software for making a model of a protein

Maryam via methods%40net.bio.net (by mzargh from yahoo.ca)
Sat May 5 07:46:23 EST 2007


Also good tutorials are available online for Pymol or Rasmol.

DK <dk from no.email.thankstospam.net> wrote:  In article , Maryam wrote:
>Check out Rasmol or Pymol.
>Mr Urpradiap wrote: Dear NG.
>I am looking for a graphic tool/software to make a model of how I think 4 
>domains of a protein resides together in the overall fold of the protein. I 
>am not looking for an advanced tool to make docking of proteins or any other 
>calculations on how the domains could fit together. I am simply looking for 
>a 3D graphic tool where i can build my hypothetical model (publication 
>grade). If I was good at paintshop I would have made the model from the 
>ground here (but I am not). I have the four domains as PDB files, that might 
>make things a bit easier?

Yes. In this case the simplest is to get Coot (google it), load your four
PDBs, use rotate/translate zone on each (after selecting first and last 
residue) to make your model, save the result, load the result into
Pymol (google it) and Pymol will make a pretty pic for you. 

Obviously, there is some learning curve involved. The easier
solution would be to find a crystallographer who can spend an hour
with you making a model and a picture of it. (Although be prepared 
for some unpleasant comments about the value of the model 
obtained this way). 

DK
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