Dear Germana,
I am not really sure if you wish to extract the solvent exposure of residues
from a given model or use solvent exposure of the template residues as an
additional restraint in the target building. The latter is not an implemented
idea in MODELLER, there are only distance, angle, dihedral angle, pairs of
dihedral angles, distance of gravity centers and minimal distances between
pairs of atoms as possible retraint types and some other more complicated
restraints depending on the previous list as forcing certain secondary element
formation etc. But if you are just interested in obtaining the various
solvent accessibilities of the model atoms/residues than it is done as you
already indicated in your top file:
WRITE_DATA FILE = 'test' , OUTPUT='psa'
in the output file test.sol and test.psa and according to the
ACCESSIBILITY_TYPE variable as the fourth column in the model file.
best wishes,
Andras
"M. Germana Paterlini" wrote:
>
> How do I (or is it possible to ) to specify the solvent
> accessibility of residues with ACCESSIBILITY_TYPE in
> MAKE_CONSTRAINTS ?
> Is there a specific RESTRAINT_TYPE associated with it ?
>
> Here is my input
>
> # Test for restraints on accessibility (?)
> READ_TOPOLOGY FILE '$(LIB)/top_heav.lib'
> READ_PARAMETERS FILE ='$(LIB)/par.lib'
> SET ATOM_FILES_DIRECTORY = './' READ_MODEL FILE = 'test.ent',
> MODEL_SEGMENT = '1:' '7:' SEQUENCE_TO_ALI ATOM_FILES = 'test.ent',
> ALIGN_CODES = 'test.ali' SEQUENCE_TO_ALI ADD_SEQUENCE = on ,
> ATOM_FILES = ATOM_FILES 'test.ini', ;
> ALIGN_CODES = ALIGN_CODES 'test-ini'
> GENERATE_TOPOLOGY SEQUENCE = 'test-ini'
> TRANSFER_XYZ BUILD_MODEL
> INITIALIZE_XYZ = off
> WRITE_MODEL FILE 'test.ini'
> SET ACCESSIBILITY_TYPE = 8
> MAKE_RESTRAINTS RESTRAINT_TYPE = 'sphere'
> WRITE_RESTRAINTS FILE = 'test-1.rsr'
> ENERGY DYNAMIC_SPHERE = off
> ENERGY
> WRITE_DATA FILE = 'test' , OUTPUT='psa'
>
> Thanks
> Germana Paterlini
>
> Department of Medicinal Chemistry
> University of Minnesota
> Minneapolis, MN 55455
--
,
Andras Fiser, PhD # phone: (212) 327 7206
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras