Hi Celestine, Did you run the "get_raw_distances.py" script first? You can do that by:
run https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py Or better: Download it to your computer and run it from there ("run" command or "File > Run Script..." from the menu). After running the script, you can use the "get_raw_distances" command. Cheers, Thomas > On May 19, 2017, at 2:26 PM, Chi Celestine <chi.celest...@phys.chem.ethz.ch> > wrote: > > Hi Thomas, > I am also interesting in getting bond distances between two pairs of > molecule. I tried running the commands to suggested but I get an error > message e.g > When I tried the following (see below) the fist command was well executed but > the second gave an error message “ SyntaxError: invalid syntax” > > I got a similar error message when I tried to execute this command D = > get_raw_distances("distname”) as well > > > Sincerely, > Celestine > > Example > fetch 2xwu, async=0 > > > > # interface polar contacts > distance iface_hbonds, chain A, chain B, mode=2 > > > > # dump (model,index) information > get_raw_distances iface_hbonds > > > ------------------------------------------------- > Celestine Chi, PhD > ETH Zürich > Laboratory for Physical Chemistry > Vladimir-Prelog-Weg 2 HCI F 222 > CH-8093 Zürich > Email: chi.celest...@phys.chem.ethz.ch > tele: 004144 63 37510 > >> On May 19, 2017, at 1:16 PM, Thomas Holder <thomas.hol...@schrodinger.com> >> wrote: >> >> Hi Ahmad, >> >> Unfortunately there is no proper API for this. But I can think of two >> approaches. Note that the results can differ because the two method do >> slightly different h-bond detection! >> >> 1) Use "cmd.find_pairs" with mode=1 on "donors" and "acceptors" selection. >> Example: >> >> sele1 = "chain A & (donors | acceptors)" >> sele2 = "chain B & (donors | acceptors)" >> radius = 3.5 >> D = cmd.find_pairs(sele1, sele2, mode=1, cutoff=radius) >> print("number of h-bonds:", len(D)) >> >> 1) Use "cmd.distance" and the "get_raw_distances" script. Example: >> >> run >> https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py >> >> sele1 = "chain A" >> sele2 = "chain B" >> radius = 3.5 >> cmd.distance("distname", sele1, sele2, mode=2, cutoff=radius) >> D = get_raw_distances("distname") >> print("number of h-bonds:", len(D)) >> >> See also: >> https://pymolwiki.org/index.php/Get_raw_distances >> https://pymolwiki.org/index.php/Distance >> https://pymolwiki.org/index.php/Find_pairs >> >> Hope that helps. >> >> Cheers, >> Thomas >> >>> On May 5, 2017, at 5:08 AM, Ahmad Abdelzaher <underoath...@gmail.com> wrote: >>> >>> I know I can can find the hydrogen bond interactions between a >>> selection and surrounding residues within a certain radius. I would >>> like to find a way to retrieve the actual count of those interactions >>> per residue. How can I do it in the API? >>> >>> Regards. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
