Tony,
Try reducing the hash_max variable by a factor of 2, 3, or 4. The
problem with large spheres is that a separate hash entry is created for each
hash cell within the sphere -- that's technically wrong, but it is how
PyMOL's naïve algorithm currently works. As a result, you can easily exceed
available RAM, which results in a crash.
Cheers,
Warren
--
mailto:[email protected]
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: [email protected]
> [mailto:[email protected]] On Behalf Of
> Tony Giannetti
> Sent: Tuesday, May 11, 2004 3:01 PM
> To: [email protected]
> Subject: Re: [PyMOL] Creating cell surface
>
> Thanks to Warren's help I was able to create a nice CGO
> sphere that makes a convincing cell membrane. And for most
> of today I was even able to render molecules placed near the
> membrane, AND it even created shadows on the CGO surface cast
> by the molecules.
>
> However, after a couple of hours it seems to have stopped working.
> Initially it would think about it and then crashn. Now,
> whenever I hit 'ray' when the large cgo sphere is on-screen
> it automatically crashes PyMol.
> I'm doing this on our lab's dual G5 using MacPyMol. I went
> back to my laptop, which was rendering the sphere just fine
> last night, and now it automatically crashes when I try to
> render just the sphere. I installed a fresh version of PyMol
> on the G5 (by unpacking the archive again) and that didn't
> help either, nor did rebooting the machine.
>
> Any ideas? I'm on a tad bit of a deadline and would like to
> get this rendered soon, preferably with the shadows. I don't
> have the patched version of pov-ray at the moment and anyways
> the output from PyMol was looking really good before it acted
> all weird.
>
>
> On 5/10/04 1:12 PM, "Warren DeLano"
> <[email protected]> was all
> like:
>
> > Tony,
> >
> > In order to enter multi-line Python code on the command
> line, you need
> > to use explicit end-of-line continuations. Otherwise, PyMOL won't
> > know where your Python code stops and PyMOL commands again begin.
> >
> > from pymol.cgo import *
> > from pymol import cmd
> >
> > set cgo_sphere_quality, 3
> >
> > def cgo_sphere(x,y,z,r,name="cgo_sphere"): \
> > # Create a CGO object \
> > obj = [ \
> > SPHERE, float(x), float(y), float(z), float(r) \
> > ] \
> > # Load it into PyMOL \
> > cmd.load_cgo(obj,name)
> >
> > # Add to PyMOL command language
> > cmd.extend("cgo_sphere",cgo_sphere)
> >
> > # end Python, begin PYMOL commands
> >
> > cgo_sphere 0,0,0,500,test
> >
> > --
> >
> > For example, I can paste the above directly into the PyMOL command
> > line (on win32), in order to get a sphere on the screen.
> >
> > A better alternative it to simply put all of that Python
> code into a ".py"
> > file and "run" it from within PyMOL.
> >
> > NOTE: PyMOL doesn't currently render large and small
> objects together
> > very efficiently, and there's precious little that you can
> do about it
> > at the present time. Increasing hash_max won't help, though
> > decreasing it can give a modest gain in performance.
> Sticking exclusively to CPK can also help.
> >
> > Cheers,
> > Warren
> >
> > --
> > mailto:[email protected]
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> > DeLano Scientific LLC
> > Voice (650)-346-1154
> > Fax (650)-593-4020
> >
> >
> >> -----Original Message-----
> >> From: [email protected]
> >> [mailto:[email protected]] On Behalf Of Tony
> >> Giannetti
> >> Sent: Monday, May 10, 2004 12:25 PM
> >> To: [email protected]
> >> Subject: [PyMOL] Creating cell surface
> >>
> >> Hey Fellow PyMolers,
> >> I should be able to figure this out but I simply haven't after
> >> much fiddling and googling. I'm trying to create a cell
> surface for
> >> a cover figure and in Molscript I usually did this by making a PDF
> >> file with a single atom, rendering it in CPK, and then blowing its
> >> atom_radius way up to several thousand angstroms to create
> a slightly
> >> curved surface on which molecules could be positioned.
> >>
> >> I'm trying this in PyMol and can't figure out the command sequence.
> >> Basically, how do I alter the radius for a single atom, especially
> >> because I don't want all atoms I draw as a surface to have
> the same
> >> radius?
> >>
> >> Alternatively I've been trying to do this with the CGO
> utility using
> >> one of Gareth's scripts I found on the web:
> >>
> >> from pymol.cgo import *
> >> from pymol import cmd
> >>
> >> def cgo_sphere(x,y,z,r,name="cgo_sphere"):
> >>
> >> # Create a CGO object
> >> obj = [
> >> SPHERE, float(x), float(y), float(z), float(r)
> >> ]
> >>
> >> # Load it into PyMOL
> >> cmd.load_cgo(obj,name)
> >>
> >> # Add to PyMOL API
> >> cmd.extend("cgo_sphere",cgo_sphere)
> >>
> >>
> >> But in adding these lines sequentially to the PyMol
> command line, or
> >> running it as a script, it fails at:
> >>
> >> def cgo_sphere(x,y,z,r,name="cgo_sphere"):
> >>
> >> and I get the following error message
> >>
> >> def cgo_sphere(x,y,z,r,name="cgo_sphere"):
> >> Traceback (most recent call last):
> >> File
> >> "/Users/delwarl/pymol/products/MacPyMOL.app/pymol/modules/pymo
> >> l/parser.py",
> >> line 144, in parse
> >> exec(com2[nest]+"\n",pymol_names,pymol_names)
> >> File "<string>", line 1
> >> def cgo_sphere(x,y,z,r,name="cgo_sphere"):
> >> ^
> >> SyntaxError: unexpected EOF while parsing
> >>
> >>
> >> Is there some other way the script is supposed to be used. .
> >> .I'm using
> >> MacPyMol 0.95.
> >>
> >> Thanks for any tips/help.
> >> Tony
> >>
> >>
> >>
> >>
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> >
> >
> >
> >
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>
>
>
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