Command Summary

$ command

Passes command to the operating system.

# comment

Echoes comment to stdout.

ALIGN [[WHOLE$\mid$*]$\mid$[zonespec [APPEND]

]]

Performs Needleman and Wunsch sequence alignment on the sequences of the two structures and derives zones from the equivalent regions in the alignment. For multiple structure fitting, ALIGN performs a pairwise alignments for the reference sequence and each mobile sequence.

It will normally be necessary to use the ATOMS command to specify that only backbone or C-alpha atoms are included in the fitting calculations.

ALLVSALL [filename]

Performs an all versus all comparison of the mobile structures when fitting multiple structures. Results are presented as tab-delimited text suitable for loading into a spreadsheet.

If the optional filename parameter is given, output is directed to the specified file. If the file cannot be opened or a filename is not specified, output appears on the screen. If the filename begins with a pipe character ($\mid$), the results are piped into the specified program.

ATOMS atm[,atm]...

Specifies the atom subset to fit.

BVALUE cutoff [ REF$\mid$MOB]

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.

BZONE

Sets fitting zones based on markers in the temperature factor (B-value) column

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.

DELRZONE zonespec

Removes a zone specification to the list of zones considered in RMS deviation calculation. DELRZONE * or DELRZONE ALL deletes all RMS deviation calculation zones.

DELZONE zonespec

Removes a zone specification to the list of zones considered in fitting. DELZONE * or DELZONE ALL removes all zone specifications.

DISTCUTOFF [cutoff $\mid$ ON $\mid$ OFF]

Specifies a distance cutoff for RMSd calculations.

FIT

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

GAPPEN val [val]

Specifies an integer gap penalty and a gap extension penalty for the sequence alignment performed by the ALIGN command. The default values for the gap penalty and gap extension penalty are 10 and 2 respectively.

HEADER [ON $\mid$ OFF]

Include PDB header and trailer records when writing structures. By default, only the coordinate section of a file is output when a structure is written.

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 $\mid$ 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 $\mid$ OFF)

Limits the range in an alignment (from 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.

MULTREF [OFF]

Sets RMSd calculations to give values to the averaged reference rather than the first mobile structure.

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.

NOFIT

Sets the fitted flag in profit allowing the user to calculate the RMSD on a structure without fitting.

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 (RESIDUE$\mid$SEQUENTIAL)

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

OCCRANK n

Sets ProFit to read the nth ranked highest occupancy atom position for alternative atom positions.

For structure files containing partial occupancies, lower occupancy atoms can be read using by setting the occupancy rank parameter to read alternative atom positions.

By default, OCCRANK is set to 1 and reads the highest ranked atom position, a setting of 2 will read the second most occupied position and a setting of 3 will read the third most occupied position, etc.

ORDERFIT

Performs a fit of all mobile structures to the reference structure. The most similar structures are fitted first.

PAIRDIST [ filename]

Prints the pairwise distances between equivalent atom pairs. If the first character of the (optional) filename is a pipe character ($\mid$), then the results will be piped into the specified program. For example:

   PAIRDIST |less

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

PRINTALIGN [FASTA$\mid$PIR] [ filename]

Prints current fitting zones as a sequence alignment. The default output is a (user-friendly) pairwise alignment with the reference and mobile sequences printed as pairs of 60-character wide lines. The optional FASTA and PIR parameters set the printout to FASTA or PIR formatting. ProFit can read PIR-formatted files using the READALIGN command.

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. Note that when used with multiple structures, the first sequence must appear twice in the alignment file. This is because it is used as both the first reference and mobile set.

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 ($\mid$), 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.

SCRIPT filename

Executes a script file.

SETCENTER residue

See SETCENTRE.

SETCENTRE residue

Specifies a single residue as the centre of fitting. Entering SETCENTRE CLEAR or SETCENTRE * will clear the centre residue.

SETREF [n]

Sets the reference structure to the nth mobile structure when fitting multiple structures.

If no structure number is given then the reference is automatically set by performing an all versus all comparison of the mobile structures then selecting the structure with the lowest overall RMSD to the other mobile structures.

STATUS[ filename]

Reports current program status. If the optional filename parameter is given, output is directed to the specified file. If the file cannot be opened or a filename is not specified, output appears on the screen. If the filename begins with a pipe character ($\mid$), the results are piped into the specified program.

SYMMATOMS [[OFF$\mid$ON$\mid$ALL]$\mid$xxx [OFF$\mid$ON]

where xxx is a three-letter amino acid code.

Enabes the auto-matching of symmetrical atoms (eg CD1 - CD2 and CE1 - CE2 of tyrosine) in ProFit

SYMMATOMS matches charged oxygens and nitrogens on arginine, aspartate and glutamate residues and the delta and epsilon carbons of phenylalanine and tyrosine residues.

It is also possible to match the nitrogen and oxygen atoms of the amide sidechains of asparagine and glutamine residues and the prochiral methyl groups of valine and leucine.

Typing SYMMATOMS will display the pairs of atoms currently matched by ProFit. Typing SYMMATOMS ON or SYMMATOMS OFF will turn symmetrical atom matching on or off.

Individual residue types, for example ASP, can be turned-on or off by typing SYMMATOMS ASP ON or SYMATM ASP OFF, respectively. Alternatively, SYMMATOMS ALL ON will turn all atom pairs on.

By default, the the matching of symmetrical atoms is turned-off

TRIMZONES

This command is used primarily with fitting zones derived using ALIGN. With pairwise alignments, the lengths of the aligned regions may vary and there may be gaps in the alignments from one structure to another. The TRIMZONES command trims the ends of the aligned zones and adds gaps allowing for a like versus like comparison by using fitting zones that are common to all the structures.

TRIMZONES is automatically called by the ALLVSALL and SETREF commands. This command is only used with multiple structures.

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 ($\mid$), 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.

WTAVERAGE [ ON$\mid$OFF ]

Sets the weighting system for the averaged reference structure to the default weighting system where the change in the coordinates of the reference structure is inversely proportional to the number of mobile strucures. The weighted averaging scheme was introduced to lower the effect that outlying structures have on the averaged reference. (Default: ON)

The alternative weighting scheme sets the coordinates of the reference stucture to the average of the reference and the mobile structures. This was the scheme used by ProFit prior to version 3.0. (WTAVERAGE OFF)

ZONE zonespec

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