Hi Chi, The file needs a .py extension to be recognized as a Python script. Microsoft Windows can be tricky when it comes to changing a file extension. I recommend to follow these steps when downloading a Python file from the PyMOLWiki:
1) Visit https://pymolwiki.org/index.php/Get_raw_distances 2) Box on the right side, right click on "Download get_raw_distances.py" 3) "Save Link As..." or "Save target as..." (depends on browser) File name: get_raw_distances.py Save as type: PY File Hope that helps. Cheers, Thomas > On May 19, 2017, at 9:41 PM, Chi Celestine <chi.celest...@phys.chem.ethz.ch> > wrote: > > Dear Thomas, > Many thanks! I copied and saved the script as a dot txt but can not run it > from file> run on pymol. Do I need yo save the file in a special folder? I > am actually really new with pymol and not vey good in scripting > > Thanks for your understanding > > Sincerely > Chi > ------------------------------------------------- > 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 5:33 PM, Thomas Holder <thomas.hol...@schrodinger.com> >> wrote: >> >> 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
