January 2025 - ChimeraX-users - RBVI Mailing Lists

Problem upgrading to the latest version 1.9
by svle＠tiscali.it 10 Jan '25

10 Jan '25

Hi, surely for my errors in uninstalling the previous version , I'm receiving the following: $ sudo apt remove --purge ucsf-chimerax Reading package lists... Done Building dependency tree... Done Reading state information... Done The following packages were automatically installed and are no longer required: libgdk-pixbuf-xlib-2.0-0 libgdk-pixbuf2.0-0 libosmesa6 libxcb-cursor0 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: ucsf-chimerax* 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 0 B of additional disk space will be used. Do you want to continue? [Y/n] (Reading database ... 524167 files and directories currently installed.) Removing ucsf-chimerax (1.9ubuntu24.04) ... Deregister desktop menu and associated mime types /var/lib/dpkg/info/ucsf-chimerax.prerm: 4: chimerax: not found dpkg: error processing package ucsf-chimerax (--remove): installed ucsf-chimerax package pre-removal script subprocess returned error exit status 127 dpkg: too many errors, stopping Errors were encountered while processing: ucsf-chimerax Processing was halted because there were too many errors. E: Sub-process /usr/bin/dpkg returned an error code (1) $ dpkg --get-selections | grep ucsf ucsf-chimerax install $ chimerax chimerax: command not found Any suggestions to recover? Thanks. Saverio

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Saving restraints
by Dyda, Frederick (NIH/NIDDK) [E] 07 Jan '25

07 Jan '25

I was wondering if there is a way to save restraints that one set up for a particular structure. For instance if I set up a bunch of "Simple Distance Restraints" in Isolde, to restrain a metal coordination environment, can I save these so I can reuse them for another .pdb file (assuming residue numbering is the same). Thanks. Happy New Year! Fred ******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 NIDDK Bldg. 5. Room 338 e-mail: Fred.Dyda(a)nih.gov Bethesda, MD 20892-0560 URGENT message: 2022476710(a)msg.fi.google.com Google map: 39.001168, -77.102048 http://www-mslmb.niddk.nih.gov/dyda/dydalab.html *******************************************************************************

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Assistance/guidance with ChimeraX
by Mahesh Chandrasekharan 03 Jan '25

03 Jan '25

Hi: First up, thank you and your team for all your efforts in creating and maintaining Chimera and ChimeraX. They are an awesome tool/package! It would be very helpful if you could please assist me with the two questions below. 1) I have a PDB downloaded from Alphafold. I would like to ‘drag out’ or reposition regions in order to enable their better visualization for a figure that I need for a grant. How can I select and reposition specific regions of a protein structure in ChimeraX? 2) The protein of my interest is a homodimer. I would like to open two copies of the relevant PDB file and manipulate them as two separate proteins. I have made a duplicate and relabeled the PDB file. However, when I open it ChimeraX along with the original, the two files seem linked, and I am unable to work on them separately. Is there a way to open two copies of the same PDB file to ‘recreate’ a homodimer? Thank you, Best, Mahesh Mahesh B. Chandrasekharan, PhD Assistant Professor of Radiation Oncology Investigator, Huntsman Cancer Institute Adjunct Assistant Professor of Hematology & Hematological Malignancies University of Utah School of Medicine 2000 Circle of Hope Room 3715 Huntsman Cancer Institute Salt Lake City, UT 84112-5540 Phone: 801-213-4220 Administrative Assistant: Coreen Rankin (801-585-3599) Lab site: https://uofuhealth.utah.edu/huntsman/labs/chandrasekharan

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Getting average of PAE values for a given region / interaction
by David S. Fay 02 Jan '25

02 Jan '25

Greetings and Happy New Year to All! My question is about broadly protein-protein interactions (PPIs. Last year several manuscripts came out proposing new metrics for assessing PPIs. This was in logical response to the growing understanding that ipTM (alone) is a fairly flawed metric, particularly for detecting interactions that involve a small number/fraction of the total residues. For those interested, I’ve pasted links to three such papers below (Coincidentally one is from a former roommate's lab, which I didn’t notice until recently!). Some may be easier to use than others (have GUIs). Tom Goddard and I emailed back and forth a bit about the relative merits of some of these metrics - nothing is perfect obviously (thank you again Tom). With respect to ChimeraX, I was wondering if there was a way to extract average PAE values after employing a cutoff. For example, "alphafold contacts /A distance 5 maxPae 5” will tell me that are "54 residue or atom pairs within distance 5 with pae <= 5”. But what if I want to know the average of those 54? Along those lines, for some PPIs there may be several spatially separated interfaces, with each one contributing to the total number. Is there an easy way to obtain the average and other metrics for each one? Some of this information I could probably find in my clunky (borderline boomer) way, by filtering, adding, and averaging values from the pairwise data (perhaps made easier by Predictome). Lastly, drawing rectangles on the PAE plot does a great job of giving coordinates and the average PAE, but it doesn’t give the range or other potentially useful data, such as the number of PAE<5 values etc. I guess I’m thinking that it could be very useful to be able to get metrics for a prescribed region of the PAE plot simply by drawing the rectangle. (And maybe there is but I missed it.) Those are my questions and thoughts. But I also wanted to express my gratitude for the ChimeraX software, and even more, the people working at ChimeraX who are always exceptionally responsive and helpful. David https://www.biorxiv.org/content/10.1101/2024.02.19.580970v1 https://www.biorxiv.org/content/10.1101/2024.10.23.619601v1 https://www.biorxiv.org/content/10.1101/2024.04.09.588596v1 David S. Fay Ph.D. Professor, Department of Molecular Biology Associate Director, National Institutes of Health Wyoming INBRE University of Wyoming email: davidfay(a)uwyo.edu

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get help with changing the cartoons ribbon to ball sticks
by Nhi Hoang 02 Jan '25

02 Jan '25

Hi. I am a sophomore at Le Quy Don High School in Danang City, Vietnam. I am using ChimeraX to display a model for my little project, and I have found a small trigger that I want to get help with. My problem is I cannot change the cartoon of selected residues from ribbons to ball sticks, after I have preset the model with cartoon ribbons. I wonder if this problem is due to the application and its limits or because of my device. I have attached an image presenting the coding and the model for a clear description of my problem. If possible, I am really willing to receive some advice from you in tackling this problem. Thank you very much. Best, Nhi Hoang. [image: image.png]

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