By default, current versions of PyMOL excludes PDB HETATMs from surface
calculations. The idea behind this is to enable you to easily surface
the protein away from solvent and ligands. To change this:
set surface_mode=1
which will cause all atoms to be included.
Cheers,
Warren
PS. surface_mode
If you can't get Premiere, the only options I know of are mpeg_encode
(any unix) or mediaconvert (IRIX specific). Unfortunately, both of
these produce noticably inferior results when compared to AVI (Cinepak)
or Quicktime (Sorenson).
Anyone know of a respectable freeware solution for making movie
Yes: use animated GIF!
Very simple to make and you can stick it into your webpages without any
horrible platform-specific plugins - it'll just start running straight
away. They also work in PowerPoint (if you really insist on using that
program).
You can make them with the ImageMagick package, wit
> 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
A great answer for intranets and PowerPoint presentations! Thanks
Daan...
You can assemble these on the fly with ImageMagick, but I've found it
takes two passes. One to make the gif, and a second to adjust the frame
rate. The whole movie assembly process can then be reduced to a single
PyMOL scr
I tried the gifmerge which worked just fine.
Thanks
Abhinav
-Original Message-
From: Daan van Aalten [mailto:d...@davapc1.bioch.dundee.ac.uk]
Sent: Wednesday, February 13, 2002 1:50 PM
To: DeLano, Warren
Cc: Abhinav Kumar; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] RE: Pymol
