unknown at dl.ac.uk wrote:
: Hi, we have recently ftp'ed a copy of the "kinemages" software.
: The Structure viewer is working fine on the Tour files provided as examples
: alongwith the package, but we are having problems with running the Kinemage
: Constructor. Kindly let us know about the kind of inputs that are required
: for getting a file which can be viewed as a kinemage.
The program PREKIN makes a kinemage from a PDB file. That is, the protein
structure you want to watch must be available in the Brookhaven Protein
Database (all the published structures are or will be). You can access
the PDB by anonymous ftp or by gopher. They also sell the database on
tape or CD-ROM (sorry, don't know mail address).
To get really nice kinemages, you usually have to change the output
from PREKIN by hand. The documentation is rather flaky about the
various parameters, so you have to try (the last time I fiddled
with PREKIN output was about half a year ago). The PREKIN output
is a normal text file so you can change it with any text editor.
If you run into troubles it usually helps to have a look at the
pre-made kinemages which come with the KINEMAGE package.
Something which I did not figure out is how to superimpose two
related structures to compare them. The last version of PREKIN
which I have seen did not support this but it would be a really
nice feature. Maybe somebody out there in netland has written
software which superimposes two given structures, either in
PDB or Kinemage format?
Hope that helps a little,
/* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */
/* email: krasel at alf.biochem.mpg.de fax: +49 89 8578 3975 */
/* "People are DNA's way of making more DNA." (R. Dawkins/anonymous) */