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mutate.pl
Usage
usage: mutate.pl [options] [PDBfile] options: [-seq index:sequence[=index:sequence]] [-minimize]
Description
This script can be used to mutate residues in an existing protein
structure. It requires a continuous single chain structure and
will not work if residues are missing.
The input structure is given either as command-line argument or
passed through standard input. The option -seq is then
used to indicate the new sequence(s) to which the input structure
should be mutated. The new sequence is given by the starting residue
number where it should replace the original sequence and an
abbreviated sequence string. Multiple new sequences can be separated
with = in order to mutate different parts of the sequence
simultaneously.
Mutations are done by reducing the input structure to a low-resolution
model consisting only of C-alpha and side chain center positions and
subsequent rebuilding of an all-atom structure with the new sequence.
The rebuilding procedure preserves C-alpha coordinates and coordinates
from all residues that are not being mutated. This generally results
in quite reasonable structures but further force-field minimization
may be desirable in order to improve the quality of the models.
The flag -minimize is available to request automatic minimization.
The minimization is done with CHARMM using distance dependent dielectric
and restraints on the non-mutated parts of the structure and requires
a recent version of CHARMM to be installed. If more extensive minimization
is needed, the utility minCHARMM.pl may be used.
Options
- -help
- usage information
- -seq index:sequence[=...]
- new sequence to be mutated to
- -minimize
- briefly minimize resulting structure
Examples
mutate.pl -seq 10:ADEF 1vii.exp.min.pdb
mutates residues 10 through 13 from VFGM in the original structure to ADEF.
ATOM 1 N MET 1 3.075 -9.691 -2.062 0.00 0.000 ATOM 2 CA MET 1 1.835 -9.001 -2.351 0.00 0.000 ATOM 3 C MET 1 0.889 -9.260 -1.188 0.00 0.000 ATOM 4 O MET 1 0.838 -10.371 -0.644 0.00 0.000 ATOM 5 CB MET 1 1.181 -9.487 -3.654 0.00 0.000 ATOM 6 CG MET 1 1.921 -9.123 -4.938 0.00 0.000 ATOM 7 SD MET 1 1.107 -9.774 -6.420 0.00 0.000 ATOM 8 CE MET 1 0.002 -8.437 -6.776 0.00 0.000 ATOM 9 N LEU 2 0.128 -8.242 -0.786 0.00 0.000 ATOM 10 CA LEU 2 -0.806 -8.363 0.321 0.00 0.000 ...
mutate.pl -seq 10:ADEF -minimize 1vii.exp.min.pdb
mutates residues and minimizes the resulting structure to relieve unfavorable
energetics
ATOM 1 N MET 1 3.116 -9.700 -2.114 1.00 0.000 PRO0 ATOM 2 HT1 MET 1 3.622 -9.265 -1.309 1.00 0.000 PRO0 ATOM 3 HT2 MET 1 3.712 -9.622 -2.962 1.00 0.000 PRO0 ATOM 4 HT3 MET 1 2.939 -10.703 -1.903 1.00 0.000 PRO0 ATOM 5 CA MET 1 1.823 -9.003 -2.332 1.00 0.000 PRO0 ATOM 6 HA MET 1 2.032 -7.944 -2.370 1.00 0.000 PRO0 ATOM 7 CB MET 1 1.137 -9.470 -3.642 1.00 0.000 PRO0 ATOM 8 HB1 MET 1 0.149 -8.964 -3.731 1.00 0.000 PRO0 ATOM 9 HB2 MET 1 0.950 -10.566 -3.592 1.00 0.000 PRO0 ATOM 10 CG MET 1 1.938 -9.167 -4.923 1.00 0.000 PRO0 ...