ucsf.edu/chimerax/docs/quickstart/index.html, pdb:1a0m) that the electron density of 4KQO did not cover the substrate molecule. I am totally ignorant in crystallography, so, how could I visualize the electron density of the substrate? by any symmetry operation / command so that I could check whether there is "electron density in the substrate" ? 2. I aligned 4KQO with the alphafold generated model, and I deleted the protein from 4KQO, and combined the two model, make a bond between the active residue with the substrate, however, I am not sure how to (1) check the bond length and angle is appropriately assigned, and (2) do energy minimization to reorientate side change to eliminate the crash with the substrate. Thank you very much for your help in advance Have a nice weekend

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Capturing output of measure center command
by ldreher＠smith.edu 12 Jul '24

12 Jul '24

Hello, I am trying to write a python script to prepare proteins for molecular docking, and as part of that I want to be able to identify and save the center coordinates of each protein. using runCommand('measure center #0') works fine, but I am at a loss as to how to capture the output of that command. Ideally I would like to save the output as a string in python. Any advice on how to go about this would be appreciated! Thanks! Laura

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Difference between command line and menus
by edith.gincel＠u-paris.fr 09 Jul '24

09 Jul '24

Dear all I am trying to check contacts between ligands and protein. I tried to use the command line, to be able to do it semi-automatically, but I don't find any contact. When I use the command line, I find contacts. Has someone experienced such problems? Thank you for your help

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