MMTSB
Tool Set Documentation

rebuild.pl

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Usage

usage:   rebuild.pl [options] [ -pdb file | seq chain ]
options: [-l refpdb min:max[=min:max...]] [-fixca]
         [-r resolution] [-o offsetx offsety offsetz]
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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          

...