ens2pdb
Converts an ensemble of structure files to a single PDB, with structures separated by MODEL records. The SEGID field is written to the ChainID field so it must be, at most, a single character. The result should be acceptable for PDB submission. Usage: ens2pdb [options] <structure files>
Options:
-psf <psf filename> - specify a psf filename. If omitted PSF info is
automatically generated from the pdb file.
-renameSegid <selection> <new name>
- renames the SEGID to a new value. This option may
be specified more than once to rename multiple
selections.
-renameResname <selection> <new name>
- renames the residue name to a new value. This
option may be specified more than once to
rename multiple selections.
-keepOccupanciesBfactors - causes occupancies and B-factor fields of the
input files to be preserved in the output.
-delete <selection> - specifies an atom selection (in the input files)
to be omitted from the output file.
-altLoc <selection> <altLoc characters>
- specifies an atom selection for which the altLoc
PDB field is to be specified. AltLoc characters
are also specified, and number of these should
match the ensemble size. Occupancies will be
taken from ensemble weights. If altLoc is not
specified for an ensemble of input structures,
then the ensemble members are all placed in
separate MODEL entries, and ensemble weights are
reported in the REMARKs section.
-altLocOccupancy <val> - The occupancy value for the preceeding -altLoc
specification. If not specified, occupancies
take a value of 1.
-weightsName <name> - specifies an entry in the EnsWeights field in the
REMARK header of the input files giving ensemble
weights. If this argument is not specified and
there is a single EnsWeights entry, that will be
used.
-weightsTerm <name> - specifies an entry in the listing of per-term
Ensemble Weights in the REMARK sectuib header of
the input files giving ensemble weights. Use only
a maximum of one of -weightsName or -weightsTerm.
-ensMemberOrder <indices> - used to rearrange ensemble members. The indices
argument should be a colon-separated list of
0-offset ensemble member indices to print.
-threeLetter - turns on three character residue names for
nucleic acids. By default, nucleic acid residue
names are converted to their single character
version.
-twoLetter - specifies two character residue names, which are
apparently used for DNA depositions.
-hetatmSel <selection> - specify which atoms should have HETATM records
instead of ATOM records.
Structure filenames which contain glob wildcards will be treated as ensembles, and each matching file will be inserted into its own MODEL entry sorted by the ensemble member number.
The result is printed to stdout.