inger.com]
> Sent: Thursday, May 28, 2015 9:17 AM
> To: Osvaldo Martin
> Cc: Tobias Martin; pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] create bonds between selections within cutoff radius
>
> Hi Osvaldo,
>
> your solution can be simplified if you use cmd.find_p
mas Holder [mailto:thomas.hol...@schrodinger.com]
Sent: Thursday, May 28, 2015 9:17 AM
To: Osvaldo Martin
Cc: Tobias Martin; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] create bonds between selections within cutoff radius
Hi Osvaldo,
your solution can be simplified if you use cmd.find_pa
Hi Thomas,
You're absolutely right. I had completely forgotten the find_pairs
function! Thanks for the clarification.
Cheers,
Osvaldo.
On Thu, May 28, 2015 at 10:17 AM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:
> Hi Osvaldo,
>
> your solution can be simplified if you use cmd.fin
Hi Osvaldo,
your solution can be simplified if you use cmd.find_pairs:
http://pymolwiki.org/index.php/find_pairs
Cheers,
Thomas
On 28 May 2015, at 09:06, Osvaldo Martin wrote:
> Hi Tobias,
>
> One possible solution will be to run the following code.
>
> import pymol
> from pymol import cm
Hi Tobias,
One possible solution will be to run the following code.
import pymol
from pymol import cmd, stored
stored.pd = []
stored.pairs = []
cmd.iterate('name pd', 'stored.pd.append(index)')
for i in stored.pd:
cmd.iterate('name si within 2.5 of index %s' % i,
'stored.pairs.append((%s,
I want to create bonds between e.g. all Pd atoms and all
Si atoms, but only within a specified cutoff radius.
bond (n. pd), (n. si) within 2.5 of (n. pd)
creates all possible bonds between all Pd atoms and all Si
atoms near enough to any Pd atom. This yields a weired
structure with very l
