Hi Jared, Thanks for your help. I have two issues with this script:
1. It only works once after I've started pymol; the second time, python.exe crashes. 2. It does create an object with *distances*, not the actual residues. Your other solution with the single word selectors should work but I'll need to refine it ;-) Cheers Markus From: Sampson, Jared [mailto:jared.samp...@nyumc.org] Sent: Thursday, October 16, 2014 6:36 AM To: Markus Heller Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Show all residues forming H-bonds 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> 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 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> 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 ------------------------------------------------------------------------------ Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? 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