January 2023 - ChimeraX-users - RBVI Mailing Lists

Macbook Pro, fans, and ChimeraX
by Lewis James martin 26 Jan '23

26 Jan '23

Hi all, Ever since I got my Macbook Pro (16-inch, 2019, 2.3GHz 8‑core Intel Core i9) I noticed the fans can go full bore for seemingly small tasks. ChimeraX is one of those - swinging a protein view around is enough to set them off, and Activity Monitor reports around 200% usage for the "UCSF ChimeraX" process. I can see that GPU usage on the inbuilt AMD Radeon Pro 5500M can get up to about 50%, too. The bottom can get quite hot - it's Summer here now, but this happens in Winter too. A couple of questions: - Is this expected (for ChimeraX, not generally)? Do other people experience this? - Does ChimeraX use the GPU for rendering? If so, what's driving the CPU spike when I move the protein on screen? Is it just from calculating the coordinate rotations? Thanks, Lewis

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Re: [chimerax-users] [Chimera-users] Rotation along symmetry axys
by Tom Goddard 25 Jan '23

25 Jan '23

Hi Leonardo, As Elaine said, rotating the view in ChimeraX does not change what is saved in the map (*.mrc) file. The data needs to be rearranged in the 3D array. That can be done with the ChimeraX "volume resample" command (in Chimera it is called vop resample) but that interpolates the data on a new grid, and it would be better to just rotate the 3D data array so you don't get interpolation errors. I made a ChimeraX command to do that "volume rotate_90" available on the ChimeraX Recipes web site. https://rbvi.github.io/chimerax-recipes/rotate_90/rotate_90.html We no longer develop Chimera so I provide this for ChimeraX. Tom > On Jan 25, 2023, at 6:14 AM, Leonardo Talachia Rosa via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera team, > I hope you are well. > > I am processing a phage dataset which presents D5 pseudossymetry. The C5 axys is aligned to the z axys. I would like to rotate the map 90 degree in the z axys, so that Z axys now separate the molecule in a C2 pseudosymmetry, in order to play with some symmetry relaxation features to refine differences in the two map vortexes. > Is there a way in chimera to rotate the map in relation to the xyz axys? The way I see, all rotate commands I know rotate the axys themselves alongside the map. > > Thank you for your time, > Kind wishes, > Leonardo > > -- > ************************* > Leonardo TALACHIA ROSA, PhD > PostDoctoral Researcher > Microbiology and Structural Biology > Instituto de Química, Universidade de São Paulo - IQ-USP > Av. Prof. Lineu Prestes, 748 - Butantã, São Paulo - SP > ************************** > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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color palette in transprency ?
by vincent Chaptal 25 Jan '23

25 Jan '23

Hi, I'm rendering a series of models using this command line (which works very well): rainbow #1 structures palette cyan:blue I would like to do the same but in a series of transparent models, with a range from 0 to 80 (or similar). Is there a command for this, I couldn't find it? Thanks a lot. Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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vector
by Dr.S.Somasundaram 25 Jan '23

25 Jan '23

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Pseudobonds change style
by Samo Lešnik 25 Jan '23

25 Jan '23

Dear ChimeraX developers, I am wondering if it is possible to change the style of pseudobonds, specifically "Distances", from "dotted disks" to "whole undotted lines"? It is very easy to do this in Chimera, with just changing the style in the graphical interface of Distances. Thank you very much, dr. Samo Lešnik

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Re: [chimerax-users] downloading pdb files from another webserver
by Rangarajan, Amith 24 Jan '23

24 Jan '23

hi, i mostly resort to using the resource from dunbrack's lab to download structures renumbered as per uniprot numbering. i currently do it using a simple .py script: [cid:14eb2e7f-deaa-4341-92eb-3f9c56db264b] i want to make this as a chimerax script that i can call from command line with open {scriptname.py} { pdbid} wondering if some one has tried to do similar things and some tips regarding which modules to use might be helpful. thanks a lot , best amith

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Memory problems with Orbital Viewer
by Michael Patzschke 24 Jan '23

24 Jan '23

Dear colleagues, I am using ChimeraX mostly for small molecular complexes, typically up to 100 atoms. I am running the code on a MacBook Pro with 16 GB of memory under macOS 11.8.8. When I try to render molecular orbitals from an orca calculation I get even for very small molecules the warning message: Estimated peak memory usage (0.0GB) is above or close to the available memory (0.0GB). Exceeding available memory might affect the stability of your computer. You may attempt to continue, but it is recommended that you lower your resolution, decrease padding, or use fewer threads. Press "Ok" to continue or "Abort" to cancel Is there any way to fix this problem? Kind regards, Michael Patzschke

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electrostatic surface of docking model
by Citterico, Matteo 23 Jan '23

23 Jan '23

Hello everyone, I am trying to visualize the electrostatic potential surface of a docking model generated with ClusPro2.0 (job: https://cluspro.bu.edu/models.php?job=898454). When I click on the electrostatic button on ChimeraX 1.3 to visualize the charge, it gives the error: "Using Amber 20 recommended default charges and atom types for standard residues. Hydrogen copy of model.000.00.pdb #/A PHE 244 H1 bonded to atom that should not have hydrogens (copy of model.000.00.pdb #/A PHE 244 C)." How can I solve this problem? Thank you for the help and always a big up to the Chimera staff! Matteo

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Coot view in ChimeraX
by Cryo EM 23 Jan '23

23 Jan '23

Hi everyone, Does anyone know of a command for getting a coot view of map in ChimeraX? I remember seeing it in chimera, so I guess there should be something of such sort in ChimeraX too? Regards and thanks

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Error in opening Chimera
by Ashfaque Rahman 22 Jan '23

22 Jan '23

Why is this error showing? What is the solution? [image: image.png]

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ChimeraX-users January 2023