RE: [modeller_usage] More Doubts - missing aminoacids in template

["Schweikardt, Thorsten" <>]

Hi Elton, 

please take a look at your template-pdb file, it does not
begin with aminoacid 2, but with aminoacid 16; same problem
for the ending aminoacid. You have to make sure your alignment
and pdb-file contain the same aminoacids. If the xray structure
analysis does not reveal all aminoacids, you have to correct
the alignment before modelling. If you want to know which aa
are missing, extract the sequence of the existing aminoacids
in the pdb-file with Modeller or DeepView (File-save-Sequence)
and compare it to the sequence you are using.

Happy modeling,

Thorsten Schweikardt
Molecular Biophysics
University of Mainz


 
> Dear Mr. Schweikardt and others,
> 
> I'm trying to model another protein (HSP) and I'm having 
> trouble again.
> Please look the second line of my alignment file
> structureX:1uy7:2:A:236:A:::-1.00:-1.00
> 
> I have followed your previous instructions for the Prion 
> protein and it doesn't
> seem to work out. Can you help me again?
> The files (.ali .log .top and) are compressed by tar -cvzf command.
> 
> Best regards,
> 
> Vasconcelos, EJR 
> 
>