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
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2013/2/11 Edward Deira <[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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