Hi folks (& Ben),
I have been building some models with disulfide patches. One of the
disulfides presents a model with basically bad geometry (cys66-cys40)
which is troubling. I have attached model and top file. (I'm using 8.2
with old style formats).
Any suggestions as to how to rectify this (fix the geometry)? I'm trying
to gauge which is the appropriate disulfide connectivity between this
model and another and this ain't helping the cause.
Joel Tyndall, PhD
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Ph / Waea +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034
SET ALNFILE = 'MIS_rec_modelII.ali'
SET KNOWNS = '2hlq_a'
SET MD_LEVEL = 'refine_1'
SET SEQUENCE = 'MIS_rec_modelII'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 5
SET DEVIATION = 4.000000
SET DO_LOOPS = 1
SET RADII_FACTOR = 0.915
SET LOOP_STARTING_MODEL = 1
SET LOOP_ENDING_MODEL = 5
SET LOOP_MD_LEVEL = 'refine_2'
SET HETATM_IO = on
CALL ROUTINE = 'model'
SUBROUTINE ROUTINE = 'special_patches'
PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '34' '58'
PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '3' '39'
PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '40' '66'