Re: Restraining a disulphide bridge

-- Roberto Sanchez, Assistant Professor Structural Biology Program, Department of Physiology & Biophysics and Institute for Computational Biomedicine, Mount Sinai School of Medicine Box 1677, 1425 Madison Avenue, New York, NY 10029 phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://physbio.mssm.edu/~sanchez/ Marc BAADEN wrote: > 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 > >