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, index))' % i)
print stored.pairs
If you run the above code you will obtain a list of tuples, each tuple
contains the indexes of the pairs Pd-Si atoms (fulfilling the "within 2.5
A" criteria). Then you should iterate over "stored.pairs" to create the
bonds between the atoms in each pair. Something like this:
for pair in stored.pairs:
cmd.bond('index %s' % pair[0], 'index %s' % pair[1])
Cheers,
Osvaldo.
On Thu, May 28, 2015 at 7:37 AM, Tobias Martin <mar...@chemie.uni-kl.de>
wrote:
> 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 long, unwanted bonds.
> I tried to iterate over the first selection, to draw only
> bonds between an Pd atom and Si atoms which are within
> range to that Pd atom like
>
> iterate (n. pd), bond id ID, (n. si) within 2.5 of (id
> ID)
>
> but get an syntax error. Is it possible to create bonds
> within an iteration?
>
> Best regards,
> tmartin
>
>
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