- ChimeraX-users - RBVI Mailing Lists

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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Camera Viewfinder
by Vytautas Raškevičius 29 Aug '23

29 Aug '23

Hi It would be nice to have camera viewfinder to make images. Like here: https://expertphotography.b-cdn.net/wp-content/uploads/2021/02/Viewfinder-v… So it would be much easier to put something in center exactly and so. VR

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How to reduce subdivision of the mesh?
by HL F 29 Aug '23

29 Aug '23

Dear ChimeraX Development Team, I hope this email finds you well. First and foremost, I would like to express my heartfelt gratitude for developing such a powerful and invaluable tool like ChimeraX. Your dedication to providing the scientific community with a free and versatile platform is truly remarkable. I am writing to inquire about a technical aspect related to exporting 3D models in ChimeraX. I'm using ChimeraX-1.1.1 to export protein meshes(surface model) into Blender. I've got a problem that the mesh is too smooth which means it has too many vertices. And that makes my Blender run very slow. Is there a way to reduce the subdivision(resolution/vertex number) of the mesh in ChimeraX? Thank you very much! Looking forward to your reply. Regards, Hualing [image: image.png]

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