Hi Fabrice, Interesting observation. PyMOL reads "metalc" bonds from mmCIF files and represents them as "zero order" bonds. Apparently this breaks double bond detection in your given example. This is something we need to fix.
Possible workarounds: 1) Load .pdb files instead of .cif files 2) Load .mmtf files, they have full bonding information, including bond orders 3) Load .cif files, but with connect_mode=4, which looks up all bond orders from the chemical components dictionary Relevant settings: https://pymolwiki.org/index.php/Fetch_type_default https://pymolwiki.org/index.php/Connect_mode Cheers, Thomas > On Mar 15, 2018, at 5:55 PM, Fabrice Carles <carlesfabr...@gmail.com> wrote: > > Dear pymol users, > > I would like to know if there is a way to change pymol2 settings in order to > fit older version. > > My problem is very simple. Pymol 2 and pymol 1.8 do not provide the same > results. > > I download and select the ATP molecule in both pymol 1.8.6.0. and 2.0.7: > > cmd.fetch('1atp') > cmd.select('lig','organic') > > Pymol 1.8.6.0 detect three double bonds between phosphate and oxygen of ATP > molecule but pymol2 does not. > Using the command below, I compare the differences between the two versions > in sdf file format. > > cmd.save('atp.sdf',selection='lig') > > diff 1atp_pymol1.8.sdf 1atp_pymol2.sdf > 2c2 > < PyMOL186 3D 0 > --- > > PyMOL2.0 3D 0 > 18,19c18,19 > < 11.1000 9.8800 -1.4300 O 0 5 0 0 0 0 0 0 0 0 0 0 > < 13.9290 9.9200 -2.7000 O 0 5 0 0 0 0 0 0 0 0 0 0 > --- > > 11.1000 9.8800 -1.4300 O 0 0 0 0 0 0 0 0 0 0 0 0 > > 13.9290 9.9200 -2.7000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 24c24 > < 15.7480 6.8350 -0.4270 O 0 5 0 0 0 0 0 0 0 0 0 0 > --- > > 15.7480 6.8350 -0.4270 O 0 0 0 0 0 0 0 0 0 0 0 0 > 38c38 > < 1 18 2 0 0 0 0 > --- > > 1 18 1 0 0 0 0 > 41c41 > < 2 19 2 0 0 0 0 > --- > > 2 19 1 0 0 0 0 > 47c47 > < 3 24 2 0 0 0 0 > --- > > 3 24 1 0 0 0 0 > > > > How can I force pymol2 to write exactly the same sdf as before ? > Is there new defaults settings in pymol2 that I can override ? > > Thanks, > > Fabrice > > Fabrice Carles - PhD student > Structural Bioinformatics & Chemoinformatics, > Institut de Chimie Organique et Analytique (ICOA) > > University of Orleans - France -- 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
