Subject: Re: [modeller_usage] prb encountered, plz help
From: Modeller Caretaker <>
Date: Sun, 24 Apr 2005 11:44:42 -0700
Cc:
rathankar rao wrote:
i had to model a protein whose ali file, top file and the log files are
present here. i couldnt model it and its always presenting some or the
other errors plz help
The error is:
pdbnam__217W> Filename for PDB code not found: 1ocs
This simply means that your PDB file has the wrong name. It should be
called 1ocs.pdb or similar (pdb1ocs.ent, 1ocs.atm are also valid names).
there was one problem in the pdb file,:
a ligand cme under the name of the heteroatom, had a residue number as
91 , which was supposed to be a number for the aminoacid. the next
residue thus continued from 92 and so on. so i changed the residue
numbers by 1. i changed the ligand atom number also as 1191 instead of
91 so that it is distinguished from the other aminoacids. despite all
these it dosent work.
There shouldn't be any need to renumber residues in your PDB file. Just
make sure you have the correct residue numbering and chain labels in
your alignment file.
i have one more doubt , if at all the protein as many chains then how do
i model it. what is the command which is used to model a protein with
chains.
You don't have to do anything special, although you should separate the
sequences for the chains in your alignment file by chain break (/)
characters.