[modeller_usage] Disulfides

[Joel Tyndall <>]

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.

Many thanks

J

--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand                     

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa

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Attachment: rec_modelII.BL00030001.pdb
Description: application/save-as

INCLUDE
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'
STOP
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'
RETURN
END_SUBROUTINE