Hi Jason, I see you have hash_max set to 400 -- that's the problem.
In empirical testing, I found that there is rarely a reason to go above 200 with this setting. Having a hash table that is too finely sampled is no better than having one too coarsely sampled. PyMOL's default of 100 is intended to avoid running out of RAM on systems with just 256 MB. If you have more RAM, then going up to 150 or 170 is usually worth it. 250 may sometimes be helpful, but 400 is almost certainly overkill. Because this is a 3D hash table, each 2X increase can potentially involve an 8X increase in memory required. set hash_max,200 set antialias,1 produces the following image in 204 seconds using 948 MB of RAM on a dual G5 http://delsci.com/img/scene1.jpg with "set light, [-0.4,0.4,-1]": http://delsci.com/img/scene1_flip_light.jpg You can mellow out that techno-green and give your scene a more natural feel with: set ray_blend_green, 0.4 set ray_blend_colors, on http://delsci.com/img/scene1_mellow.jpg And then, it helps to back off on the green color itself, so that those spheres don't look so over-lit: set_color green, [0.25,0.75,0.25] rebuild Now you've got a reasonably balanced image... http://delsci.com/img/scene1_final.jpg Cheers, Warren > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Jason Vertrees > Sent: Saturday, April 24, 2004 11:03 PM > To: PyMol Users List > Subject: [PyMOL] Does (PDB) size really matter? > > Warren, > > Thanks! I was setting 'hash_max' higher and higher (but my > memory monitor always showed at least 90 megs free at the > least). I'll try the lower hash_max; I'll try lower this time. > > I think we have a really great movie in the works, and as I > play with PyMol more and more, I can make much cooler things. > You've got some great software here! > > My 0.96b2 PSE file is bzipped, for all to download, at > http://www.vertrees.org/~tree/scene1.pse.bz2 it's about 2.7 > MB; The 0.95 PSE file is > http://www.vertrees.org/~tree/095_scene1.pse.bz2. > atom_count is about 85,000 for them. > > The movie script is as in the previous message. > > As of now, I'll try smaller hash_max's and also if that's not > good, reduce the size of my circular lipid bilayer. > > Many thanks for the quick response! > > Regards, > > -- Jason > > > -- > Jason Vertrees > BSCB Graduate Student @ UTMB, Galveston > javer...@utmb.edu :: http://www.bscb.utmb.edu > > > ------------------------------------------------------- > This SF.net email is sponsored by: The Robotic Monkeys at ThinkGeek > For a limited time only, get FREE Ground shipping on all orders of $35 > or more. Hurry up and shop folks, this offer expires April 30th! > http://www.thinkgeek.com/freeshipping/?cpg=12297 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
