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
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@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
Thanks, I'll check them out.
Wen-Shyong Tzou
Elaine Meng meng@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@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
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@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@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
Hi Wen-Shyong, Yes, you can do combinations (and/or/not) in command-line atom specifications, see explanation and examples at:
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#combinations http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html
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 ----- 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@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@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@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
Thank you! It does help. Paris
Elaine Meng meng@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:
< http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#combin...
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html
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
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@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@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@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
participants (2)
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Paris Tzou