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
