[chimerax-users] NMR CSPs

[Elaine Meng]

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