- ChimeraX-users - RBVI Mailing Lists

save "side view" settings
by vincent Chaptal 05 Sep '23

05 Sep '23

Hi, I opened the side view dialog window and adjusted the view planes for a nice figure. I would like to save the parameters so I can go back and modify the figure at a later stage, but the setting are not stored in the "view matrix" command. Could you tell me which command can save these settings? (I'm using chimeraX 1.5). Thank you. Best 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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Zone map around center of rotation?
by Oliver Clarke 01 Sep '23

01 Sep '23

Hi, Surface zone allows one to carve the map in a sphere around a selected atom (with “nearAtoms”). When navigating around the map, it would be convenient to be able to use the center of rotation as a reference point instead. Would it be possible at some point to add a “nearCofR” option to surface zone to facilitate this? In Chimera, I had kind of a hack-y way to do this, by placing a marker atom at the center of rotation and using that as the reference, but this option is not yet available in ChimeraX. Cheers Oli

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Set defaults for molecule display?
by Oliver Clarke 01 Sep '23

01 Sep '23

Hi, Is there anyway to set default preferences for molecule display? Currently it seems to vary (I think?) based on the number of atoms in the model - so relatively small proteins will load as ribbons, while larger ones will load in sphere representation. I would rather set a default such that all molecules load as ribbons, rainbow colored by chain. Is this possible? Cheers Oli

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morph for non-protein atoms?
by Alexis Rohou 01 Sep '23

01 Sep '23

Hello, The documentation for morph reads very protein-centric, and testing it with default options certainly makes it look like ligands are removed. Is there a way to have ligands included in a morph (assuming the same atoms are present in both models)? Cheers, Alexis

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getting HEX code from molecule
by Matzov Donna 01 Sep '23

01 Sep '23

Hello, I was wondering if there's a command that would give me the HEX code of a particular atomspec. Using the "pick from screen" option in the color editor is somewhat helpful samples the colors that are the results of shadows so I can't really the exact color. Thanks, Donna Matzov, PhD Department of Structural Biology Weizmann Institute of Science The Shalev-Benami Lab<https://www.weizmann.ac.il/Structural_Biology/Shalev-Benami/home>

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Structure Comparison->Morph conformations
by Revan Katte 01 Sep '23

01 Sep '23

Hello, For morphing my structures, I'm using ChimeraX 1.6.1, but I cannot find structure comparison and morph conformations in the tool menu. Could you please assist me with this? Thank you! Revan -- Revan Katte, Ph.D. Postdoctoral Research Associate, Prof. Maolin Lu Laboratory, Department of Cellular and Molecular Biology, The University of Texas Health Science Center, Tyler, Texas 75708, USA. E-mail: *Revansiddha.Katte(a)uthct.edu <Revansiddha.Katte(a)uthct.edu>* Professional Website: Google Scholar <https://scholar.google.com.tw/citations?user=phuOXjgAAAAJ&hl=en> LinkedIn <https://www.linkedin.com/in/dr-revan-katte-3b53a788/>

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More shades in color byattribute
by Enrico Martinez 01 Sep '23

01 Sep '23

Dear Chimera-X users ! I am using ChimeraX to color pdb file according to its structural flexibility determined in the b-factor column color byattribute bfactor palette rainbow range 2,100 This info is taken directly from the rmsf calculations of short MD trajectory and stored in a single pdb structure in the b-factor column. Technically It works very well, however in the case of flexible systems, the most of the structures is colored in "red". I enclose a screenshot of an example image along with the corresponded rmsf chart. Would it be possible to define the gradient of the coloring in more accurate fashion in order that the red zones could have more shades ? I believe this could be fine-tuned via the "range 2, 100 " attribute and / or switching to other palettes e.g. 'Paired-12' , which naturally has more shades compared to 'rainbow' .. I would be grateful for any further suggestions ! Yours with thanks, Enrico

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Render by attribute - custom rmsd
by Dominik Sordyl 31 Aug '23

31 Aug '23

Hi, I am developing the custom plugin for sequence alignment and structure superposition, that will have it's own sequence viewer. I would like to use 'Render by attribute" feature of ChimeraX 1.16. But without using 'matchmaker ... show True' I do not have such option. Is there a way to pass the rmsd values for superimposed structures' residues to be available for 'render by attribute'? While looking through the ChimeraX source code, I have noticed that it uses Sequence Viewer headers to store rmsd, but I can not figure out how can I add such thing to my plugin. Best, Dominik

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Trouble installing plugin
by BARRY E DEZONIA 30 Aug '23

30 Aug '23

I am having trouble installing a plugin I am developing. It works on one system I am using at work and fails on my system at home. The home system has the latest daily build on it. The work system has an earlier daily build on it. This is what I try to do inside chimerax: devel install ~/dev/bphon/chimerax-plugin/tut_tool_qt And this is the installation error: open /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.pyTraceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.py", line 49, in <module> assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main module" AssertionError: Cannot run __pip-runner__.py as a non-main module Error opening python file /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.py Any idea what is happening? I may have run into this problem some time ago on the work computer and fixed it but I honestly don't know. Please forward this to the bugs email list of it should go there instead. Thanks. Sorry for yet another question. You guy seems very busy with mail recently.

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Coloring by Ca-RMSD
by Abhilash Padvannil 30 Aug '23

30 Aug '23

Hello, I am working with a multi-subunit protein. I aligned current structure with a previously determined structure using mm command. I am trying to color my protein using RMSD. Chimerax is however, coloring only one-subunit by RMSD, the other chains have default colors. Is there a way to color the whole molecule with RMSD attribute. Thanks Abhilash.

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