February 2024 - ChimeraX-users - RBVI Mailing Lists

Save docked tool size?
by Guillaume Gaullier 14 Feb '24

14 Feb '24

Hello chimerax-users, I recently started using ChimeraX in more custom ways for specific analyses, for which I need several tools displayed at once. I need some docked and others floating. So the "Save tool position" option is very helpful. However, it saves window size only for floating tools, not docked ones, so I have to resize the docked tools at every restart (their position is saved correctly, but not their size relative to the main ChimeraX window). This happens for the model panel and log, that I have docked to the right of the 3D display: they systematically start much wider than I want (and than I resized them to last time I started ChimeraX). This doesn't happen for a custom button panel that I have docked to the right of the toolbar (but maybe because the command file generating the panel sets a fixed size explicitly?). I have not checked whether this happens with other tools. Is this normal behavior? If so, is there any way I can make docked tools remember not only their position but also their size? A quick search in the documentation didn't answer this question. Thank you, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Feature request; sort by last time file was modified in save window
by m.c.feasey2＠newcastle.ac.uk 12 Feb '24

12 Feb '24

The content of this message was lost. It was probably cross-posted to multiple lists and previously handled on another list.

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Chimera Script
by Dixson, Jamie 12 Feb '24

12 Feb '24

Hello, I would like to use the Matchmaker comparison in ChimeraX (specifically the 'across all' RMSD value given) to compare 10,000+ structures so I would like to incorporate it into a python script in a jupyter notebook. I am very familiar with scripting with python in jupyter notebooks but I am not as familiar with getting two scripts to work together as appears to be needed to use matchmaker in an existing jupyter script. The script I am attempting to use is found below. I wrote it following some of the guidance in your documentation. ``` #Chimera Command Line import chimera import os from chimera import runCommand as rc # use 'rc' as shorthand for runCommand from chimera import replyobj # for emitting status messages file1='C:/Users/jamie/Downloads/temppdb1.pdb' file2='C:/Users/jamie/Downloads/temppdb2.pdb' structure1=rc("open " + file1) structure2=rc("open " + file2) rc("mmaker structure1 structure2") ``` I get the error 'No chimera module' I try to install chimera using 'pip install chimera' and it won't install. Can you offer any guidance on getting this to work? Best, Jamie Dixson

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Automatisation of the movie record / encode
by Enrico Martinez 11 Feb '24

11 Feb '24

Dear Chimera-X users! Typically when I load multi model pdb using open coordset true I may record my movie automatically using the context menu. I need to script this process selecting the resolution and the quality of the encoding using movie record size 3840,2160 supersample 3 movie encode format h264 quality highest output ./my_movie.mp4 The only problem is that when I type the first command it asks me to "play" and then "stop" the pdb ensemble for the number of frames which should be present in the resulting video. Is it possible to define in the scipr that the movie should take the selected number of frames in the selected range and then automatically start to encode the movie ? Many thanks in advance Enrico

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Setting transparency for multi-frame PDB
by Enrico Martinez 09 Feb '24

09 Feb '24

Dear ChimeraX users! I am working on visualization of protein-ligand complex from MD trajectory loaded as multiframe pdb via open coordset true Here is my script: #coloring ligand options color ligand & C gold style ligand sphere #transparency surface protein color byattribute kdh protein target rs palette sandybrown:coral:orangered novalue gray transparency protein 5 surfaces select zone ligand 4 protein transparency sel 55 surface The problem is only in the transparency which could be set only on the first frame but then disappears when I browse movie. How could I modify my scipr to keep the transparency on all frames ? Many thanks in advance ! Enrico

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Surface representation for small compounds
by Enrico Martinez 09 Feb '24

09 Feb '24

Dear ChimeraX users I am also experimenting on the representation of the surfaces of small compounds surface ligand gridSpacing 0.5 probeRadius 1.2 color ligand white target s transparency 90 This creates a relatively large transparent surface around the small compound. How would it be possible to reduce the volume of the surface ? Also I did not understand how to change the style of the surface among dot/mesh etc since adding style dot did not work. I would appreciate any further creative examples of how to change the representation of a small compound in the case when I need to make it more "coarse-graining" , hiding some precise details of the structure ? Many thanks in advance ! Enrico

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Colour patterns for ligand atoms
by Enrico Martinez 09 Feb '24

09 Feb '24

Dear ChimeraX users ! I am experimenting with some unusual coloring of the ligand atoms represented as balls and sticks. the following commands color ligand atoms: size ligand atomRadius +3.0 color ligand & C gold target a color ligand goldenrod target a However, the following command does not work w/o any error message rainbow ligand & C palette cornflowerblue:red:gold target a I've also tried without any success. style ligand ball ringFill off rainbow ligand & C palette cornflowerblue:red:gold target f Any additional suggestions e.g. for the situation when I would like to alternate the colors for the ligand atoms in a regular fashion : e.g. the first atom white, the first black, the third white, the forth black etc ? Many thanks in advance ! Cheers Enrico

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Llama2 cannot be used as an alternative to the mailing list
by Pranav Shah 09 Feb '24

09 Feb '24

As the subject states. (see attached image for context) So thank you Elaine (and rest of the CX team) for your tireless and infinite capacity to support users! :) Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Fourier transformation of the 3D volume
by Dmitry Semchonok 08 Feb '24

08 Feb '24

Dear colleagues, How to get the Fourier transformation of the 3D volume? thank you. Kind regards, Dmitry

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Re: ChimeraX: AlphaFold data saving help
by Tom Goddard 06 Feb '24

06 Feb '24

Hi Tony, Good. I didn't see the sleep issue mentioned in our ChimeraX documentation. We'll add that. Tom > On Feb 6, 2024, at 2:35 PM, Anthony Newcombe <ant.newcombe(a)gmail.com> wrote: > > Ah ok thanks Tom! > > My PC does go into sleep mode, I'll turn this off and try again! > > Many thanks for the help > > Best wishes > > Tony > > Anthony Newcombe > Brook Lodge > Lisnacunna > Ballinascarthy > Clonakilty > Cork > > On Tue, Feb 6, 2024 at 10:25 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Tony, >> >> If you let your computer sleep when the ChimeraX AlphaFold job is run on Google Colab it will probably lose the results. Google intends Colab to be for interactive use. So I suggest setting your computer not to sleep when running a prediction. There is more discussion of AlphaFold prediction not downloading on the ChimeraX mailing list >> >> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… >> >> including how you can get the results if Google Colab has not closed the session and deleted them (happens within a few hours). >> >> Tom >> >> >>> On Feb 6, 2024, at 5:57 AM, Anthony Newcombe via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hello ChimeraX team >>> >>> I am evaluating ChimeraX (non-commercial use) but have an issue you may be able to help with. When I run a structure prediction: >>> >>> Tools > structure prediction > AlphaFold >>> >>> I enter two primary sequences and hit ‘predict’ >>> >>> The simulation completes, but nothing opens in ChimeraX, also there is no data saved in the location below. I have tried alternative locations, but no data is saved >>> >>> ~/Downloads/ChimeraX/AlphaFold/prediction_[N] >>> >>> Do you know how I obtain saved predicted results ChimeraX? Do I need a paid service for this? >>> >>> Many thanks >>> >>> Tony >>> >>> Anthony Newcombe >>> Brook Lodge >>> Lisnacunna >>> Ballinascarthy >>> Clonakilty >>> Cork >>> _______________________________________________ >>> 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/ >>

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