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Re: [modeller_usage] Modelling a multiheme cytochrome

> Many thanks for your previous help with my copper binding proteins
> and I will apologies in advance for the length of this query!  I
> require some guidance with a modelling problem I am having.  I am
> attempting to model the structure of a 258 residue segment of a
> decaheme cytochrome, I have template models covering the positions of
> the 10 hemes and the first 223 residues.  I have also implemented
> several distance and bond angle restraints on the heme binding
> residues in an attempt to correctly orientate them around the hemes,
> however when I run modeller some of the restraints don’t seem to take
> affect.  A specific example is residue 258 that (if I have
> implemented the script correctly) should be within 2.0A of the Fe
> atom from heme 268, however, in the final model it is 50A away from 
> the heme and has been pulled 50A  apart.
> The following is the complete script I have used for my modelling
> attempts:

The script looks fine to me, except for the second 'select_atoms'
function at the end of the script. You never call that function, so it's
redundant and can be removed. (The first select_atoms method should do
the correct thing though; the second uses the obsolete pick_atoms
method, so wouldn't work if you called it anyway.)

You should check to make sure your restraints are acting on the correct
atoms. Check the residue numbers and chain IDs against those in the
MtrA.ini file.

Check the log file to see violations of your restraints. The restraints
may be being violated if they clash with other restraints on the system.
For example, Modeller already builds a set of restraints on your ligands
and the protein-ligand distances to maintain template coordination; see
http://salilab.org/modeller/9v6/manual/node65.html. If these restraints
conflict with your own then you may want to override the
nonstd_restraints method.

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage