sure, you are welcome to update the PyMOLWiki page. Cheers, Thomas
On 16 Oct 2014, at 15:57, Markus Heller <mhel...@cdrd.ca> wrote: > 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
