Hi folks, I'm a newbie and am having trouble getting started. Sorry to be dense. Using the command line on a single protein chain O select :32-42,44-49.O or rep sphere :43:56:59:60:61:63:65:67:68:70:71:72:73:74:75:78:110:113.0 only seems to work on the last residue. Thus I'd have to write a separate command for each residue. Could you tell me what I've missed please! John
On Jan 17, 2005, at 7:52 AM, John Nixon wrote:
I'm a newbie and am having trouble getting started. Sorry to be dense. Using the command line on a single protein chain O select :32-42,44-49.O or rep sphere :43:56:59:60:61:63:65:67:68:70:71:72:73:74:75:78:110:113.0 only seems to work on the last residue. Thus I'd have to write a separate command for each residue. Could you tell me what I've missed please!
Hi John, Don't worry, this was almost right! You can think of the chain ID as part of the residue specification, so that you need to put it on each residue number or range of residue numbers: select :32-42.o,44-49.o rep sphere :43.o:56.o:59.o:60.o:61.o:63.o:65.o:67.o:68.o:70-75.o:78.o:110.o:113.o which is somewhat more of a pain to type, unfortunately. The reason is that theoretically there could be another chain that doesn't have an ID, so residue numbers not together with a specification of chain O would specify residues in the no-ID chain. There are a few more examples in http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ atom_spec.html#hierarchy I hope this helps, Elaine ---- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 17, 2005, at 10:21 AM, Elaine Meng wrote:
rep sphere :43.o:56.o:59.o:60.o:61.o:63.o:65.o:67.o:68.o:70-75.o:78.o:110.o:113.o
which is somewhat more of a pain to type, unfortunately. The reason is that theoretically there could be another chain that doesn't have an ID, so residue numbers not together with a specification of chain O would specify residues in the no-ID chain.
I would add that there a couple of ways to avoid having to type a long atom spec like the above repeatedly. One is to edit the previous command so that you "reuse" the atom spec part (also you can use up-arrow to get back to a command that isn't the immediately previous one). Another way is to use the 'alias' command so that a long piece of text can be replaced with a much shorter one, e.g.: alias site :43.o:56.o:59.o:60.o:61.o:63.o:65.o:67.o:68.o:70-75.o:78.o:110.o:113.o rep sphere site color red site Aliases are remembered in session files. Finally, any series of commands (including 'alias') can be put into a file and read in using the 'source' command. Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu
As another fairly newbie, may I also suggest using the sequence window, setting the selection mode on 'Append', and using the mouse to select the residues you want. For me this is easier than the typing. Ann Mullin Research Scientist Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) amullin@tulane.edu On Jan 17, 2005, at 12:21 PM, Elaine Meng wrote:
On Jan 17, 2005, at 7:52 AM, John Nixon wrote:
I'm a newbie and am having trouble getting started. Sorry to be dense. Using the command line on a single protein chain O select :32-42,44-49.O or rep sphere :43:56:59:60:61:63:65:67:68:70:71:72:73:74:75:78:110:113.0 only seems to work on the last residue. Thus I'd have to write a separate command for each residue. Could you tell me what I've missed please!
Hi John, Don't worry, this was almost right! You can think of the chain ID as part of the residue specification, so that you need to put it on each residue number or range of residue numbers:
select :32-42.o,44-49.o
rep sphere :43.o:56.o:59.o:60.o:61.o:63.o:65.o:67.o:68.o:70-75.o:78.o:110.o:113.o
which is somewhat more of a pain to type, unfortunately. The reason is that theoretically there could be another chain that doesn't have an ID, so residue numbers not together with a specification of chain O would specify residues in the no-ID chain.
There are a few more examples in
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ atom_spec.html#hierarchy
I hope this helps, Elaine ---- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
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Ann Mullin -
Elaine Meng -
Eric Pettersen -
John Nixon