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.hed@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...