[chimerax-users] NMR CSPs

[Bohg, Claudia]

Dear Elaine,


thanks for that fast and detailed answer. This looks doable, I hope I can make it work (:


Would it also be possible to color the residues in Chimera and save it in a way that I can open it with Chimera X?


Many thanks.


Best,

Claudia


________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: 24 March 2020 23:35:37
To: Bohg, Claudia
Cc: chimerax-users at cgl.ucsf.edu
Subject: Re: [chimerax-users] NMR CSPs

Hi Claudia,
ChimeraX doesn't yet have reading an attribute assignment file.

However, you can create and assign custom attributes using the "setattr" command.  You could reformat your chemical shift data into a ChimeraX command file (a text file of ChimeraX commands, with filename something.cxc) where each value is assigned in a "setattr" command, and then simply open that file in ChimeraX to execute all the commands.

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files>

Here is an example .cxc file that creates/assigns an attribute named "kdh" with values assigned per amino acid residue type:
<http://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle_hydrophobicity.cxc>

... for example, one command in that file is

setattr :asp res kdh -3.5 create t

Instead of specifying residues by name like :asp  you could specify by residue number, optionally including chain if you have more than one chain, e.g.

setattr /A:201 res csp 0.022 create t

... repeating for all the residues to which you want to assign values. ( I assumed this is a residue attribute.  You could alternatively create a per-atom attribute, see setattr manual page.)

Then you can use ChimeraX command "color byattribute" to do the coloring.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute>

However, ChimeraX does not yet have a color key.  You could get fancy by making a color key in Chimera and then combining it with the image from ChimeraX as discussed in this previous post.
<http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-March/000452.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 Mar 24, 2020, at 1:12 PM, Bohg, Claudia <Bohg at fmp-berlin.de> wrote:
>
> Hey,
> is it somehow possible to use this attribute in Chimera X?
>
> http://www.cgl.ucsf.edu/chimera/data/nmrcolor-nov2017/nmrcolor.html
>
> Best,
> Claudia

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