[chimerax-users] Inquiry: Map sequence conservation onto a protein structure

[Gomez Barillas, Andrea]

Dear ChimeraX developers,

I am trying to map sequence conservation onto a protein structure. I am using ChimeraX version (version 1.4 (2022-06-03).

For this purpose, I was trying to use a tutorial from 2014 for Chimera for Mapping Sequence Conservation onto Structures (Showing Sequence Conservation in Chimera (ucsf.edu)<https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html>).

It seems that some the tools mentioned in this tutorial are no longer available, or maybe work differently. Specifically, the tutorial's "Case 4" (calculating values outside of
Chimera but showing them in Chimera) has you set an attribute, and then render/color the structure based on the attribute.

The Tools > Structure Analysis > Define attribute mentioned in the tutorial is no longer available. I was as able to assign values directly to structure residues in a text file and
read it in using the command defattr instead. The next step would be to use the tool Render by Attribute for coloring but I cannot find this option anymore.

Is there a different command I can use for this step, or a new functionality built into ChimeraX I could use for my purpose of mapping sequence conservation onto the structure?

One relevant point is that I already have my sequence identify values calculated from another program, and I want to import those values.


Thank you in advance for your help,
Andrea



Showing
 Sequence Conservation in Chimera<https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html>
Example
 2B Chimera session: ConSurf-1hd2-chimera19.py [show this last!] (result of submitting 1hd2 to the ConSurf server and choosing to show results in Chimera; alignment has 150 sequences including that of the query, 1hd2) . Given a protein structure, the ConSurf
 server estimates the evolutionary conservation of amino acid positions based on the phylogenetic relations between homologous ...
www.cgl.ucsf.edu



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20230113/c3b33402/attachment.html>