Dear PyMOLers,
You might remember that some time ago I posted a message asking whether
it was possible to make PyMOL display nucleic acids similarly to
Ribbons (i.e. with backbone and bases represented by a ribbon and
cylinders, respectively).
At the time there was unfortunately no simple way of doing so, however,
Kevin Weeks later on kindly suggested me a first way to display base
cylinders within PyMOL.
Based on Kevin's suggestion, I have now written a program - nuccyl -
that allows to get the kind of representation we were looking for in a
semi-automated way. As usual, pictures are much more meaningful than
words, so you can see what I mean by having a look at some examples
(static pictures and downloadable PyMOL session files) here:
http://www.mssm.edu/students/jovinl02/research/nuccyl.html
As explained much more throughly on the same page, which includes a
step-by-step tutorial, you can either use RNAView to identify base
pairs in your nucleic acid, or manually write a simple file containing
this information. nuccyl will use this data to calculate coordinates
for base cylinders which can be then displayed by PyMOL.
If you are interested, you can download the program from the same link.
I hope you will find nuccyl useful; please let me know of any problem
you encounter, and of course suggestions and criticisms will always be
welcome.
Ciao,
Luca
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Luca Jovine, Ph.D.
Brookdale Department of Molecular, Cell & Developmental Biology
Mount Sinai School of Medicine
Annenberg Building, Room 25-18
One Gustave L. Levy Place, New York, NY 10029-6574, USA
Voice: +1.212.241-8620 FAX: +1.509.356-2832
E-Mail: lucajov...@mac.com - luca.jov...@mssm.edu
W3: http://www.mssm.edu/students/jovinl02
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