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