How large is large? With enough RAM, PyMOL can do molecular surfaces up to perhap a hundred thousand atoms or so, but above that, you probably need to fall back on Gaussians as illustrated in the script below:
Cheers, Warren # load a whopping big PDB load one_million_atoms.pdb, struct spectrum count, selection=struct # give ourselves a responsive UI as spheres set sphere_mode,1 # === now create a pseudo-fcalc map (a 3D volumetric scalar field) === # set the B-factors nice and high for smoothness alter all, b=40 # ~10 A map resolution set gaussian_resolution, 10 # ~10 A map spacing with a 10 A surrounding buffer # (you may need to vary this) map_new map, gaussian, 10, struct, 10 # create a surface from the map isosurface surf, map, 1.0 # now color the map based on the underlying protein ramp_new ramp, struct, [0,10,10], [-1,-1,0] color ramp, surf disable ramp -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com > -----Original Message----- > From: Crystal K. Chuang [mailto:ckchu...@lbl.gov] > Sent: Tuesday, December 16, 2008 5:11 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] PyMol memory vs. computer memory > > Hello, > > When I try to add a surface to a very large structure and > PyMol gives me the error message "PyMol just ran out of > memory and crashed...." am I receiving this message due to > limitations of the PyMol program, or do I need to install > more memory on my computer? > > Thanks > -Crystal > > > > -------------------------------------------------------------- > ---------------- > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las > Vegas, Nevada. > The future of the web can't happen without you. Join us at > MIX09 to help pave the way to the Next Web now. Learn more > and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009 .visitmix.com/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
