Hey Martin, rank? I didn't know that one :p Checking your structure, it seems to me that:
ID is the numbering as in the PDB file rank is a numbering from 1 to N, following the order of atoms in the PDB file index is an internal index to an array that contains the atoms, sorted by element The index changes when atoms are deleted, whereas the ID and the rank do not. Loading the structure to two different objects, gives the exact same labels: load lig.pdb, lig1 load lig.pdb, lig2 label all, "%d-%d-%d"%(ID,rank,index) I don't think I can help you much further than this :S Maybe Jason can shed some more light on the issue. May the source be with you. Tsjerk On Mon, Nov 1, 2010 at 10:02 AM, Martin Hediger <ma....@bluewin.ch> 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 > > > > > On 31.10.10 18:31, Tsjerk Wassenaar wrote: > > Hi Martin, > > So it seems I was right :D > > ID is an atomic property, read from the PDB file, whereas index is an > 'internal' identifier. Following Jasons comments, ID is not changed upon > additions/deletions, whereas index does. > > For your purpose, you probably want to make sure that the IDs are identical > for corresponding atoms. > > Hope it helps, > > Tsjerk > > On Oct 31, 2010 3:35 PM, "Martin Hediger" <ma....@bluewin.ch> wrote: > > Hey, Thanks for your earlier response on the issue. > Its quite important to me right now, since I am trying to interpolate > between two states of the same structure and therefore (let me call it > 'physical') atom numbering has to be perfectly identical. > I looked into it but i cant quite get my following observation into > agreement with what you said. > I have a PDB file with 920 atoms. Starting from the top, with no 'TER' or > 'MODEL' or other PDB syntax elements, on line 909 of that file an ATOM is > stated (hydrogen), with the number '909' at the "line-909".split()[1] > position. > When I open the file in PyMOL and let it display LABELS>ATOM_IDENTIFIERS>ID, > I get '909' displayed in the model. Changing the value at '909' in the PDB > file to 950, reloading and redisplaying the 'ID' labels, presents '950' also > in the PyMOL viewer, even if the ATOM is still on line 909 in the PDB file. > How can this behavior be explained with regard to what we were talking about > previously? What label-type is required to display the actual, > non-label-dependent index of the atom in the system? Does the functionality > depend on whether there are more detailed atom descriptors available, like > residue type or chain id? > > Thanks one more time for any help on this. > Martin > > > > > > > > Am 25.10.10 17:03, schrieb Jason Vertrees: > >> > Hi Martin& Tsjerk, > > There is a another difference between the two >> > aside from the > off-by-o... -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ------------------------------------------------------------------------------ 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
