> Pymol isn't very good at handling many spheres. Slanderous! ...but true with default settings. However:
./pymol -O 1 monster_large_file.pdb Will enable PyMOL to display, manipulate, and render at least a million spheres per GB of RAM. Also try -O values up through 5 for alternate approaches for handling large numbers of spheres. -O 5 uses a shader program on cards which support it in to create pixel-perfect OpenGL spheres. (BTW that's a capital O, not a zero). Cheers, Warren > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Tsjerk Wassenaar > Sent: Friday, July 28, 2006 1:14 AM > To: philippe.garteise...@ou.edu > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] problem: choking on big files > > Hi Philippe, > > Pymol isn't very good at handling many spheres. However, > Povray is extremely efficient with raytracing scenes > consisting of spheres and if you know the perspective you > want to have the image from, you can convert your atom set to > spheres (with desired radii) and apply the view from Pymol. > If you would like, I can send you the script (Povray > macro) to export the Pymol view to Povray. > > Best regards, > > Tsjerk > > On 7/25/06, philippe.garteise...@ou.edu > <philippe.garteise...@ou.edu> wrote: > > Hi again, list. > > > > I need help on how to render an unconventional > (non-protein) pdb file with a big number of atoms in it. Even > with no display (console mode), pymol still crashes due to > insufficient memory. > > A different hardware is out of the question and a smaller > file would defeat my purpose, so I would like to simplify the > representation. What i do is to 'show sphere', then 'set > sphere_scale,0.01'. However, it seems it takes the same > amount of memory for pymol to display small or large spheres > (i thought that by using very small sphere_scale, pymol would > tend to treat each atom more and more as a single pixel). The > dots representation is also very complex to display I > believe. In my case the line display can not be used either. > > > > Are there some settings to increase the memory allocated to pymol ? > > Are there settings of the dots representation so that only > one dot is represented for each atom ? > > Any additional ideas are of course welcome ! > > > > Thanks in advance ! > > > > Garteiser Philippe > > OMRF, Cardiovascular Biology dpt. > > Doctoral candidate, OU Bioengineering > > Advisors: Dr. Tim Mather, Dr M. Uli Nollert 12600 N Macarthur Crown > > Pointe apt. #1423 Oklahoma City, OK 73142 > > home: (405) 603 7091 > > work: (405) 271 4924 > > > > "It does not pay to leave a live > > dragon out of your calculations" > > - Tolkien > > > > > > > > > > > ---------------------------------------------------------------------- > > --- Take Surveys. Earn Cash. Influence the Future of IT Join > > SourceForge.net's Techsay panel and you'll get the chance to share > > your opinions on IT & business topics through brief surveys -- and > > earn cash > > > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEV > > DEV _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > -- > > Tsjerk A. Wassenaar, M.Sc. > Groningen Biomolecular Sciences and Biotechnology Institute > (GBB) Dept. of Biophysical Chemistry University of Groningen > Nijenborgh 4 9747AG Groningen, The Netherlands > +31 50 363 4336 > > -------------------------------------------------------------- > ----------- > Take Surveys. Earn Cash. Influence the Future of IT Join > SourceForge.net's Techsay panel and you'll get the chance to > share your opinions on IT & business topics through brief > surveys -- and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge > &CID=DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
