From: Michael B. <mb...@uv...> - 2003-11-11 21:08:18
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Hi all, newbie question here; I think this is a question about syntax for the 'select' command. I study a homodimeric enzyme, which has been crystallized in various ligand-bound states. For example, I have loaded and aligned two different pdb files, and so there are actually four Lysine 465's on different chains and from different pdb files. If the first loaded pdb file is called 'abc' and the second is called 'xyz' how do I build a 'select' command to specify that I want create a unique selection element for K465 in one monomer (chain A) of the 1fyf file? My guess is that I need to use a combination of 'and' operators while specifying the name,resi,and chain that I want, but there seems to be so many possible ways to write this that the likelihood of my getting it right by trial and error is looking pretty small right now ;0) BTW, Also having trouble with command syntax for renaming (alter-ing?) the selection names for entire pdb files that appear in the right column of the viewer window... Is there some thread in the archive, or section of one of the pdf manuals that goes deeper into this syntax issue with 'real-life' examples? If so, please point out what I've missed, so I can minimize repetition on this list. Thanks, --Michael Bovee University of Vermont |
From: Robert C. <rl...@po...> - 2003-11-11 22:15:43
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Hi Michael, * Michael Bovee <mb...@uv...> [2003-11-11 16:08] wrote: > I think this is a question about syntax for the 'select' command. I > study a homodimeric enzyme, which has been crystallized in various > ligand-bound states. For example, I have loaded and aligned two > different pdb files, and so there are actually four Lysine 465's on > different chains and from different pdb files. If the first loaded pdb > file is called 'abc' and the second is called 'xyz' how do I build a > 'select' command to specify that I want create a unique selection > element for K465 in one monomer (chain A) of the 1fyf file? > > My guess is that I need to use a combination of 'and' operators while > specifying the name,resi,and chain that I want, but there seems to be > so many possible ways to write this that the likelihood of my getting > it right by trial and error is looking pretty small right now ;0) Yes, you just need to include the object name in there, so you could use select ak465, (abc and chain A and resi 465) select bk465, (abc and chain B and resi 465) select xk465, (abc and chain A and resi 465) select yk465, (abc and chain B and resi 465) or you could shorten the selection string: select ak465, (abc & c. a and r. 465) or use the shorthand notation: select ak465, /abc//a/465 > BTW, > Also having trouble with command syntax for renaming (alter-ing?) the > selection names for entire pdb files that appear in the right column > of the viewer window... You can copy an object to another (and thereby have a different name for it). load big_long_pdb_file_name.pdb create big_long_pdb_file_name, 1fyf Then you will have two objects, named "big_long_pdb_file_name" and "1fyf", so then you can delete one: delete big_long_pdb_file_name Of course if the problem is the default name that is used, you can just specify that when you load the file in the first place: load big_long_pdb_file_name.pdb, 1fyf Cheers, Rob -- Robert L. Campbell, Ph.D. <rl...@po...> Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2 |