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" <war...@delanoscientific.com> 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:war...@delanoscientific.com
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax (650)-593-4020
>
>
>> -----Original Message-----
>> From: pymol-users-ad...@lists.sourceforge.net
>> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
>> Tony Giannetti
>> Sent: Monday, May 10, 2004 12:25 PM
>> To: pymol-users@lists.sourceforge.net
>> 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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