[modeller_usage] Modelling of a copper binding cluster

Dear all,

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!

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))

Any guidance that could be given on this problem would be much appreciated!

Regards

Stephen Hearnshaw