[Chimera-users] Auto-associate define attribute/render by attribute

[Elaine Meng]

Hi Joe,
Not sure I understand completely, but did you know that you could include chain in the specification in the attribute file?  E.g. instead of “:3” it could be “:3.A”  for residue 3 in chain A.  It is any command-line specifier, so it could also include the model number.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile>

You would still have to figure out the numbering correspondence to write the attribute files, however.

An alternative approach is to create a custom header file for the sequence or sequence alignment in Multalign Viewer, which would automatically also become an attribute of any associated structures.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavAttributes>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/defineheader.html#headerformat>

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

> On Nov 26, 2019, at 7:40 AM, Healey, Joseph <J.Healey.1 at warwick.ac.uk> wrote:
> 
> Hi Chimera team,
> I’m working on a script to automatically render proteins in a complex by attributes (in this case, a number of scores obtained from different immunogenicity prediction algorithms). I currently have the script outputting attribute files as intended, but ideally I’d like to define the same attributes across all the chains of the model, which are made up of a number of different proteins.
>  
> Is there any way for me to define the attribute file, or utilise some functionality to auto-associate an attribute file with all of the chains which have the correct sequence (similarly to how the sequence alignment input works at the moment?). Currently the attribute file is only using ‘numbered’ coordinates (:1, :2, :3…etc) , rather than the actual sequence.
>  
> Since there’s no chain information in the attribute files, I’m not sure how I can go about connecting it to the right structure, other than manually at the moment? 
> Many thanks, 
> Joe