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genchain.pl
Usage
usage: genchain.pl [options] [[-m | -s | -pdb | -primo | -primo2 | -htrna] 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]
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 chain in MONSSTER format
- -s
- generate off-lattice SICHO chain
- -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[=...]
- not sure
- -setres num:
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.
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 ...