Dear Marco,
It is possible to restrain any kind of spatial restraint (angle, distance etc.) in Modeller, using external data from experimental results (additional NMR constraints) or some preliminary knowledge as in your case.
e.g. in your case you can introduce distance restraints among the three residues. the easiest way is to include in your top file a redefined SPECIAL_RESTRAINTS routine, with the desired values and parameters.
I include an example below, which restrains 2 distances between atoms of residues 166 and 336 and 191 and 336.
For the details of the parameters, please look up the manual. #################### SUBROUTINE ROUTINE = 'special_restraints' ADD_RESTRAINT ATOM_IDS = 'NH1:166' 'O1:336',; RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1 ADD_RESTRAINT ATOM_IDS = 'NE2:191' 'O4:336',; RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1
RETURN END_SUBROUTINE #################
Andras
MarcoBocola wrote: > > Hello from Marburg, > > I want to do homology modelling on serine hydrolases with highly > conserved > fold and reasonable AA-identity. > So the difficulty is to model the active site correctly with respect to > the catalytic triade and the backbone nitrogens in the oxyanion hole. > > These few amino acids should be overlayed as exact as possible. > > Is there a straightforward way to contstrain modeller only for these > higly conserved topology of the catalytic residues within one Angstroem, > thus remaining the catalytic hydrogen bond network intact. > > Any hints on possible protocolls appreciated. > > Marco