[Chimera-users] How can I load a list of residues of protein?
paristzou at gmail.com
Tue Oct 30 20:00:36 PDT 2018
Thank you! It does help.
Elaine Meng <meng at cgl.ucsf.edu> 於 2018年10月30日 週二 下午11:18寫道：
> Hi Wen-Shyong,
> Yes, you can do combinations (and/or/not) in command-line atom
> specifications, see explanation and examples at:
> Also aliases can be combinations of aliases. If you already defined (with
> alias) set1 and set2, something similar to your example would be
> alias combined set1 | set2
> alias intersected set1 & ~ set2
> I hope this helps,
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Oct 29, 2018, at 9:28 PM, Paris Tzou <paristzou at gmail.com> wrote:
> > Is it possible to do set operation like
> > alias common_set set_A & set_B
> > alias subtract_set set A not set_B
> > Thanks a lot
> > Wen-Shyong
> > 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.
> > <
> > 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
> > >
> > > 15,C
> > > 16,C
> > > 17,C
> > > 263,A
> > > 264,A
> > > 265,A
> > >
> > > Thank you very much.
> > > Paris Tzou
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