MMTSB
Tool Set Documentation

genchain.pl

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Usage

usage:   genchain.pl [options] [[-m | -s | -pdb | -primo | -primo2] file] | [-rnd num]
options: [-r resolution] [-g gridsize]
         [-float] [-center] [-ca]
         [-o offsetx offsety offsetz]
         [-l min:max[=min:max=...]]
         [-setres num:name[,num:name]]
         [-seq seqfile]
         [-dcd dcdinp dcdout]
         [-nsel selection]
Show source


Description

Generates SICHO chains with a single particle per amino acid residue located at the side chain center of mass. The script works in either one of four different modes.

If a PDB file is given with -m a corresponding MONSSTER compatible lattice chain is generated. The grid size for representing the chain in MONSSTER can be given with -g, the default value is 100 lattice units. The grid size is used to position the chain in the center of the grid and ensure that the structure fits within the grid dimensions. An offset in lattice units can also supplied explicitly with -o. The option -l is available for the modeling of loops or fragments in order to provide residue ranges describing regions where no structure is available. If this option is given the known part of the chain generated from the PDB file is connected by random chain fragments for the specified unknown residues.

In the second mode, selected with -rnd a completely random, MONSSTER-compatible chain is generated. The number of virtual particles is given as the argument of -random. The -g and -o are available as in the PDB mode. In particular the -g option to specify the grid size is more important in this mode to restrict the more extended random chains to the grid size used in MONSSTER.

Please note that MONSSTER requires additional terminal residues at either end of the chain. The MONSSTER output chains in the first two modes have therefore two more residues than requested or present in the PDB file.

The third mode is chosen with -s. It is used to generate simple chains with arbitrary resolutions and offsets, specified with the -r and -o options, from the given PDB file. If if the MONSSTER model resolution of 1.45 is used chains generated in this mode are usually not suitable for use with MONSSTER due to additional constraints that need to be satisified in valid MONSSTER chains (see the documentation of checkchain.pl for more information). The -l option is also not available in this mode.

The fourth mode selected with -pdb is similar to the third mode. It generates simple chains from a PDB file but writes out a pseudo-PDB file instead of a MONSSTER chain file. This output PDB file has atom entries with the atom name SC for side chain centers. In this mode C-alpha atoms are included for each residue if the -ca flag is given.

If the option -nocenter is specified, the molecule read from a PDB file is not centered at the origin. This may be desirable to preserve the original spatial position, e.g. if a part of a larger molecular assembly is modeled on the lattice. By default, the molecule is centered unless one of the -l, -pdb or -s options are specified. -center is available to request centering in this case. Please note, that the SICHO chain has to fit inside the lattice grid which is always centered around the origin and will not be shifted to accomodate a molecule located far from the origin.

The option -setres can be used to change individual residue names in PDB-type output files. This is useful for mutating residues by first generating a low-resolution model from the original amino acid side chain center and then rebuilding a mutated amino acid. If more than a few residue names are changed as in most homology modeling applications it is more convenient to supply the complete new amino acid sequence with a MONSSTER sequence file given with -seq.

Options

-help 
usage information
-m 
generate SICHO chains that conform to MONSSTER requirements
-s 
generate simple SICHO chains including off-lattice chains
-pdb 
generate SICHO/C-alpha model in PDB format
-primo 
generate PRIMO model
-rnd num 
generate random sequence
-r resolution 
resolution of lattice projection
-g gridsize 
lattice grid size (should match MONSSTER)
-float 
generate off-lattice model
-center 
center model
-ca 
generate C-alpha coordinates with SICHO model
-o offsetx offsety offsetz 
coordinates of lattice origin
-l min:max[=...] 
generate random chains for the given residue fragments (for loop modeling) while generating SICHO sites from PDB file otherwise
-setres num:name[,...] 
mutate residues
-seq seqfile 
sequence file to provide sequence of entire structure

Examples

genchain.pl 1vii.exp.pdb
generates a MONSSTER chain from a PDB file and writes the chain to standard output

    38
    50   44   42
    49   44   45
    49   45   49
    46   42   49
    43   45   49
    44   42   52
    48   43   51
    47   48   50
    44   46   54

...


genchain.pl -g 80 -rnd 87
generates a random MONSSTER chain with 87 residues for a grid size of 80 units and writes the chain to standard output

    89
    32   41   37
    35   42   38
    38   42   39
    41   42   38
    41   38   38
    42   35   38
    45   37   38
    50   37   38
    51   32   36

...


genchain.pl -r 1.0 -s 1vii.exp.pdb
generates a simple (non-MONSSTER) chain for a lattice with 1 A resolution.

    36
    50   42   44
    50   43   51
    46   39   50
    41   43   51
    42   38   55
    48   39   54
    46   47   53
    41   45   58
    47   43   60

...


genchain.pl -l 10:21 1vii.exp.pdb
generates a MONSSTER chain from the given PDB file with random sidechain positions for residues 10 through 21.

    38
    48   45   43
    50   44   46
    50   45   51
    47   43   50
    44   45   50
    44   42   54
    48   43   53
    47   48   52
    44   46   55

...


genchain.pl -ca -pdb 1vii.exp.pdb
generates a pseudo-PDB file with simple (non-MONSSTER) side chain centers and C-alpha positions

ATOM      1  SC  MET     1      -0.472  -8.215  -6.418  1.00  0.00          
ATOM      2  CA  MET     1       0.292  -8.839  -3.377  1.00  0.00          
ATOM      3  SC  LEU     2       0.051  -6.358   1.625  1.00  0.00          
ATOM      4  CA  LEU     2      -1.241  -7.824  -0.028  1.00  0.00          
ATOM      5  SC  SER     3      -4.399 -11.276   0.426  1.00  0.00          
ATOM      6  CA  SER     3      -4.651  -9.514  -0.199  1.00  0.00          
ATOM      7  SC  ASP     4      -9.416  -7.024   0.277  1.00  0.00          
ATOM      8  CA  ASP     4      -7.413  -7.518   1.539  1.00  0.00          
ATOM      9  SC  GLU     5      -8.645 -12.010   5.593  1.00  0.00          
ATOM     10  CA  GLU     5      -7.065  -9.365   4.887  1.00  0.00          

...


genchain.pl -setres 2:PHE -ca -pdb 1vii.exp.pdb
generates a pseudo-PDB file as in the previous example but with the name of the second residue changed to PHE.

ATOM      1  SC  MET     1      -0.472  -8.215  -6.418  1.00  0.00          
ATOM      2  CA  MET     1       0.292  -8.839  -3.377  1.00  0.00          
ATOM      3  SC  PHE     2       0.051  -6.358   1.625  1.00  0.00          
ATOM      4  CA  PHE     2      -1.241  -7.824  -0.028  1.00  0.00          
ATOM      5  SC  SER     3      -4.399 -11.276   0.426  1.00  0.00          
ATOM      6  CA  SER     3      -4.651  -9.514  -0.199  1.00  0.00          
ATOM      7  SC  ASP     4      -9.416  -7.024   0.277  1.00  0.00          
ATOM      8  CA  ASP     4      -7.413  -7.518   1.539  1.00  0.00          
ATOM      9  SC  GLU     5      -8.645 -12.010   5.593  1.00  0.00          
ATOM     10  CA  GLU     5      -7.065  -9.365   4.887  1.00  0.00          

...


genchain.pl -seq new.seq -pdb -ca 1vii.exp.pdb | rebuild.pl -fixca -pdb
this command demonstrates how to build a homology model from a template with a different sequence. In the example the 1VII structure in 1vii.exp.pdb is used as the structural template while the new sequence is provided in new.seq. genchain.pl generates a low-resolution model with sidechain centers and C-alpha positions. rebuild.pl is then used to rebuild the all-atom model for the new sequence onto the fixed C-alpha backbone.

ATOM      1  N   MET     1       1.633  -8.698  -3.945  1.00  0.00          
ATOM      2  CA  MET     1       0.292  -8.839  -3.377  1.00  0.00          
ATOM      3  C   MET     1       0.261  -8.540  -1.890  1.00  0.00          
ATOM      4  O   MET     1       1.167  -8.853  -1.133  1.00  0.00          
ATOM      5  CB  MET     1      -0.224 -10.267  -3.569  1.00  0.00          
ATOM      6  CG  MET     1      -0.313 -10.704  -5.022  1.00  0.00          
ATOM      7  SD  MET     1      -1.135  -9.486  -6.067  1.00  0.00          
ATOM      8  CE  MET     1       0.254  -8.468  -6.559  1.00  0.00          
ATOM      9  N   LEU     2      -0.739  -7.814  -1.399  1.00  0.00          
ATOM     10  CA  LEU     2      -1.241  -7.824  -0.028  1.00  0.00          

...