Hi Markus -
First, you need to run the python script from the wiki page (save it as, e.g.
polarpairs.py). Then, to run pure Python code within a pml file, you’ll need
to enclose those lines in a python block
(http://www.pymolwiki.org/index.php/Python) using ‘python’ and ‘python end’.
For example, to list all the H bonds between chains A and B:
###
run path/to/polarpairs.py
python
# the example from http://www.pymolwiki.org/index.php/Polarpairs
pairs = polarpairs('chain A', 'chain B')
for p in pairs:
dist = cmd.get_distance('(%s`%s)' % p[0], '(%s`%s)' % p[1])
print p, 'Distance: %.2f' % (dist)
python end
###
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Oct 15, 2014, at 6:17 PM, Markus Heller
<mhel...@cdrd.ca<mailto:mhel...@cdrd.ca>> wrote:
Jared,
I'm a newbie to pythom/PyMOL; how do I get this to work in a pml script? A
pointer to an example script would be enough .
Thanks
Markus
From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Friday, October 10, 2014 4:17 PM
To: Markus Heller
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] Show all residues forming H-bonds
Actually, an even better option is Thomas' polarpairs.py script:
http://www.pymolwiki.org/index.php/Polarpairs, which considers the H-bond angle
as well as distance.
Apologies for the multiple emails, but I hope that is closer to what you're
looking for.
Cheers,
Jared
On Oct 10, 2014, at 7:10 PM, Sampson, Jared
<jared.samp...@nyumc.org<mailto:jared.samp...@nyumc.org>> wrote:
Hi Markus -
Ah, sorry, I misunderstood your request at first.
What about the "acceptors" and "donors" selectors?
http://www.pymolwiki.org/index.php/Single-word_Selectors
e.g.
select hbond_residues, byres ((acceptors within 3.5 of donors) or (donors
within 3.5 of acceptors))
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Oct 10, 2014, at 6:41 PM, Markus Heller <mhel...@cdrd.ca> wrote:
Hi Jared,
Thanks for the reply.
This is NOT what I'm looking for. As you stated, distance mode 2 yields the
*distances* as dashes, but not the actual residues. I don't want the dashes,
but I want the residues (i.e. the donors and acceptors) in selectable objects.
I hope it's clearer now what I'm after .
Cheers
M
From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Friday, October 10, 2014 3:33 PM
To: Markus Heller
Subject: Re: [PyMOL] Show all residues forming H-bonds
Hi Markus -
Under the GUI "action" menu A > find > polar contacts, you'll find several
options which will create a new object with all the specified distances as
dashes.
This is also available with `distance` command.
http://www.pymolwiki.org/index.php/Distance
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Oct 10, 2014, at 2:45 AM, Markus Heller <mhel...@cdrd.ca> wrote:
Hello list,
subject says it all. The 2 options I came across search the www are:
http://sourceforge.net/p/pymol/mailman/message/7562444/http://sourceforge.net/p/pymol/mailman/message/7562444/
and DistancesRH
(http://www.pymolwiki.org/index.php/DistancesRH)http://www.pymolwiki.org/index.php/DistancesRH
Is this current state-of-the-art, true-and-tried, or is there something more
powerful hiding out there?
Thanks
Markus
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