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

[Elaine Meng]

Dear Andrea,
Chimera and ChimeraX are two different programs, and even though many things are similar, there are differences in how they work. As you said, you were using a tutorial that was written for Chimera.  If you want to follow that tutorial, you have to use Chimera instead of ChimeraX.   However, we are no longer developing Chimera, so it is better to use ChimeraX if you can.

There is a ChimeraX tutorial for coloring by sequence conservation here:
<https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-coloring.html>

ChimeraX also allows defining your own attribute (not described in that tutorial) by opening a defattr file, same text-file format as read by Chimera.  However, there is no tool in the tools menu.  You just need to name the text file something.defattr and simply open that file with the "open" command or menu: File... Open.  Define attribute files in ChimeraX:
<https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html>

Secondly, ChimeraX also has coloring by attribute but it is not exactly the same as in Chimera.  You can either 
(1) use command "color byattribute":
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute>
This is what the ChimeraX coloring by conservation tutorial uses.
- OR -
(2) if you get a recent daily build of ChimeraX (this feature is newer than the 1.5 release), you can user Render by Attribute.  We just started adding Render by Attribute to ChimeraX so it does not have as many options as the Chimera one yet.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 13, 2023, at 1:27 PM, Gomez Barillas, Andrea via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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)). 
> 
> 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
> 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
> 
> 
> 
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users