Dear Professor Sali,
although I tried to thoroughly read through your documentation,
and found several references (and examples) to patching disulphide
bridges, I could not get it to work for my particular case.
I tried to use Modeller v6a (but we also have Modeller4 in the lab,
if that would make any difference).
My case might be a bit special:
I have got an Xray structure, with missing sidechains+residues.
One Cysteine is present, the second missing, There are only 2 in
the structure, and there has to be a disulphide bridge between
them.
I only need a homology model where missing residues and sidechains
are completed. So my usual modeller script looks like this:
INCLUDE
SET ALNFILE = '1fep.ali'
SET KNOWNS = '1fep_xr'
SET SEQUENCE = '1fep_ok'
SET ATOM_FILES_DIRECTORY = '.'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 10
SET DEVIATION = 2.0
SET RAND_SEED = -12312
CALL ROUTINE = 'model'
Using xray coordinates from 1fep_xr.atm.
Now I wanted to add something like
PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '487' '494'
which leads to an error of
Run READ_TOPOLOGY and GENERATE_TOPOLOGY first.
Now I wonder, is this the right way to add my disulphide restraint ?
If yes, then what kind of topology should I use and how ?
Do I need to build an initial complete model first, and my 10 models
afterwards ?
Thank you very much in advance,
Best wishes,
Marc Baaden
--
Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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