[PyMOL] secondary structure and many more questions

[Jason Y. <jk...@br...>]

Hello All,
    I had a few questions:

1) Is there a way to find out what secondary strucuture has been 
assigned by the automatic algorythem?
I assume there must be a python command that will dump the output of the 
utility to the screen or to a file.


2) Is there any information available for any of the other util programs?

3) Is it possible to color the chain by B-factor?

4) I have a heme moiety, I can get the program to display the FE atom, 
but I'm not sure how to increase the sphere size of the atom so that I 
can exagerate it, it is possibe? something close to the set atomradius 
command in molscript.

5) For some strange reason it recognizes the Nitrogens on the heme 
differently and colors some of them blue and others pink. I tried to 
manually set it like I could for the Fe, but I think that I am not 
getting the atom type/name correct. Is there a list of atom names?

6) Is there a way to make a C-alpha trace? other than ribbons something 
that will draw straight bonds between C-alpha's?

7)  Is it possible to change the color of the mesh (not the isomesh) 
relatve to helix color ie what are the command line commands. I have 
tied color red, mesh and that didn't seem to work, same question for the 
surfaces as well.

8) Is it possible to have a "ball and stick" representation?

9) What is the command to output a pov ray file?

10) How do you get two color helicies, ie the equivalent to planecolour2 
in molescript?


So far the program is running great. The stereo works very well for me. 
I have it running on a dual AMD athlon 1.4GHz, with an Oxygen GVX1 
graphics card and 1 gig of  DDR ram under the Windows 2000 pro OS.


Thanks,


Jason Yano