how to select multiple residues in multiple chains
I work a lot with symmetrical, multi subunit structures and in order to select say residue 45 in every subunit, I must one at a time go in and in the sequence finder select the residue in each chain and then color it. Is there a way to select all of the same number residues (say number 45, might be an alanine) in the structure displayed and color only those. If you select alanine, it will select every single alanine in the structure. Chimera seems to be a really powerful program, but I am pulling my hair out trying to get it to do something productive in a timely fashion. thanks, eric.
On Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote:
I work a lot with symmetrical, multi subunit structures and in order to select say residue 45 in every subunit, I must one at a time go in and in the sequence finder select the residue in each chain and then color it. Is there a way to select all of the same number residues (say number 45, might be an alanine) in the structure displayed and color only those. If you select alanine, it will select every single alanine in the structure. Chimera seems to be a really powerful program, but I am pulling my hair out trying to get it to do something productive in a timely fashion. thanks, eric.
Hi Eric, It depends how the residues and chains are defined in the PDB file, but often it will be the same residue number but in different chains. In that case, it is fairly simple to select using a command. For example, in PDB 1e9i there are chains A-D, each comprising essentially the same sequence. To select residue 45 in all four chains: command: select :45.a-d or command: select :45.* Or, to select residue 45 in just chains A and D: command: select :45.a,45.d (To show the command line, choose Favorites... Command Line from the menu). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
Elaine's suggestions for using the command line are the easiest way to do what you want. However, if for some reason you prefer to use the menus, you can use the Select menu to change the "selection mode" to "append". This will allow you to build up selections since selecting new items won't deselect previous items. You can then do operations (like color) on the aggregate selection rather than having to do them separately. You can also save selections you've built up by using "Name Selection..." in the Select menu. If you save a session, named selections will be remembered in the session. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Nov 1, 2005, at 9:13 AM, Elaine Meng wrote:
On Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote:
I work a lot with symmetrical, multi subunit structures and in order to select say residue 45 in every subunit, I must one at a time go in and in the sequence finder select the residue in each chain and then color it. Is there a way to select all of the same number residues (say number 45, might be an alanine) in the structure displayed and color only those. If you select alanine, it will select every single alanine in the structure. Chimera seems to be a really powerful program, but I am pulling my hair out trying to get it to do something productive in a timely fashion. thanks, eric.
Hi Eric, It depends how the residues and chains are defined in the PDB file, but often it will be the same residue number but in different chains. In that case, it is fairly simple to select using a command. For example, in PDB 1e9i there are chains A-D, each comprising essentially the same sequence. To select residue 45 in all four chains:
command: select :45.a-d or command: select :45.*
Or, to select residue 45 in just chains A and D:
command: select :45.a,45.d
(To show the command line, choose Favorites... Command Line from the menu). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
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participants (3)
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Elaine Meng -
Eric Gillitzer -
Eric Pettersen