Aha, that makes sense now. Would it be worth to clarify this in the pymolwiki (http://www.pymolwiki.org/index.php/Show)? That's where I got my version from ...
Cheers Markus -----Original Message----- From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] Sent: Thursday, October 16, 2014 10:44 AM To: Markus Heller Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] h_add breaks surface? Hi Markus, > # hide non-polar hydrogens > hide (h. and (e. c extend 1)) This will hide all representations -- including surface -- for non-polar hydrogens. I guess what you rather want is to remove those non-polar hydrogens, so that they will not be included in the surface calculation. # remove non-polar hydrogens remove (h. and (e. c extend 1)) Hope that helps. Cheers, Thomas On 16 Oct 2014, at 13:34, Markus Heller <mhel...@cdrd.ca> wrote: > Thomas, > > If you comment out the h_add line in the pml script below, the surface looks > good. If it's in there, it's broken for me. > > Cheers > Markus > > <broken_surf.pml> > > # load the PDB file > fetch 3CIY, async = 0 > > # add hydrogens > h_add > > # hide everything but show cartoon > hide lines > #as cartoon > > # show protein surface > show surface, all > > # deselect all to avoid little pink squares deselect > > # hide non-polar hydrogens > hide (h. and (e. c extend 1)) > > # finally, raytrace and save a PNG > ray > png broken_surf.png > > </broken_surf.pml> > > -----Original Message----- > From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] > Sent: Wednesday, October 15, 2014 4:18 PM > To: Markus Heller > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] h_add breaks surface? > > Hi Markus, > > I can't reproduce this. Do you have an example? > > Thanks, > Thomas > > On 15 Oct 2014, at 18:32, Markus Heller <mhel...@cdrd.ca> wrote: > >> Hi all, >> >> I updated to 1.7.2.3. I noticed that >> >> h_add >> >> breaks the surface rendering for me, meaning the surface representation >> shows lots of holes/missing parts (before and after ray). It doesn't matter >> if h_add is placed before or after the surface is generated. >> >> Has anybody else noticed that, or does this occur just for me? >> >> Thanks >> Markus >> >> -- >> Markus Heller, Ph.D. >> NMR Scientist >> CDRD - The Centre for Drug Research and Development >> 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: >> (604) 827-1147 >> Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | >> www.cdrd.ca -- Thomas Holder PyMOL Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho _______________________________________________ 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
