[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: Restraining a disulphide bridge



Dear Marc,

Did you add the PATCH command within the 'special_patches' routine? You should have something like this in your top file (Please see FAQ #6 in the modeller manual).

SUBROUTINE ROUTINE 'special_patches'
  PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '487' '494'
END_SUBROUTINE

This should work even if you have missing atoms in one of your CYS residues.

Best Wishes,

Roberto

--
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