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 a
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 ra
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 ind
Hi Tsjerk,
I am still wondering about how the numbering is done.
Given a PDB file looking like this (some random molecule):
HETATM1 C LIG 1 -4.242 2.555 -0.814 1.00
0.00 C
HETATM2 C LIG 1 -2.736 2.361 -0.665 1.00
0.00 C
HETATM3
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 identica
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 follo
Hi Martin & Tsjerk,
There is a another difference between the two aside from the
off-by-one characteristic. PyMOL has to keep track of atoms, so a
simple 'index' could work. But, then when the user removes an atom
from the middle of a structure, do we shift indices above it down?
(This could mak
Thanks Tsjerk (on both occasions).
As a matter of fact, I'm kind of making a living out of writing a Python
script once in a while, so thats no worry ;)
What I was trying to get at was that I was trying to understand how
certain PyMOL scripts work, and naturally from that become able to
improve
Never get used to that only-reply-to-sender policy...
-- Forwarded message --
From: Tsjerk Wassenaar
Date: Mon, Oct 25, 2010 at 12:30 PM
Subject: Re: [PyMOL] What is the difference between Atom ID and Index
To: Martin Hediger
Hi Martin,
ID is indeed the atom id from the coord
