Hi Michael, * Michael Bovee <mbo...@uvm.edu> [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. <r...@post.queensu.ca> 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
