Re: [PyMOL] How to select nucleic/protein separately
Dear PyMOL people, Please can anyone tell me if there's any way to draw/ray so that a selection exactly fills the frame? At the moment, I'm using `zoom complete=1` (restricted to the protein) and then I'm auto cropping the resulting image (with `convert -trim`). This is solution is good enough but please can anyone tell me if there's a better way I could be doing it? Many thanks for any help. Tony Lewis On 30 November 2017 at 12:00, Tony Lewis wrote: > Dear PyMOL people, > > Please can anyone tell me if there's a standard way to select either of > nucleic / protein separately? > > I can use `polymer` to get both together but I can't see a standard way > to distinguish nucleic / protein within that. > > I'm currently using something like `resn A+C+G+U+DA+DC+DG+DT` to identify > nucleic but that's inadequate because it misses out various resn values (eg > BRU, OMG etc) that are part of modified DNA/RNA. > > The thing is: PyMOL clearly *knows* which bits are protein versus nucleic > because it draws the cartoons accordingly. So it feels like I should be > accessing this info from PyMOL rather than trying to hack together a list > of resn values. > > -- 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
Re: [PyMOL] Upgraded from 1.7 to 1.9: Different behavior
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 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
[PyMOL] Upgraded from 1.7 to 1.9: Different behavior
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: 1. all molecules have the same color. Changing color isn't applied automatically anymore 2. The hydrogen sticks are tiny. how do I make them the same size again? (least important issue) 3. 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 -- 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
