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: |
> | 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 |
> +-------------------------------------------------------------------------+
--
,
Andras Fiser, PhD # phone: (212) 327 7206
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras