Check this page:
http://pymol.sourceforge.net/newman/user/S0220commands.html
On the middle of the page.

you would probably need:
select id 2338 or
select index 2338  (Probably this)

The id, is the id number which is provided external in the pdb file. Normally the column after "ATOM".
Beside the id number, pymol assign an internal index.
This is handsome, if your xyz file, pdb file does not have an id.

 

Troels Emtekær Linnet
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Mobil:
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2011/8/22 Yotam Avital <yotama9@gmail.com>
The xyz file format opens easily with pymol (pymol fileName.xyz).  I can find the id that pymol gives to the ``atom'' via the GUI but I don't know what to do with it. I tried select 2338 (a valid number) but I get

Selector-Error: Invalid selection name "2338"

2011/8/22 Troels Emtekær Linnet <tlinnet@gmail.com>
Is this a .pdb file which can be opened with pymol?

Can you provide a file that pymol accepts?
Can you in some way find the id number?
Check out these commands in pymol:


print cmd.get_names()
print cmd.get_pdbstr("chain A")
print cmd.get_pdbstr("chain A").splitlines()
print cmd.get_pdbstr("chain A").splitlines()[3]
print cmd.identify("chain A and name N")[0]
print cmd.identify("chain A and name C")[-1]

Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE
04107 Leipzig, Tyskland
Mobil:
+49 1577-8944752



2011/8/22 Yotam Avital <yotama9@gmail.com>
Hi. 

I have a xyz file in the following form:

C    0     0     0
O    0     0     1
O    0     0     2
C    0     0     6
O    0     0     5
O    0     0     4
.
.
.

How can I select an atom from the list? How can I measure an atom from that list?
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