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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