Re: [modeller_usage] question about unusual bond length, bond angle, Chirality deviations
To: "Song, Hyundeok (songhk)" <>
Subject: Re: [modeller_usage] question about unusual bond length, bond angle, Chirality deviations
From: Modeller Caretaker <>
Date: Thu, 15 Apr 2010 13:24:54 -0700
Cc: "" <>
On 04/14/2010 08:08 PM, Song, Hyundeok (songhk) wrote:
After alignment, I used loop patch to generate the model. I thought
using loop modelling gives more accurate structure for homology
modelling.
No, loop modeling will probably give better structures for the loop
regions than regular homology modeling, since homology modeling doesn't
do any refinement of the loops. But it won't affect the aligned regions
at all.
When I checked model pdb structure, it gave the warning
message "unusual bond length, bond angle, Chirality deviations". I
think this error comes from 70 fasta sequence length difference
between model and template as suggested from Modeller Caretaker.
Your original question suggested you had a single 70-residue long loop.
Looking at your alignment, I now see that that's not the case - you have
several shorter loops. Thus there aren't really any parts of the
template you can remove.
My question: In order to generate best model from Modeller, which
residues of template should I delete?
It depends on what you want to use the model for. It may be that the
warning you're getting can be ignored. Or you have several loops in your
structure, so you should concentrate your loop refinement on just the
loops that you are most interested in (for example, loops that are close
to a ligand binding site or an interface region). Just doing default
loop modeling will try to simultaneously refine all of the loops.