[PyMOL] pymol on OS 10.1

[<wg...@ch...>]

Hi Warren, et al:

I just returned from a conference where I gave my first pymol-based 
presentation on an ibook G3 500MHz using the native version (the 
X-windows version, as previously noted, was impossibly slow).  I have to 
say it was a resounding success.  I used it to present both structures 
with electron density maps from a variety of viewpoints and then also to 
show several movies of 5 states sampled from the hammerhead ribozyme 
reaction coordinate.  It worked really really well, but I could use 
advice on how to do a couple of things more intelligently:

1.  I used pymol in conjunction with a powerpoint presentation.  I found 
the quickest way to do this was to have pymol open simultaneously with 
powerpoint, and to use the escape key to toggle back and forth.  I tried 
using a hyperlink to a one-line applescript I wrote to launch pymol with 
a script of what I planned to show, but this approach was much slower.  
Has anyone found a better way to do this, so I can get an essentially 
instantaneous hyperlink?

2.  I noticed that the electron density carving seemed a bit buggy, and 
I only got it to work by putting the map in in 3 pieces.  When I tried 
to cover the whole molecule at once the program seg faults.  I used the 
same map, I just covered it in 3 pieces rather than 1 and it seemed to 
work fine.  This happened with two structures having the same sequence, 
yet the approach that worked for the first didn't work for the second, 
so I spent about 2 hours hunting for the magic combination that 
prevented pymol from crashing.  Is this a known bug, my idiocy, or what?

3.  Using RNA, if I try to draw a bond between O2' of one residue and 
O2' (for example) of another, it does not work, but a bond between two 
O2s work fine.  I also found this failed when I edited the pdb file to 
be either some letter to replace the prime or an *.  I tried \ to no 
avail.  Is this a bug or am I doing something stupid again?

Otherwise it was great, and after about 2 or 3 hours of work, I found 
the absence of an external GUI to be more of a help than a hinderance as 
it forced me to learn the command language with all of its functionality.

This is a superb program.  Thank you so much for doing this.  Is it 
possible to buy an academic license as a mechanism for sending some 
financial support from my very modest grant?

Bill Scott