Shamelessly hijacking this thread...
...but the index page for the Wiki
http://www.pymolwiki.org/index.php/Category:Commands has not been updated for
the last 10 year, according to the footer. In other words the "find_pairs"
function is not on the index. Makes me wonder, what else is missing?!
What is the current status with regards to updates on the Wiki? Is there anyone
from the community with time and capability willing to take this up and
maintain this resource or are we just letting this wither away?
Cheers,
Carsten
-----Original Message-----
From: Thomas Holder [mailto:[email protected]]
Sent: Thursday, May 28, 2015 9:17 AM
To: Osvaldo Martin
Cc: Tobias Martin; [email protected]
Subject: Re: [PyMOL] create bonds between selections within cutoff radius
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 <[email protected]> wrote:
> 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 <[email protected]>
> 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
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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