[Chimera-users] How can I load a list of residues of protein?

[Paris Tzou]

Thanks, I'll check them out.


Wen-Shyong Tzou



Elaine Meng <meng at cgl.ucsf.edu> 於 2018年10月29日 週一 上午12:12寫道：

> Hi Paris,
> What do you want to do with these  residues, only select them?  You could
> just make that list into a command file.  E.g.
>
> select :15.c
> select :16.c
>
> (etc.) and name this plain text file something.cmd or something.com.
> Then opening it will execute the commands. By default each selection
> command will replace the previous (so that would only select one residue at
> a time) but if you first choose menu: "Select… Selection mode… append” it
> will then accumulate the selections instead.
>
> Of course, the command file could do other things like coloring instead of
> selection.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile
> >
>
> However, I’m guessing you really want to do several different things with
> this set of residues.  In that case,  just give the set(s) of residues
> different short names with the “alias" command.  Then you can keep doing
> things easily to that set including selecting/deselecting it.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
>
> However, the alias needs all the residues that you want to give a single
> name to be in a single command, e.g.
>
> alias myres1 :15-17.C,263-265.A
>
> ….and/or multiple sets with multiple names…
>
> alias cres :15-17.C
> alias ares :263-265.A
>
> Then later you can just use them in other commands,
>
> select myres1
> color orange cres
> color dodger blue ares
>
> These alias commands can be quite long if your residue list is long, but
> you’d only have to enter a given alias once, and the alias command itself
> could be in a command file.  I’ve often done this for making paper figures
> where I want to easily color certain sets of residues (domains, catalytic
> sites, mutation hotspots, etc.)
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Oct 27, 2018, at 7:31 PM, Paris Tzou <paristzou at gmail.com> wrote:
> >
> > Dear all,
> >   I want to load a file containing a lit of residues of protein which is
> already shown in Chimera. I don't want to manually select the residues
> under investigation through "Favorite -- Sequence". Is there a way of doing
> this ?  I know I can do it using command line like:select
> #0:15-17.C,263-265, 300-310.A. Instead, I can have a text file with content
> like:
> >
> > 15,C
> > 16,C
> > 17,C
> > 263,A
> > 264,A
> > 265,A
> >
> > Thank you very much.
> > Paris Tzou
>
>
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