[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] missing residues



On 5/4/12 12:22 AM, Mary Varughese wrote:
Did you mean that i should edit the template(for missing residues) pdb
so that it contains the co-ordinates of the missing residues only.
Yes (plus a few extra either side of the insertion). Since the alignment 
file must match the sequence in the *entire* PDB file, either you need 
to include the unused PDB sequence in the alignment (just misalign it so 
Modeller doesn't use it in the model - see FAQ #2) which can be a little 
awkward, or modify the PDB to remove the unused residues.
But what you mean by overlap the regions a little so that modeller can
figure out the conformation of the missing regions?
If you look at the alignment in my previous email, you'll see that the 
model is aligned with both A and B for two residues on each side of each 
insertion. If you don't do that, Modeller won't know how to connect the 
missing regions with the rest of the protein.
	Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage