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
