Atom's ID is specific to a molecule (or object - can someone please correct me?), thus if you have several molecules, and all of them contain atom with the specified ID, they all will be selected. Regarding listing the atoms within a selection (from http://www.rubor.de/bioinf/tips_advanced.html):
list=[] iterate (name ca),list.append((resi,resn)) print list alternatively you can do something like this: iterate mySelection, print "ID %s, name %s,elem %s, partial_charge %f"%(ID,name,elem, partial_charge) see "help iterate" for more details about this command. On 1/10/07, Jonathan Arthur <jart...@med.usyd.edu.au> wrote:
Hello all, I am trying to select all atoms with 4 Angstroms from a particular atom, in this case the O of the OH group in a tyrosine residue. I executed the following commands select oh, id 341 select close, all within 4 of oh where the first command creates a named selection for the particular atom I am interested in and the second selects the nearby atoms. My problem is, there seems to be too many atoms selected and, when I check a few bond distances, I definitely have atoms selected further than 4 Angstroms away. What am I doing wrong? Also, once the selection is correct, is there any easy way to get a text list of all of these nearby atoms? Thanks for your help. Regards, Jonathan -- Dr Jonathan Arthur Sydney Bioinformatics Medical Foundation Building, K25 University of Sydney NSW 2006 Phone: +61 2 9036 3132 Fax: +61 2 9036 3233 Email: jart...@med.usyd.edu.au ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
