[chimerax-users] NMR CSPs

[Elaine Meng]

Well, it depends on why you want this in ChimeraX rather than in Chimera, considering that ChimeraX doesn't yet have Color Key or a Render by Attribute graphical interface.  

Is it because you want fancy lighting on the molecular surface, so that only the coloring is the important part?  Or, did you want to select or specify the residues by attribute value in ChimeraX?  I didn't mention it, but after using "setattr" in ChimeraX to create/assign the attribute you can specify the residues by these values in the command line.

For getting the molecular surface colored by attribute in ChimeraX, I think the methods already described may be better and more direct than any approaches available in the near future for coloring in Chimera and then transferring to ChimeraX.   The main effort in what I already described is to reformat your attribute assignment file used in Chimera to a setattr command file for ChimeraX.

Elaine

  
> On Mar 25, 2020, at 1:13 AM, Bohg, Claudia <Bohg at fmp-berlin.de> wrote:
> 
> 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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