June 2023 - ChimeraX-users - RBVI Mailing Lists

Missing Vina on ChimeraX
by Luigi Marongiu 03 Apr '24

03 Apr '24

Dear sir or madam, I am using UCSF ChimeraX version 1.5 (2022-11-24). I have been trying to use AutoDock Vina but there is no such command in my version. How do I install it into ChimeraX (as shown in many tutorials, Vina is part of Chimera)? Thank you. Best regards, Luigi Marongiu Ph.D., B.Sc. (Hons.)

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Colouring clipping plane
by GOVAERTS Cédric 20 Jan '24

20 Jan '24

Hi ChimeraX team. I’m trying to get an image of a protein whose surface is colored by electrostatic properties but clipped halfway. I would like the clipping plane to be white, not red/blue according to the electrostativ properties of the residues insides the protein. However, I don’t’ seem to be able to do that. -If I color everything white and then click on Molecular-Display “electrostatic”, the clipping plane also gets the electrostatic coloring [Graphical user interface Description automatically generated] -If I color everything white and then click on Molecular-Display “hydrophobic” or “rainbow” it works, the clipping plane remains white. [cid:image002.png@01D94092.6E8A2390] Can you help me getting the white clipping plane with electrostatic surface ? Thanks a bunch Cedric — Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

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ISOLDE and secondary structure restraints
by Guido Hansen 17 Nov '23

17 Nov '23

Hi all, I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess: Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script? Cheers, Guido -- PD Dr. Guido Hansen Group Leader UNIVERSITÄT ZU LÜBECK INSTITUT FÜR BIOCHEMIE Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen(a)biochem.uni-luebeck.de www.biochem.uni-luebeck.de [1] Ratzeburger Allee 160 23562 Lübeck Links: ------ [1] http://www.biochem.uni-luebeck.de

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Feature request: replace residues in model with residues from other model
by Vorländer,Matthias Kopano 16 Nov '23

16 Nov '23

Dear ChimeraX team, Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted. Many thanks in advance, Matthias

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Fourier transform tool in chimeraX?
by Das, Abhinaba 06 Jul '23

06 Jul '23

Dear ChimeraX community, I stumbled upon a link<https://www.cgl.ucsf.edu/chimera/data/downloads/1.2470/docs/ContributedSoft…> discussing a Fourier Transform tool in Chimera. However, I encountered an issue while trying to locate it in my Chimera version (running the command "start Fourier Transform" resulted in an error). My objective is to generate a Fourier space diffraction pattern of a helical reconstructed volume by performing its Fourier transform. I am curious to know if this functionality is available in either Chimera or ChimeraX. Could you kindly provide some guidance on this matter? Thank you in advance for any advice. Abhi

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Volume Series tool missing
by Jarrett Bowman 30 Jun '23

30 Jun '23

Hello, I am trying to use the volume series tool on ChimeraX version 1.6.1 for Windows. It doesn't appear to be in my download of ChimeraX possibly along with other tools. A tutorial I am following shows this picture: [image: image.png] While this is what I have: [image: image.png] Any help would be greatly appreciated! Jerry Bowman

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toolshed plugin upload - disk quota exeeded
by Lugmayr, Wolfgang 30 Jun '23

30 Jun '23

hi, i tried to upload a new starmap release and run into the following error: OSError at /submit_app/ [Errno 122] Disk quota exceeded: '/usr/local/projects/chimerax/www/production/cxtoolshed3/media/pending_releases/ChimeraX_StarMap-1.2.15-py3-none-any.whl' Request Method: POST Request URL: https://cxtoolshed.rbvi.ucsf.edu/submit_app/?expect_app_name=ChimeraX_StarM… Django Version: 4.2.1 Exception Type: OSError Exception Value: [Errno 122] Disk quota exceeded: '/usr/local/projects/chimerax/www/production/cxtoolshed3/media/pending_releases/ChimeraX_StarMap-1.2.15-py3-none-any.whl' Exception Location: /wynton/home/ferrin/cxtoolshed/production-site/lib/python3.8/site-packages/django/core/files/move.py, line 63, in file_move_safe Raised during: cxtoolshed3.submit_app.views.submit_app Python Executable: /usr/bin/python3 Python Version: 3.8.16 Python Path: ['/usr/lib64/python38.zip', '/usr/lib64/python3.8', '/usr/lib64/python3.8/lib-dynload', '/wynton/home/ferrin/cxtoolshed/production-site/lib64/python3.8/site-packages', '/wynton/home/ferrin/cxtoolshed/production-site/lib/python3.8/site-packages', '/usr/lib64/python3.8/site-packages', '/usr/lib/python3.8/site-packages', '/usr/local/projects/chimerax/www/production'] Server time: Fri, 30 Jun 2023 04:53:50 -0700 can you please have a look at the problem? cheers, wolfgang -- Multi-User Cryo-EM Facility @ Centre for Structral Systems Biology (CSSB) @ Deutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 Gebäude 15 (E.247) 22607 Hamburg, Germany Tel.: +49 40 8998-87706 Email: wolfgang.lugmayr(a)cssb-hamburg.de http://www.cssb-hamburg.de/

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Constrained Movement
by Derek Ng 29 Jun '23

29 Jun '23

Hi, Thanks so much for ChimeraX! The tool is amazing so far. Is it possible to do the Constrained Movement GUI feature from the old Chimera in ChimeraX? I couldn’t find it in the GUI nor documentation. Thanks in advanced! Derek

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alphafold PAE map color (bluered), alphafold contacts palette option and selecting interacting residues under certain PAE values
by ahramkim1128＠gmail.com 29 Jun '23

29 Jun '23

Dear ChimeraX team, I have been working with analyzing AlphaFold-predicted structures in ChimeraX and have a few queries/suggestions. 1. Color palette for PAE Maps: One of the outputs from ColabFold is a PAE map rendered in a blue-white-red color palette. I find this color scheme very useful, and the command "alphafold pae #1 palette bluered" is working well for changing the color gradient into blue-white-red in PAE map. I was wondering if it could be integrated as a clickable option in the PAE map settings in ChimeraX, similar to the existing "Color plot rainbow" or "Color plot from structure" options. 2. Alphafold contacts color palette: I'm also interested in changing the color palette for alphafold contacts to match the bluered color scheme. While I attempted to change the color palette using the command "alphafold contact #1 /A to /B distance 5 palette bluered", it resulted in all contacts being colored red, without the expected color gradient. I'm curious if there's an alternative approach or if this could be an added feature in future updates. 3. Residue selection and visualization based on PAE cut-off: Lastly, I'm looking for a method to selectively visualize the connections between certain residues based on a PAE cut-off. For example, using the command "alphafold contacts /A to /B distance 5", I can visualize all the residue connections between A and B under a distance of 5. However, this also displays connections that are poorly predicted (i.e., yellow or red lines corresponding to PAE >15). I'd appreciate if you could suggest a way to filter these poorly predicted connections or provide an option for this in the software. Thank you in advance! Best regards, Ah-Ram

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Measuring Tilt of Helices
by Das, Abhinaba 29 Jun '23

29 Jun '23

Dear ChimeraX users, I’m trying to measure the tilt of the helices with respect to the helical axis (i.e. the z-axis). As depicted in the image below, I was wondering if it would be possible to draw a line parallel to the z-axis, traversing through the stack of helices, and another perpendicular to the z-axis and finally measure the angle between the axis passing through the helix (generated by define axis command) and the perpendicular drawn to the z-axis. [cid:image001.png@01D9A9E2.A0B8D0F0] Thanks in advance Abhi

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ChimeraX-users June 2023