March 2024 - 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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question about pb file
by Renee Garza 02 Apr '24

02 Apr '24

Hi there! I've been saving pb files and see that the colors are of varying shades and transparency. I have looked at the link regarding the color key however some colors in the pb files are not in the list. I'm wondering if there's a place to look at the degree of confidence based on color somewhere or a way to have the output with the general color like red, blue, orange, yellow, etc. instead of very specific shades. Thanks, Renee

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Can α-carbon trace and bond be adjust for PBC?
by qz.chen＠tamu.edu 02 Apr '24

02 Apr '24

Hi, I want to use ChimeraX to visualize the protein slab simulation in the condensed phase as the link below. Unlike typical protein simulations, simulations of the condensed phase slab often need to keep the atoms inside the box for more accurate visualization. This means that particles between proteins may be jumping, leading to unreasonable lines appearing in the visualization. I have not found a way to adjust this in ChimeraX. https://www.biorxiv.org/content/10.1101/2020.08.05.237008v1.full Is there a way to limit the maximum distance between carbon and bond among particles? Thanks!

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Define axis along z?
by Oliver Clarke 01 Apr '24

01 Apr '24

Hi, For symmetric EM volumes, it would be useful to be able to easily create an axis corresponding to the molecular symmetry axis - generally coincident with a vector parallel to the Z-axis of the box, directly through the center. Is there an easy way to create such an axis in ChimeraX for an arbitrary map? It would be useful to have such an axis in order to rotate a volume around the molecular symmetry axis, even in the absence of a model (this is fairly easy to do if a model is present using define axis). This might be a useful generic extension to "define axis", if there isn't already an easy way to do so. Cheers Oli

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Difficulty with Z-translation - bug?
by Oliver Clarke 01 Apr '24

01 Apr '24

Hi, I can't seem to get the mousemode "Z-translate selected models" to work properly. I have "translate selected" set to Alt+left-drag, so per the docs ("assigned button + Ctrl (in that order) switches to Z-translation instead"), Alt+Ctrl+left-drag should translate the selected model in Z. It does not, or at least in any reproducible manner. Watch the selected yellow marker in the side view here on the right hand side: https://www.dropbox.com/scl/fi/vds0cwu0zizclg64vlxqc/z_translate_bug.mov?rl… 1. Initially I translate in x-y using Alt-drag - works fine. 2. I try to translate in z using alt-ctrl-drag - nothing happens 3. I keep trying translate in z, and eventually it "works" - but if you look closely you will see that the movement of the marker is not synced up with the direction/speed of the mouse cursor. Is this a bug? I remember testing this when it was initially implemented and I thought it worked fine so I suspect so...? Cheers Oli

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*.mdb files from MOE (chemcomp)
by Krishnan Raman 29 Mar '24

29 Mar '24

how to convert docking poses from MOE software to be read into chimerax? thanks Krish CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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pTM and ipTM Score Access
by Haley V Goodwin 27 Mar '24

27 Mar '24

Hello! I am using ChimeraX to use AlphaFold Multimer. I have read from a couple of places that AF provides pTM and ipTM scores to evaluate the quality of the models. I was wondering how I access these values from ChimeraX. I have looked through the results zip file, but can’t seem to find where these values may be stored. Thank you so much for your help! Best, Haley Goodwin

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Re: isolde write phenixRsrInput (how to restrain ions?)
by Shahid, Taha (Dr.) 27 Mar '24

27 Mar '24

Hi Tristan, That worked perfectly - many thanks for your help! Phenix.metal_coordination didn’t like for_phenix.cif file created by Isolde write phenixRsrInput, but I was able to create the edits file by saving the model file as a PDB from ChimeraX directly. Cheers and happy Easter, Taha On 25 Mar 2024, at 16:15, Tristan Croll <tcroll(a)altoslabs.com> wrote: You don't often get email from tcroll(a)altoslabs.com. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> ***CAUTION:*** This email was sent from an EXTERNAL source. Think before clicking links or opening attachments. Hi Taha, I'm very glad you find ISOLDE useful! Regarding magnesium (and metal ions in general): ISOLDE itself doesn't currently try to write extra Phenix restraints for these, but you can use the program phenix.metal_coordination to generate an edits file that you can add to the phenix.real_space_refine input. That should automatically create a set of bond and angle restraints for all metals in the model. Best, Tristan On Mon, Mar 25, 2024 at 3:46 PM Shahid, Taha (Dr.) via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear Tristan, I find ISOLDE invaluable for my work. Not only has it enabled me to build models of the highest quality, but been hugely instructive in giving me an instinctive ‘feel' for protein structure. I am having a minor problem with magnesium ions moving out of density when I run phenix.real_space_refine with settings output by isolde write phenixRsrInput. I typically specify restrainPositions true and includeHydrogens true as well. Is there a way to restrain these ions as well (perhaps an edit I could make to the real_space_refine.eff file)? Many thanks, Taha _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT

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change chain description
by Joshua Arribere 27 Mar '24

27 Mar '24

Hello, When I load a pdb into chimerax, a table appears with the chain IDs and associated descriptions. I would like to change the chain descriptions. How do I do that? Thank you, J

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Apple's cpus for trajectory visualisation
by Enrico Martinez 26 Mar '24

26 Mar '24

Dear ChimeraX users ! I wonder about the performance on the modern Apple CPUs: using several Apple's models as a benchmark, I tested Chimera-X on the 2015 and 2017 iMacs equipped with the i7 8 cores and then on the 2023 Macbook Pro equipped with the Apple m2pro chip. In the end, although the modern hardware was much more stable (never mind when loading large netcdf trajectories, as I reported in the case of the 2015 iMAC), I only noticed a slight increase in performance during film editing. As a benchmark, I took a very large model containing the membrane with an embedded oligomer and loaded a trajectory of 5500 frames in Chimera-X. I used surface rendering with 0.4 grid spacing for everything. While everything worked fine, I was able to produce a short 30-second film of 750 frames in about 1h30 on the m2pro, which was almost the same as on my imac 2015. Is there any way to improve the performance of film-making on modern Apple CPUs? Many thanks in advance Enrico

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