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Re: [modeller_usage] Modelling of a copper binding cluster

 wrote:

I require some guidance with a modelling problem I am having.  I am
attempting to model a short 11 residue sequence around a template taken
from the small molecule database:

ATOM      1  SG  CYS A   1       4.774   5.927   9.587  1.00  0.00
ATOM      2  CB  CYS A   1       4.175   7.673   9.917  1.00  0.00
ATOM      3  SG  CYS A   2       5.091   3.544   6.534  1.00  0.00
ATOM      4  CB  CYS A   2       6.560   3.252   7.614  1.00  0.00
ATOM      5  SG  CYS A   3       1.160   3.172   6.513  1.00  0.00
ATOM      6  CB  CYS A   3       0.028   2.178   7.542  1.00  0.00
ATOM      7  SG  CYS A   4       0.936   5.818   9.617  1.00  0.00
ATOM      8  CB  CYS A   4      -0.419   4.795  10.238  1.00  0.00
ATOM      9  SG  CYS A   5       2.942   2.405   9.819  1.00  0.00
ATOM     10  CB  CYS A   5       4.547   1.918  10.664  1.00  0.00
ATOM     11  SG  CYS A   6       2.713   6.590   6.171  1.00  0.00
ATOM     12  CB  CYS A   6       2.800   5.754   4.601  1.00  0.00
HETATM   13 CU   CU1 A   7       2.896   4.649   9.731  1.00  0.00
HETATM   14 CU   CU1 A   8       4.201   5.454   7.463  1.00  0.00
HETATM   15 CU   CU1 A   9       3.182   2.965   7.621  1.00  0.00
HETATM   16 CU   CU1 A  10       1.497   5.188   7.518  1.00  0.00
END

I require the first 4 CYS residues of the template structure to align with
4 CYS residues from my query sequence (as shown in the following
alignment), and for the orientation of these residues around the copper
cluster to be maintained


P1;TemplateTest

Structure:templatetest:1:A:10: : : : :
C-C-----C-CCC....*

P1;Ace1

Sequence:Ace1: : : : : : : :
CRCDEGEPCKC--....*

I have performed an unrestrained alignment that produced a model, but was
unable to keep the CYS residues in the correct orientation and moved the
polypeptide 80A away from the copper cluster!
See http://salilab.org/modeller/9v6/manual/node65.html for the restraints Modeller generates on ligands. The main protein-ligand restraints are on ligand-CA distances and your template has no CA atoms, so none of these will be restrained. You will have to add your own restraints, either manually or by using Restraints.make_distance(). 


Attempts to restrain the system, by putting distance restraints between
the SG atoms of the CYS residues and coppers have been unsuccessful.  The
following is an example of the commands I have been trying as a distance
restraint.

        rsr.add(forms.upper_bound(group=physical.xy_distance,
                               feature=features.distance(at['CU:7:A'],
                                                         at['SG:1']),
                               mean=2.28, stdev=0.01))
It's hard to say what your problem is without seeing your full script, but what I can say is that unless you have done something very unusual, that restraint won't work! By default Modeller numbers residues sequentially starting from 1 in the model (it does not use the template numbering) and if you have only a single chain, by default it gives it no chain ID. So there is no 'CU:7:A' atom in the model - your Cu resides will be labeled 12 through 15.
Given that you are presumably running this script without seeing any errors, that suggests that your restraints are not being added. Maybe you have made a "MyModel" subclass but are mistakenly using the regular automodel rather than your new MyModel class later in the same script? 

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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