Hi Daniel,
yes, it it.
You have a backbone only trace in one template and another template with full atom details but you wish to use only the sidechain conformations from this latter one to build a model which then can be refined further on.
At some point you will need to optimise the model with the nmr derived backbone traces and the side-chain conformers coming from the different source, because you can not expect that they will perfectly fit in the new environment.
Maybe the simplest way to account for the information coming from the two sources is simply use both templates (one which has only backbone information and the other one with full atom details) then let Modeller do to combine the different information. Since the two templates will have identical sequences to each other and to the target the restraints derived from the two templates will be weighted equally.
A more sophisticated approach is to redefine a routine which is responsible for extracting the restraints from the templates in such a way, that from one template (let us call it for further reference "daniel_MNCH_only.pdb" you extract the mnch restraints while from the full atom template ("daniel_SCDH_only.pdb") you extract the side chain restraints only which will be combined and refined in the model. So you construct an alignment with the two templates and the target (daniel_MNCH_only.pdb, daniel_SDCH_only.pdb and target.pdb). All the three sequences are identical. Then you write the standard model building routine using these two templates but in the top file include additionally the routine below to redefine the restraint extraction. The template names must be replaced (at several places) in the routine below accordingly, (and be identical in the above mentioned alignment file.)
SUBROUTINE ROUTINE = 'mkhomcsr'
MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo', ADD_RESTRAINTS = OFF
### MNCH restraints! READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = daniel_MNCH_only.pdb SEQUENCE MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_RESTRAINTS = ON SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.3, SPLINE_MIN_POINTS = 5 MAKE_RESTRAINTS RESTRAINT_TYPE = 'omega_dihedral', ADD_RESTRAINTS = ON
### SDCH restraints ! READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = daniel_SDCH_only.pdb SEQUENCE MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi1_dihedral', ADD_RESTRAINTS = ON MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi2_dihedral', ADD_RESTRAINTS = ON MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi3_dihedral', ADD_RESTRAINTS = ON MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi4_dihedral', ADD_RESTRAINTS = ON
### MNCH restraints!!! READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = daniel_MNCH_only.pdb SEQUENCE SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.7, SPLINE_MIN_POINTS = 5 # Only do the standard residue types for CA, N, O, MNCH, SDCH dst rsrs # (no HET or BLK residue types): SET RES_TYPES = 'STD'
SET DISTANCE_RSR_MODEL = 5, MAXIMAL_DISTANCE = MAX_CA-CA_DISTANCE SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = on SET RESTRAINT_GROUP = 9 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA' PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA' MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAINTS = 'ON'
SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_N-O_DISTANCE SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = off SET RESTRAINT_GROUP = 10 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'N' PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'O' MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAINTS = 'ON'
### MNCH restraints !!! READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = daniel_MNCH_only.pdb SEQUENCE
SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-MC_DISTANCE SET RESIDUE_SPAN_RANGE = 1 2, RESIDUE_SPAN_SIGN = off SET RESTRAINT_GROUP = 23, RESTRAINT_STDEV = 0.5 1.5 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH' PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'MNCH' MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAINTS = 'ON'
SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-SC_DISTANCE SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = on SET RESTRAINT_GROUP = 26, RESTRAINT_STDEV = 0.5 2.0 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH' PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'SDCH' MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAINTS = 'ON'
# Generate intra-HETATM and HETATM-protein restraints: CALL ROUTINE = 'hetatm_restraints'
# Generate intra-BLK and BLK-protein restraints: CALL ROUTINE = 'blk_restraints'
# Special restraints have to be called last so that possible cis-proline # changes are reflected in the current restraints: CALL ROUTINE = 'special_restraints'
CONDENSE_RESTRAINTS WRITE_RESTRAINTS FILE = CSRFILE SET RESIDUE_SPAN_RANGE = -999 -999, RESIDUE_SPAN_SIGN = on
RETURN END_SUBROUTINE
best,
Andras
Daniel John Rigden wrote: > > Hi everyone > > Is it possible to get MODELLER to transfer side chain conformations to a > new backbone? > > I have some backbone traces derived from dynamic studies. I'd like to > transfer the side chains from the original structure prior to refinement > and further studies. > > Any help much appreciated. > > Thanks > > Daniel Rigden > > +-------------------------------------------------------------------------+ > | Dr Daniel John Rigden | > | CENARGEN/EMBRAPA | e-mail: daniel@cenargen.embrapa.br | > | Parque Estacao Biologica | http://www.cenargen.embrapa.br | > | PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741 | > | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3624 | > +-------------------------------------------------------------------------+