Hi Thomas, To have same stick size for hydrogens, set stick_h_scale to 1.0, see: https://pymolwiki.org/index.php/stick_h_scale
I don't think that PyMOL's behavior for loading multi-entry .sdf files has changed. If get the same behavior in 1.7.2.1 and any other version. The entries are loaded into one object as discrete states, with the same (carbon) color. Adding hydrogens to discrete objects was never supported. Are you sure you didn't load .sdf files "multiplexed" in the past? This would split the states into individual objects. load targets.sdf, multiplex=1 If your example really behaves different in 1.9 and 1.7, then it would be great if you could send me the input files. Thanks, Thomas > On Dec 14, 2017, at 9:18 AM, Thomas Strunz <beginn...@hotmail.de> wrote: > > I've upgraded some of the users to version 1.9.0.0 due to moving to windows > 10. It's the build from Christoph Gohlke. > > We use it mainly for one purpose and to make it easier I created a short pml > script to load the data and apply settings. However pymol doesn't behave the > same anymore. > > The script: > > reference.sdf > targets.sdf > preset.pretty(selection='all') > set valence, 1 > set stick_radius, 0.2 > > In version 1.7.2.1 this would load the 2 files and all mols in file 2 had a > different coloring than in file 1. Also hydrogen hat the same stick size as > the other bonds. I could go to hide/show to remove/add the hydrogens. > > In Version 1.9.0.0 this is different: > > • all molecules have the same color. Changing color isn't applied > automatically anymore > • The hydrogen sticks are tiny. how do I make them the same size again? > (least important issue) > • If I hide all the hydrogens I can't make them appear again. > For 3: there is no options unde rshow menu to show the hydrogens again. If I > go to Action menu and add hyrodgens I get an error: > AddHydrogens-Error: can't modify a discrete object. > > So how can i show hide hydrogens? > > Thanks for the help. > > Thomas -- 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
