[chimerax-users] creating an annotated structure

[Melissa Jurica]

Perfect!  Thank you.

Melissa

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Melissa S. Jurica, Ph.D.
Professor, Molecular, Cell & Developmental Biology
Center for Molecular Biology of RNA
University of California, Santa Cruz
1156 High Street
Santa Cruz, CA 95064

Office: 450 Sinsheimer Labs	Lab: 434 Sinsheimer Labs 
Office phone (831) 459-4427	Lab phone (831) 459-2463	Fax (831) 459-3139
http://www.mcd.ucsc.edu/faculty/jurica.html <http://www.mcd.ucsc.edu/faculty/jurica.html>
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> On Jun 30, 2020, at 3:22 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Melissa,
> (A) In ChimeraX you can create named sets of atoms with the "name" command, and then save a session with your structure(s) which would also include the definitions of the named sets.   These sets will show up in the Select menu and in the Basic Actions tool so that others could select and act upon them easily without having to know the residue numbers, and can give them mnemonic names (or semi-mnemonic, given you don't want them to be too long).
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html>
> 
> (B) You could share the ChimeraX session, or (lighter-weight and less version-dependent) you could share a ChimeraX command script (.cxc file, just a text file of Chimera commands) that opens the structure and creates the named sets.
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files>
> 
> (C) However, I think the best way if you have any familiarity or willingness to write simple HTML is to make a web page with explanations that lead people though the structure, and include links that execute ChimeraX commands when the page is opened in ChimeraX's own browser.  E.g. just "open URL" in the command line will open that web page in Chimerax's browser.  These special execution links are a simple HTML tag explained here: 
> <http://rbvi.ucsf.edu/chimerax/docs/user/tools/helpviewer.html>
> 
> ....and you can see many examples of such HTML files in the tutorials (and view their source).
> <http://www.rbvi.ucsf.edu/chimerax/tutorials.html>
> 
> This web page approach will also allow you to include links to the sources of the data being shown.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jun 30, 2020, at 1:12 PM, Melissa Jurica <mjurica at ucsc.edu> wrote:
>> 
>> Can you provide some guidelines for how one could create an annotated structure to share with colleagues?  For example, I would like to annotate the cancer associated mutations of a protein, making it easy for someone to select and visualize the associated residue in a structure.  Ideally, these annotations could be grouped and sorted. Even better, they could be linked to other resources.  
>> 
>> Thanks 
>> Melissa
> 

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