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rebuild.pl
Usage
usage: rebuild.pl [options] [ -pdb file | seq chain ]
options: [-l refpdb min:max[=min:max...]] [-fixca]
[-r resolution] [-o offsetx offsety offsetz]
Description
Rebuilds an all-atom representation from a low resolution SICHO
protein model based on side chain centers. Either a sequence file
in MONSSTER format (see: genseq.pl)
and a SICHO chain file with the model coordinates or, if the flag
-pdb is given, a pseudo-PDB file
with side chain centers and optional C-alpha atoms (see: genchain.pl)
are required as arguments.
The following additional options are available: The -l option can be used
or loop modeling to provide template coordinates from a PDB file and a range
of residues. Only the specified residues are then rebuilt while the template structure
is used to provide coordinates for the remaining residues.
The options -r and -o relate to the representation of the
input chain. A different resolution of the lattice projection (other than the
MONSSTER default of 1.45 Å) can be specified with -r. With the
option -o it is possible to shift the input chain in lattice units
before the reconstruction. This may be useful for loop modeling when the chain
was shifted as a whole during lattice-based modeling and has to be shifted back
before it can be matched with the original PDB template.
No further minimization is done with this script. Subsequent minimizations of the
output generated with this script using minCHARMM.pl
or minAmber.pl is recommended to obtain structurally and
energetically improved reconstructions.
Options
- -help
- usage information
- -pdb file
- read chain in PDB format
- -fixca
- keep C-alpha positions from input
- -l refpdb min:max[=...]
- rebuild only specified residue range while taking coordinates from reference PDB otherwise
- -r resolution
- resolution of lattice projection
- -o offsetx offsety offsetz
- origin of lattice grid
Examples
rebuild.pl 1vii.seq 1vii.exp.chain
rebuilds an all-atom model from MONSSTER sequence and chain files
ATOM 1 N MET 1 -0.194 -8.104 -7.197 1.00 0.00 ATOM 2 CA MET 1 0.003 -8.457 -5.787 1.00 0.00 ATOM 3 C MET 1 -1.063 -8.084 -5.005 1.00 0.00 ATOM 4 O MET 1 -1.911 -7.297 -5.189 1.00 0.00 ATOM 5 CB MET 1 1.249 -7.765 -5.230 1.00 0.00 ATOM 6 CG MET 1 1.340 -6.286 -5.568 1.00 0.00 ATOM 7 SD MET 1 1.095 -5.957 -7.324 1.00 0.00 ATOM 8 CE MET 1 -0.693 -5.998 -7.430 1.00 0.00 ATOM 9 N LEU 2 -1.411 -8.302 -3.794 1.00 0.00 ATOM 10 CA LEU 2 -2.099 -8.601 -2.614 1.00 0.00 ...
rebuild.pl -l 1vii.exp.pdb 10:21 1vii.seq 1vii.exp.chain
rebuilds residues 10 through 21 using the MONSSTER sequence and chain files. The rest
of the structures is taken from the PDB file given with -l
ATOM 1 N MET 1 1.177 -10.035 -3.493 1.00 0.00 ATOM 2 CA MET 1 0.292 -8.839 -3.377 1.00 0.00 ATOM 3 C MET 1 -0.488 -8.912 -2.063 1.00 0.00 ATOM 4 O MET 1 -1.039 -9.937 -1.709 1.00 0.00 ATOM 5 CB MET 1 -0.674 -8.793 -4.565 1.00 0.00 ATOM 6 CG MET 1 -0.091 -7.889 -5.657 1.00 0.00 ATOM 7 SD MET 1 -0.153 -8.747 -7.255 1.00 0.00 ATOM 8 CE MET 1 -0.971 -7.432 -8.193 1.00 0.00 ATOM 9 N LEU 2 -0.523 -7.832 -1.331 1.00 0.00 ATOM 10 CA LEU 2 -1.241 -7.824 -0.028 1.00 0.00 ...
rebuild.pl -pdb 1vii.exp.chain.pdb
rebuilds an all-atom structure from side chain centers and C-alpha positions
from a pseudo-PDB file
ATOM 1 N MET 1 1.728 -8.815 -3.806 1.00 0.00 ATOM 2 CA MET 1 0.386 -8.942 -3.267 1.00 0.00 ATOM 3 C MET 1 0.369 -8.646 -1.744 1.00 0.00 ATOM 4 O MET 1 1.278 -8.965 -0.992 1.00 0.00 ATOM 5 CB MET 1 -0.147 -10.360 -3.484 1.00 0.00 ATOM 6 CG MET 1 -0.308 -10.746 -4.945 1.00 0.00 ATOM 7 SD MET 1 -1.172 -9.489 -5.906 1.00 0.00 ATOM 8 CE MET 1 0.209 -8.568 -6.579 1.00 0.00 ATOM 9 N LEU 2 -0.623 -7.905 -1.272 1.00 0.00 ATOM 10 CA LEU 2 -1.072 -7.936 0.104 1.00 0.00 ...