June 2023 - ChimeraX-users - RBVI Mailing Lists

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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Daily build issues
by BARRY E DEZONIA 29 Jun '23

29 Jun '23

Hello, My colleague and I are trying to install daily build(s) of chimerax. A few weeks ago, on Ubuntu 20.04, I installed the daily build for that OS just fine. Now I am trying to show my work to a colleague. We need a daily build because our work relies on a bug fix that was recently made. Anyhow he is on ubuntu 22.04 and needs to install the version appropriate for his OS. When we do so it complains that "libssl3" is missing. And when we find instructions on how to install it apt says the dependency for "glibc" can't be satisified because the version required is newer than the one installed. Now rather than messing with my colleague's system too much I'd like to know your recommendations for getting the daily build installed. Thanks.

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IMOD Generated Model and Tomogram are Offset
by Guilliams,Bradley 29 Jun '23

29 Jun '23

Hi All, I have been working with a tomogram and corresponding model in IMOD and when I load these files into ChimeraX the model and tomogram are offset (see included image). At the highest plane of the tomogram, it intersects roughly halfway up the model. Any advice on how to fix this would be much appreciated! Cheers, Bradley Bradley Guilliams (he/him/his) PhD Candidate Ackerson Research Group Analytical Resources Core - Imaging & Surface Science (ARC-ISS) Department of Chemistry Colorado State University

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Save only the sequence that is present in the model
by Eric Pettersen 28 Jun '23

28 Jun '23

> Begin forwarded message: > > From: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> > Subject: Save only the sequence that is present in the model > Date: June 28, 2023 at 6:53:11 AM PDT > To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> > > > Dear ChimeraX team, > > I would like to save only the sequence of a chain that is actually modelled. As I would like to do this for many files it would be great if this would work via scripting. Is this possible? > > Many thanks, > Matthias

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Docking scores only as integers??
by thomas.wein＠lmu.de 28 Jun '23

28 Jun '23

Dear all, I'm reading glide Docking results into ChimeraX. In the ViewDockX table or charts the docking score is displayed only as integers. However, typical score valus are "-4.1234" or "-8.9876", I only see the "-4.000" etc. For the correct numbers I have to go into the original files which is somehow time consuming. Is there any possibility to get a "real" score value displayed? Thanks Thomas

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