- ChimeraX-users - RBVI Mailing Lists

measure neighboring distance of histidine side chain
by HONG ZHAN 05 Apr '22

05 Apr '22

Dear all, I am interested to get a list of distances between histidine residues in my built model. Because I would like to see which crosslinker can potentially help to maintain the structure better during purification. I have noticed that I can measure one residue in chain A to all other atoms in chain B using contact function, however, I want to get a list of distances between any histidine imidazole (neighboring distance), is there a way to do that in ChimeraX? Super thanks in advance. Best, Hong

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display options for model with 2 chains
by Mauricio Losilla 05 Apr '22

05 Apr '22

Hi, I am new to ChimeraX, thank you for making this great software available. I loaded a pdb file that has 2 amino acid chains aligned (chimerax.png). These chains are a model (gray) and template (purple). As you can see, the two chains look weaved or blended. I would much prefer to display the uninterrupted template around to model, to visually represent their fit. Is there a way to do this? I am attaching a second image (ideal_display.png, generated elsewhere) with the visual outcome I am after (the purple chain is the template, the rainbow-colored chain is the model). Thank you *Mauricio Losilla, PhD* Integrative Biology; and Ecology, Evolution, & Behavior Michigan State University he, him, his

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Trouble with imports in ChimeraX bundle
by William Hofsøy 05 Apr '22

05 Apr '22

Hi, I have been doing some restructuring and refactoring of my project and started having trouble with my imports and modules not being found. previously all my imports were relative for instance: "from . import tool" However this is a bit impractical now that I have a folder structure, so I have been trying to use absolute imports like from "src.toolname.pythonfile import class" but it seems my folder structure differs from how it is after installing it into ChimeraX. I am using pycharm as my editor and the automatic import paths they set up also fails, meanwhile i looked at the sys.path and there the structure is chimerax/packagename where packagename contains the files contained in my src. So I was wondering if there is a way to set this up properly?

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Selection of the specific state from multi-model PDB
by Enrico Martinez 05 Apr '22

05 Apr '22

Dear ChimeraX users! Working in ChimeraX with multi-model PDBs I may use the following command to close all states but not the first (1.1): close #1.2-end How could I keep only the desired state (e.g I would like to display only the state #1.5 and close others)? Many thanks in advance Cheers Enrico

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Feature Request From Chimera
by Anderson, Jacob 05 Apr '22

05 Apr '22

Love ChimeraX - the UI is really enjoyable! I was curious if I could put in a plug for biomtSet true option to be ported to ChimeraX's sym command! I expect a lower priority, but would love to use this tool in ChimeraX in some future version.

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Re: [chimerax-users] [Chimera-users] Question regarding chimerax module
by Tom Goddard 04 Apr '22

04 Apr '22

Hi Prathvi, There is no ChimeraX Python library yet, it is only distributed as a standalone application including its own Python. But we have funding to make a library for PyPi and/or Anaconda so that should happen in the next year. You can use the ChimeraX Python Jupyter shell to try out Python code, menu entry Tools / General / Shell. Tom > On Apr 2, 2022, at 10:30 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello again Elaine, > > Is it possible to install the chimerax module in anaconda for usage in jupyter notebook? > > -- > Prathvi Singh, > Research Fellow, > Department of Biological Sciences & Bioengineering, > Indian Institute of Technology, Kanpur-208016 > _______________________________________________ > 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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Re: [chimerax-users] ChimeraX-users Digest, Vol 64, Issue 4
by Martti Tolvanen 04 Apr '22

04 Apr '22

As a pragmatic solution to the task of seeing both chains even when one is sometimes behind the other (as is inevitable with any superimposed models), you could make one ribbon semi-transparent. -Martti -----Original Message----- From: chimerax-users-request(a)cgl.ucsf.edu [mailto:chimerax-users-request@cgl.ucsf.edu] Sent: 2. huhtikuutata 2022 22:00 To: chimerax-users(a)cgl.ucsf.edu Subject: ChimeraX-users Digest, Vol 64, Issue 4 Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users or, via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..."

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Saving ChimeraX log, saving protein sequence to file
by Elaine Meng 03 Apr '22

03 Apr '22

Hi Prathvi, These answers are both for ChimeraX so I CC'd the chimerax-users list. (1) ChimeraX command "log save" saves it as HTML <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html> (2) in ChimeraX, open the structure, show the sequence of the chain of interest (menu: Tools... Sequence... Show Sequence Viewer, choose chain if there is more than one chain preset). Showing the sequence can also be done with the ChimeraX "sequence chain" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#chain> Then in the sequence viewer window, the context menu has a choice to save the contents (File... Save As...). <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context> You show a context menu in ChimeraX with Ctrl-click or right-click (depending on your system) in the tool window. <https://rbvi.ucsf.edu/chimerax/docs/user/window.html#context-menu> In Chimera, #2 is similar, use main tools menu to show sequence, use sequence-viewer tool's menu to save it to file. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 2, 2022, at 9:51 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thanks a lot Elaine. It helped enormously. I just have 2 more questions: > > 1. After running the dssp command in chimeraX, is there a command to save the reply log to file using a command? I searched for it & landed up at: https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003739.html but chimeraX throws the "Unknown command" error. > > 2. Is there a way to extract polypeptide sequence from a PDB file & save as a FASTA file or even a simple text file which simply contains a string representing the amino acids as single letters alphabets? >

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How to draw the surface of cavity
by 令怡 01 Apr '22

01 Apr '22

Dear ChimeraX Staff, Hello! I would like to know if there's a way to display the cavity like this? I've been studying for a long time without a clue. Thank you for your attention! Best Regards, Lingyi | | Xu, Lingyi Ph.D. | | Zhejiang University School of Medicine | 签名由网易邮箱大师定制

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Analysis of Hydrogen bonds in multi-model pdb
by Enrico Martinez 01 Apr '22

01 Apr '22

Dear ChimeraX users! Another question related to the analysis of the multi-model pdb obtained from protein-ligand docking calculations. I am using ChimeraX to visualise protein-ligand interactions between each pose predicted by docking and protein in my script: # calculate H-bond in first 10 frames of the multi-model pdb hbonds #1.1-10&protein restrict #1.1-${hb_poses}&ligand coordsets false interModel false makePseudobonds false log true intraRes false saveFile output.log Is it possible to print (or save somewhere?) the number of the state that has 1) the maximal number of the hydrogen bonds? 2) has a particular hydrogen bond of my interest? Cheers, Enrico

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