Figures of proteins - Figures of proteins (Dec/09/2005 )

I wonder where can i get this kind of figure (see below) or other related figure types for a protein?

Which database to use?




Thank you.

depends on what you want

i use expasy.org as database, download .pdb file with coordinates for protein of interest, than swissprotpdbviewer to arrange everything (colours etc.). as additional step i use povray (a raytracer) to brush up the quality and that's it.

swissprot PDB viewer is easy to use, and you can do a lot with, like calculate distances between two residues, with Chimera (you can download from UCSF website), you will have a nice molecule to show. the software is a little heavier, I only use it to show the molecule for a presentation for example and use the other one to think about the molecule.

here you can find the PDB number of your molecule of interest :http://www.infobiogen.fr/srs71bin/cgi-bin/wgetz?-page+query+-newId+-l+pdb

once you have the number, you can fetch the PDB file from internet using the PDB number and chimera software.

have a lot of fun

I wonder where can i get this kind of figure (see below) or other related figure types for a protein?

Which database to use?




Thank you.

i didn't know chimera, looks like a really powerful program. thank you very much laurence for this tip

depends on what you want

i use expasy.org as database, download .pdb file with coordinates for protein of interest, than swissprotpdbviewer to arrange everything (colours etc.). as additional step i use povray (a raytracer) to brush up the quality and that's it.

http://www.expasy.org/spdbv/

the documentation is quite okay, you'll understand how to do that stuff, if special problem ask again.

Hi,

if you want a quick solution then use VMD or Rasmol.... these are much smaller than the fantastic Swiss Deep View but should allow you to produce images without having to learn a complicated package.

VMD is extra nice as it is simple and allows you to do the PovRay trace which allows you to make images far more impressive than the one shown above.

The new PDB site provides images of all structures, generated by a variety of molecular viewing programs. http://pdbbeta.rcsb.org/pdb/Welcome.do

Personally I can't stand the swiss deepview or whatever it is called. I use Pymol instead.