> You can bypass the requirement for having secondary structure in the PDB
> file by explicitly assigning secondary structure using the alter command.
Ah. This is probably what I was looking for.
> PyMOL just stores one bit of secondary structure information per residue
> (the "ss" property of the CA atom). Just remember to set cartoon mode to
> "auto" after making changes in order to force an update of the graphical
> cartoons.
How does this affect movies involving conformation changes? Secondary
structure info from the first frame appears to carry over into the others-
whereas in reality some helixes or sheets change to varying degrees. This
leads to warping in something like calmodulin. Would I need to render
frames separately and run 'alter'?
> It should be pretty straighforward to write a Python script which
> assigns secondary structure based on any file format. Of course, from a
> Python python script, the above commands would look like
Definitely a good idea, since I'm using a combination of Perl and Python
with many intermediate files right now, and the result is not pretty. I'd
much rather do everything in Python (which, unfortunately, I'm much less
familiar with).
However, I'm finding that using PyMOL as a module is failing. I built
from source and have everything installed in /usr/local/python, and when I
try to do 'from pymol import cmd, util' I get this:
Traceback (most recent call last):
File "./render.py", line 7, in ?
import pymol
File "/usr/local/pymol/modules/pymol/__init__.py", line 24, in ?
import _cmd
ImportError: shared object not open
I do have /usr/local/python/modules in the shared library path
(/etc/ld.so.conf under SuSE 7). I'm not quite sure what's going on... all
I really need to do is execute a .pml file and run a few system calls for
now, until I create something more rigorous.
thanks,
Nat
