Keywords: ProFit

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# Command Summary

$ command
  Passes command to the operating system.

ALIGN
  Performs Needleman and Wunsch sequence alignment on the sequences of the two structures and derives zones from the equivalent regions in the alignment.

ATOMS atm[,atm]...
  Specifies the atom subset to fit.

BVALUE cutoff [ REFMOB
  ] Specify a B-value cutoff. Any atoms with B-values greater than this value will be ignored completely. A negative cutoff specifies that atoms with B-values less than the absolute cutoff should be ignored. The optional `REF` or `MOB` parameter restricts B-value checking to the specified structure.

BWEIGHT
  Weight the fitting by the inverse of the mean of the B-values in the equivalent atoms.

CENTER [ OFF
  ] See `CENTRE`.

CENTRE [ OFF
  ] Cause the coordinates to be written (using the `WRITE` or `MWRITE` commands), with the centre of geometry located at the origin instead of in the same coordinate frame as the reference set.

FIT
  Performs the actual fitting. Returns the RMS deviation over the atoms included in the fit.

GAPPEN val
  Specify an integer gap penalty for the sequence alignment performed by the `ALIGN` command.

HETATOMS
  Read HETATM records with subsequent `MOBILE` and `REFERENCE` commands.

IGNOREMISSING
  Ignore any atom mismatches and proceed with the fitting. Such atoms are listed as warnings.

ITERATE [ (limit OFF)
  ] Switches on (or off) iterative updating of the zones for fitting. The `ITERATE` command may be followed by an optional distance cutoff (default: 3.0Å) or by the keyword `OFF' to switch off iterative zone calculation.

LIMIT (pos1 pos2 OFF)
  Limits the range in an alignment (from ALIGN or READALIGNMENT) used to derive zones. `LIMIT OFF` restores the default behaviour.

MATRIX
  Displays the centres of geometry, rotation matrix and translation vector.

MOBILE [ XMAS
  ] filename Reads a mobile PDB structure. If compiled with XMAS support, then the XMAS keyword specifies that the input is in XMAS format.

MULTI filename
  Reads a file of files containing a list of structures for multiple fitting.

MWRITE [ ext
  ] Write the results of multiple structure fitting. The structures are written back using the same filenames with which they were read, but with the extension changed to that specified. If no extension is given, then `.fit' is used. Note therefore, that you must have write permission to the directory from which the input files were read.

NFITTED
  Reports the number of atom pairs fitted.

NOHETATOMS
  Do not read HETATM records with subsequent `MOBILE` and `REFERENCE` commands.

NOIGNOREMISSING
  Restore the default behaviour of issuing an error message for any atom mismatches and halting the fitting proceedure.

NOWEIGHT
  Normal, non-weighted fitting.

NUMBER (RESIDUESEQUENTIAL)
  Specifies whether zones are based on residue numbers in the PDB file or on sequential numbering (running through all chains).

QUIET [ OFF
  ] Switches on (or off) quiet mode. In quiet mode, warning messages are suppressed and progress of iterative zone updating and multiple structure fitting is not reported.

QUIT
  Exits from the program.

RATOMS atm[,atm]...
  Specifies atoms over which to calculate the RMS deviation. Fitting must already have been performed.

READALIGNMENT filename
  Reads an alignment in PIR sequence file format and sets zones based on that alignment.

REFERENCE [ XMAS
  ] filename Reads a reference PDB structure. If compiled with XMAS support, then the XMAS keyword specifies that the input is in XMAS format.

RESIDUE [ filename
  ] Gives a by-residue RMS deviation. If the first character of the (optional) filename is a pipe character (), then the results will be piped into the specified program. For example:

         RESIDUE |less

  will cause the results to be displayed on the screen using the `less` pager program.

RMS
  Recalculate the RMS deviation over the zones and atoms currently defined with `RZONE` and `RATOMS`.

RZONE zonespec
  Adds a zone specification to the list of zones considered in RMS deviation calculation. `RZONE *` or `RZONE` `CLEAR` resets the zones for RMSD calculation to be the same as that specified with the `ZONE` command.

STATUS
  Reports current program status.

WEIGHT
  Weight the fitting by the mean of the B-values in the equivalent atoms.

WRITE [ REFerence
  ] filename Writes the fitted structure to a PDB file. If the first character of the filename is a pipe character (), then the results will be piped into the specified program. For example:

         WRITE |less

  will cause the coordinates to be displayed on the screen using the `less` pager program.

  If the `REFERENCE` keyword is given (only the letters `REF' are required), then the reference set will be written. This is used in conjunction with the `CENTRE` command.

ZONE zonespec
  Adds a zone specification to the list of zones considered in fitting. `ZONE *` or `ZONE` `CLEAR` removes all zone specifications.

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