Re: [modeller_usage] modeling homodimer with hetero atoms
To: NUTAN CHAUHAN <>
Subject: Re: [modeller_usage] modeling homodimer with hetero atoms
From: Modeller Caretaker <>
Date: Fri, 18 May 2012 08:09:06 -0700
Cc: "" <>
On 5/18/12 1:20 AM, NUTAN CHAUHAN wrote:
I am trying to model a homodimer with heteroatoms from a homodimer
template. when make homodimer without heteroatoms it goes fine but when
i try to build homodimer with heteroatoms it doesn't run and shows some
errors regarding alignment mistakes.
OK, so the problem is your alignment doesn't match your PDB. You just
need to fix that.
What should be the alignment look like?
The alignment looks fine, but of course you didn't attach your PDB file
so there's no way to independently tell whether they match. But the
Modeller error message below looks pretty clear to me:
Alignment .....PDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKH
PDB ....PDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHE
Match ***** * * *
(The formatting got a little messed up in the email, but if you look in
the original log file it should be lined up properly.) You have one more
'.' in your alignment file in the B chain than you have in the PDB.
Either you deleted one too many HETATM residues from your PDB file, or
you added one too many to your alignment file.