[Chimera-users] named selections

[Elaine Meng]

Hi Ajith,
We are very happy to hear you will be the "Chimera guy" for your  
group, and that the tutorials are useful!  But sometimes it is hard to  
find certain things, which is why we have the chimera- 
users at cgl.ucsf.edu list (recommended rather than sending mail to me  
individually).

It sounds like you really want to use aliases rather than named  
selections.  See the "alias" command:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>

and also how to specify particular models, residues, chains, etc:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html 
 >
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierarchy 
 >

For example, to alias residues 10-42 and 55 in chain A and 80-100 in  
chain B:

alias myresidues :10-42.a,55.a,80-100.b
color red myresidues

These would be the residue numbers in the structure, which are not  
always the same as in a sequence file.

Session files are not friendly/intended for viewing as text.  Aliases  
are saved in sessions, but you would just use the alias command  
without arguments to list the definitions of the existing aliases.   I  
hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


On Mar 30, 2010, at 8:05 PM, Ajith Harish wrote:

> Hi Elaine,
> I will not bother you with too many questions after this last one  
> (at least for a while ;-)). There are a lot of features to explore  
> and I am playing with it and have learnt quite bit today. Also the  
> tutorials on the website are very helpful. I am soon going to be the  
> "Chimera Guy" of our group ;-)
>
> But there was one feature I could not figure out. Is it possible to  
> name sections without actually selecting the sequence from the GUI.  
> I need color different parts of large ensembles. Different domains  
> in multiple chains of a single pdb file. For now I open the sequence  
> of one chain at a time form the "Tools > sequence > sequence" and  
> then pick the residues (amino/nucleotide) based on the numbering  
> from the corresponding Fasta file from PDB and then name it from  
> "Select > Name Selection". Is it possible to assign names on a FASTA  
> file?
>
> I also looked into the session.py file. I could not relate the  
> numbers corresponding to my names in the session file to the residue  
> numbers or the residues. It would be great if I could assign names  
> in a file and then acess the names to color. Even better would be  
> assign colors to those named selections.
>
> Thanks much for your help.
> Best wishes,
> Ajith
>