That's pretty slick.
Alternatively you can delete the "drawn bonds" using the builder module. Then
show nb_sphere for the Fe atom. If you have access to the CSD I would grab one
from there
Hope this helps
From: Troels Emtekær Linnet [mailto:[email protected]]
Sent: Tuesday, 12 February 2013 3:17 a.m.
To: Edward Deira
Cc: [email protected]
Subject: Re: [PyMOL] representing ferrocene in pymol
How about.
import select_sites
sites 1a3l
set_bond stick_radius, 0.1, resi 213
extract Fe_atom, resi 213 and name Fe
Wiki
http://www.pymolwiki.org/index.php/Select_sites
http://www.pymolwiki.org/index.php/Set_bond
Best
Troels
Troels Emtekær Linnet
Ved kløvermarken 9, 1.th<http://1.th/>
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Mobil: +45 60210234<tel:%2B45%2060210234>
2013/2/11 Edward Deira <[email protected]<mailto:[email protected]>>
Dear all,
How can I "accurately" represent ferrocene in pymol, without using CONECT lines
in the pdb file ?
By "accurately" I mean at least including the C-C bonds; I'd rather not have
any Fe-C bonds, but if they are present I can live.
I've been trying to figure out how to do this using atom selections, or trying
to get gonds between the nonbonded...
Any hints are welcome,
all the best
Ed.
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