[Chimera-users] Thank you

Ajith Harish ajith at life.illinois.edu
Tue Mar 30 22:49:38 PDT 2010

Hi Elaine,

Thanks again for your patient and detailed emails. Yes I do understand that I should sign up for the mailing list and minimize asking you alone, that way others with similar questions would also get to see the solution.

I have a better idea now for most things I plan to do and hopefully not many more complicated tasks. Hopefully I will manage to get my group to use Chimera more often after a demo.

Best wishes,

On Mar 30, 2010, at 11:27 PM, Elaine Meng wrote:

> 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

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