Thanks Hongbo Zhu. Great summary of the topic. Rank rules. Martin
On 01.11.10 11:57, Hongbo Zhu wrote: > ID is the>>external-index-number<<, which is parsed from columns 7-11 > of the PDB file (Atom serial number). > Try pymol command: > select id 110 > > RANK is the order of the atoms as they are listed in the PDB file > (0-based). Therefore, the nitrogen is at rank 11 (line 12). > Try pymol command: > select rank 11 > > INDEX is the>>internal-index-number<< of the atom. Obviously, the atoms > get their internal indices based on their names as atoms of the same > name are grouped together. > Try pymol command: > select index 1 > > PyMOL suggests that > " Atom indices are fragile and will change as atoms are added > or deleted. Whenever possible, use integral atom identifiers > instead of indices. " > > > I suppose you should use>>RANK<<, if you like to "find a way to get the > 'linenumber-dependent' index of an atom". > > cheers, > Hongbo Zhu > > > On 11/01/2010 10:02 AM, Martin Hediger wrote: >> Hi Tsjerk, >> I am still wondering about how the numbering is done. >> Given a PDB file looking like this (some random molecule): >> >> HETATM 1 C LIG 1 -4.242 2.555 -0.814 1.00 0.00 C >> HETATM 2 C LIG 1 -2.736 2.361 -0.665 1.00 0.00 C >> HETATM 3 H LIG 1 -4.461 3.588 -1.106 1.00 0.00 H >> HETATM 4 C LIG 1 -4.961 2.214 0.487 1.00 0.00 C >> HETATM 5 H LIG 1 -4.615 1.908 -1.617 1.00 0.00 H >> HETATM 6 H LIG 1 -2.333 3.133 0.004 1.00 0.00 H >> HETATM 7 H LIG 1 -2.247 2.493 -1.637 1.00 0.00 H >> HETATM 8 C LIG 1 -2.409 0.977 -0.105 1.00 0.00 C >> HETATM 9 H LIG 1 -4.728 2.975 1.243 1.00 0.00 H >> HETATM 10 C LIG 1 -4.549 0.837 1.003 1.00 0.00 C >> HETATM 11 H LIG 1 -6.045 2.243 0.329 1.00 0.00 H >> HETATM 110 N LIG 1 -3.097 0.727 1.164 1.00 0.00 N >> HETATM 13 H LIG 1 -4.907 0.053 0.324 1.00 0.00 H >> HETATM 14 H LIG 1 -5.027 0.653 1.972 1.00 0.00 H >> HETATM 15 H LIG 1 -1.329 0.896 0.057 1.00 0.00 H >> HETATM 16 H LIG 1 -2.677 0.200 -0.831 1.00 0.00 H >> HETATM 17 H LIG 1 -2.789 1.419 1.847 1.00 0.00 H >> >> What PyMOL-function returns me the 'physical' index in the array of >> atoms? So for atom '12' (nitrogen), (with label '110') I would like '12' >> displayed in the PyMOL viewer. Right now, 'ID' displayes '110', 'RANK' >> displays '11' and 'INDEX' displayes '1'. >> >> After deleting row 4, again for atom labeled '110' nitrogen, 'ID' >> displayes '110', 'RANK' displayes '10' and index displayes '1'. >> >> I'm not sure now if this is in agreement with what we have said so far. >> What I dont like too much about relying on 'ID' is the fact that if the >> labels get changed (or none are present), its not possible to tell >> anymore which atom has which index. Thats why i was hoping to find a way >> to get the 'linenumber-dependent' index of an atom. >> >> Thanks for your help so far. >> >> Martin >> >> >> > ------------------------------------------------------------------------------ > Nokia and AT&T present the 2010 Calling All Innovators-North America contest > Create new apps& games for the Nokia N8 for consumers in U.S. and Canada > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store > http://p.sf.net/sfu/nokia-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
