Markus, I'll create an account for you. Cheers, Thomas
On 20 Oct 2014, at 14:33, Markus Heller <mhel...@cdrd.ca> wrote: > Would if I could. > > How do I sign up for the PyMOLWiki? > > THanks > Markus > > -----Original Message----- > From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] > Sent: Thursday, October 16, 2014 1:48 PM > To: Markus Heller > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] h_add breaks surface? > > 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
