#$


   $ command
   
   Any command preceeded by a $ is passed to the operating system.
   This is useful for directory listings, typing or editing files,
   etc.
#REFERENCE


   REFERENCE filename

   Reads a reference PDB structure. Reading a structure will cause
   any zones or atoms specified for RMS calculation to be reset.
   By default, HETATM records will be ignored. (Use the HETATOM 
   command to change this, or start ProFit with -h.)
#MOBILE


   MOBILE filename

   Reads a mobile PDB structure. This will be fitted to the Reference
   structure. Reading a structure will cause any zones or atoms 
   specified for RMS calculation to be reset.
   By default, HETATM records will be ignored. (Use the HETATOM 
   command to change this, or start ProFit with -h.)
#FIT


   FIT

   Performs the actual fitting. Returns the RMS deviation over the
   atoms included in the fit. Any zones or atoms specified for RMS 
   calculation will be reset to those specified for fitting. Should
   RMS deviations be required over different areas of structure or
   groups of atoms, the RZONE and RATOMS commands should be used to
   specify the appropriate atoms. The RMS over these atoms will be
   displayed immediately.
#ATOMS


   ATOMS atm[,atm]...

   Specifies the atom subset to fit. * fits all atoms. A ~ or ^ may
   be used to inverse the selection. If specified, it must be placed
   at the start of the atom list.

   Wildcards are also allowed. A % or a ? may be used to match a
   single letter at any point in the specification while a * may be
   used to match all remaining characters (thus C* is allowed,
   but *G is not). The special characters may be escaped by 
   preceding them with a \. 

   The PDB atom name field is 4 characters wide followed by a space. 
   The first two characters are the right-justified element type, so
   for normal protein and DNA atoms consist of a space followed by a N, 
   C, O, S or P. Thus the atom name field for a C-alpha contains
   " CA ". HETATMs such as calcium will contain the two characters
   CA in the first two fields. i.e. "CA  ". When you specify an atom
   type it is matched against the atom name field from the SECOND 
   CHARACTER ONWARDS, unless you preceed it with a <. Thus to match
   a C-alpha you use "CA", but to match Calcium, you use "<CA".

   If atom names contain spaces (e.g. in heme groups) the whole atom
   specification must be enclosed in double inverted commas.
   
   Examples:
   ATOMS CA             Fit only C-alphas
   ATOMS <CA            Fit only calcium atoms
   ATOMS <CA,CA         Fit calciums and C-alphas
   ATOMS N,CA,C,O       Fit N, C-alpha, C and O
   ATOMS *              Fit all atoms
   ATOMS ~N,CA,C,O      Fit all atoms except N, C-alpha, C and O
   ATOMS C*             Fit all carbon atoms
   ATOMS ?G*            Match all atoms at the gamma position
   ATOMS C4\*           Match the C4* atoms in DNA
   ATOMS "N A,N B,N C"  Fit atoms with names containing spaces
#ZONE


   ZONE CLEAR|((*|(X...[,n][/m])|(j-k))[:(*|(X...[,n][/m])|(j-k))])
   where X...      is an amino acid sequence
         n         is a number of residues
         m         is the occurrence number
         j and k   are residue specifications of the form
                   [chain]renum[insert]
         Optional items are in square brackets
         Alternatives are marked by a | and grouped in parentheses

   Specifies residue zones to be fitted. Each zone is added to those
   currently active. To clear all zones (i.e. fit all residues), the
   ZONE CLEAR command may be given. ZONE * has the same effect.

   In Residue Number mode, the residue numbers may be preceded by a 
   chain name. In Sequential Number mode, chain names will be ignored.

   Insertion codes may follow a residue number in Residue Number
   mode.

   Negative residue numbers must be escaped with a \

   Note that sequence-specified zones automatically imply sequential
   numbering.
   
   Examples:
   ZONE 24-34           Fits 24-34 in Reference with 24-34 in Mobile
   ZONE H5-H10          Fits 5-10 in chain H of Reference with the
                        same region in Mobile
   ZONE H*              Fits just the H chains
   ZONE 24-34:25-35     Fits 24-34 in Reference with 25-35 in Mobile
   ZONE L25A-L30        Fits residues 25A-30 in the L chain
   ZONE -10:50-59       Fits up to 10 in Reference with 50-59 in Mobile
   ZONE \-4-10:\-1-13   Fits residues -4 to 10 with -1 to 13 in Mobile
   ZONE *:1-100         Fits all in Reference with 1-100 in Mobile
   ZONE CAR:VNS         Fits first occurence of CAR in Reference with
                        first occurence of VNS in Mobile
   ZONE CAR,10:VNS,10   Fits 10 residues from first occurence of CAR 
                        in Reference with first occurence of VNS in 
                        Mobile
   ZONE CAR,5/2         Fits 5 residues from second occurence of CAR
                        in both structures
   ZONE 24-34:EIR,11    Fits 24-34 in Reference with 11 residues from
                        first occurence of EIR in Mobile
#ALIGN


   ALIGN

   Performs Needleman and Wunsch sequence alignment on the sequences
   of the two structures and displays the alignment. Any fitting zones
   are automatically cleared and replaced with zones derived from the
   equivalent regions in the alignment.
   
   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.
#READALIGNMENT


   READALIGNMENT filename

   Reads an alignment in PIR sequence file format and sets zones based
   on that alignment. Any previously defined fitting zones are 
   automatically cleared first.

   The file format is standard PIR with the two sequences represented
   by separate entries  i.e. each must have a header of the form:

   >P1;xxxxx
   title text .......

   If the PIR file contains multiple chains, it will be rejected. The
   alignment is specified by introducing dash (-) signs into the
   sequence.

   The first sequence will be assumed to be that of the reference
   structure and the second is that of the mobile structure. Any other
   sequences in the file are ignored.
   
   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.
#RATOMS


   RATOMS atm[,atm]...

   Specifies atoms over which to calculate the RMS. Fitting must 
   already have been performed. Any RZONE spcifications which have 
   been given will be considered in the calculation. The RMS over 
   the specified atoms is displayed. * includes all atoms. A ~ 
   or ^ may be used to inverse the selection. If specified, it must 
   be placed at the start of the atom list.

   Wildcards are also allowed. A % or a ? may be used to match a
   single letter at any point in the specification while a * may be
   used to match all remaining characters (thus C* is allowed,
   but *G is not). The special characters may be escaped by 
   preceding them with a \. 

   The PDB atom name field is 4 characters wide followed by a space. 
   The first two characters are the right-justified element type, so
   for normal protein and DNA atoms consist of a space followed by a N, 
   C, O, S or P. Thus the atom name field for a C-alpha contains
   " CA ". HETATMs such as calcium will contain the two characters
   CA in the first two fields. i.e. "CA  ". When you specify an atom
   type it is matched against the atom name field from the SECOND 
   CHARACTER ONWARDS, unless you preceed it with a <. Thus to match
   a C-alpha you use "CA", but to match Calcium, you use "<CA".

   If atom names contain spaces (e.g. in heme groups) the whole atom
   specification must be enclosed in double inverted commas.
   
   Examples:
   RATOMS CA            RMS over C-alphas
   RATOMS <CA           RMS over calcium atoms
   RATOMS <CA,CA        RMS over calciums and C-alphas
   RATOMS N,CA,C,O      RMS over N, C-alpha, C and O
   RATOMS *             RMS over all atoms
   RATOMS ~N,CA,C,O     RMS over all atoms except N, C-alpha, C and O
   RATOMS C*            RMS over all carbon atoms
   RATOMS ?G*           RMS over all atoms at the gamma position
   RATOMS C4\*          RMS over the C4* atoms in DNA
   ATOMS "N A,N B,N C"  RMS over atoms with names containing spaces
#RZONE


   RZONE CLEAR|((*|(X...[,n][/m])|(j-k))[:(*|(X...[,n][/m])|(j-k))])
   where X...      is an amino acid sequence
         n         is a number of residues
         m         is the occurrence number
         j and k   are residue specifications of the form
                   [chain]renum[insert]
         Optional items are in square brackets
         Alternatives are marked by a | and grouped in parentheses

   Specifies residue zones over which to calculate the RMS. Each zone 
   is added to those currently active. The RZONE CLEAR command will
   cancel any RMS calculation zones that have been specified causing
   the RMS to be calculated over the same zones used for fitting.
   RZONE * has the same effect. Any RATOMS specifications which have 
   been given will be considered in the calculation.
   
   In Residue Number mode, the residue numbers may be preceded by a 
   chain name. In Sequential Number mode, chain names will be ignored.

   Insertion codes may follow a residue number in Residue Number
   mode.

   Negative residue numbers must be escaped with a \

   Note that sequence-specified zones automatically imply sequential
   numbering.
   
   Examples:
   RZONE 24-34          RMS of 24-34 in Reference with 24-34 in Mobile
   RZONE L25A-L30       RMS of residues 25A-30 in the L chain
   RZONE 24-34:25-35    RMS of 24-34 in Reference with 25-35 in Mobile
   RZONE -10:50-59      RMS of up to 10 in Reference with 50-59 in Mobile
   RZONE \-4-10:\-1-13  RMS of -4 to 10 with -1 to 13 in Mobile
   RZONE *:1-100        RMS of all in Reference with 1-100 in Mobile
   RZONE H*             RMS over just the H chain
   RZONE CAR:VNS        RMS of first occurence of CAR in Reference with
                        first occurence of VNS in Mobile
   RZONE CAR,10:VNS,10  RMS of 10 residues from first occurence of CAR 
                        in Reference with first occurence of VNS in 
                        Mobile
   RZONE CAR,5/2        RMS of 5 residues from second occurence of CAR
                        in both structures
   RZONE 24-34:EIR,11   RMS of 24-34 in Reference with 11 residues from
                        first occurence of EIR in Mobile
#RMS


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


   WRITE [REFerence] filename

   Writes the fitted structure to a PDB file. If the filename begins
   with a pipe character (|), the coordinates are piped into the
   specified program.

   If the REFERENCE parameter is given then the reference set will be
   written. This is only useful if the CENTRE command has been used!
#MATRIX


   MATRIX

   Displays the centres of geometry, rotation matrix and translation
   vector. The translation vector is the vector between the centres
   of geometry. Thus to superimpose the mobile structure on the 
   reference structure using these data, you should translate the
   mobile to the origin, apply the rotation matrix, translate back to
   the original centre of geometry and finally apply the translation 
   vector.
#STATUS


   STATUS

   Reports current program status.
#QUIT


   QUIT

   Exits from the program.
#NUMBER


   NUMBER (RESIDUE|SEQUENTIAL)

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

   In Residue Number mode, the residue numbers may be preceeded by a 
   chain name. In Sequential Number mode, chain names will be ignored.
#RESIDUE


   RESIDUE [filename]

   Gives a by-residue RMS on the currently specified RATOMS (or ATOMS
   if RATOMS has not been specified) over the currently specified
   RZONE (or ZONE if RZONE has not been specified).

   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 (|), the results are piped into the
   specified program.
#HETATOMS


   HETATOMS

   Read HETATM records with subsequent MOBILE and REFERENCE commands.
   This is the default if the -h flag has been given on starting
   ProFit.
#NOHETATOMS


   NOHETATOMS

   Do not read HETATM records with subsequent MOBILE and REFERENCE 
   commands. This is the default unless the -h flag has been given 
   on starting ProFit.
#WEIGHT


   WEIGHT

   Weight the fitting by the mean of the B-values in the equivalent
   atoms. Normally, you wouldn't use this with real B-values, but
   with some other weight parameter (e.g. SSAP scores).
#BWEIGHT


   BWEIGHT

   Weight the fitting by the inverse of the mean of the B-values in 
   the equivalent atoms. This is useful for genuine weighting by
   B-values (i.e. mobile atoms will be less heavily weighted).
#NOWEIGHT


   NOWEIGHT

   Normal, non-weighted fitting.
#GAPPEN


   GAPPEN val

   Allows you to specify an integer gap penalty for the sequence
   alignment performed by the ALIGN command. (Default: 5)
#BVALUE


   BVALUE cutoff [REF|MOB]

   Allows you to specify a B-value cutoff. Any atoms with B-values
   greater than this value will be ignored completely in both the
   fitting and RMS calculations. The B-value may not be higher than
   this value in either the reference or the mobile structure.
   For example, if you specify 10, then atoms with B-values greater
   than 10 will be ignored.

   If the cutoff you supply is negative, any atoms with B-values
   less than the absolute value you specify will be ignored.
   For example, if you specify -10, then atoms with B-values less
   than 10 will be ignored.

   The optional REF or MOB parameter restricts checking of B-values
   to the specified structure.

   Specify BVALUE * to allow all BValues
#IGNOREMISSING


   IGNOREMISSING

   By default, atom mismatches during fitting caused by atoms 
   missing in one of the two structures causes the program to report 
   an error. This command causes the program to issue a warning,
   but to proceed with the fitting, ignoring the mismatched atom(s).
   (See NOIGNOREMISSING.)
#NOIGNOREMISSING


   NOIGNOREMISSING

   Restores the default behaviour of reporting an error and stopping
   the fitting procedure if atom mismatches occur during fitting.
   (See IGNOREMISSING.)
#NFITTED


   NFITTED

   Reported the number of atom pairs fitted in the last fitting
   operation. Note that this is not the number of residues fitted
   unless you are only fitting on CA atoms.
#ITERATE


   ITERATE [limit | OFF]

   Iterates the fitting zones during future FIT commands. 

   Note that this immediately does an "ATOMS CA" since iteration of
   zones is only performed on C-alpha atoms. See notes below if you
   want to calculate an RMSD over other atoms.

   After the initial fit on the specified zones, the zones are updated
   such that residue pairs with C-alpha atoms within 'limit' Angstroms
   (default 3.0A) are included and those more distant are excluded. 
   The optimum set of equivalences is obtained using a dynamic 
   programming method.

   After updating the zones, the structures are refitted and the
   procedure iterates to convergence (typically 3 or 4 cycles). The
   RMSD on C-alpha atoms is shown after each cycle unless the QUIET 
   command is given.

   As stated above, the ITERATE command implies ATOMS CA. Having
   fitted on C-alpha atoms, you can of course display the RMSD over
   other atom sets in the usual way using the RATOMS command (e.g.
   RATOMS N,CA,C,O will display the backbone RMSD).

   Should you wish to refit on another atom set using the iterated 
   zones, simply use ITERATE OFF to switch off iteration, select the
   atom set required using the ATOMS command and use FIT to refit the
   structures in the usual way. For example, to fit on backbone atoms:

   ITERATE OFF
   ATOMS N,CA,C,O
   FIT
#MULTI


   MULTI filename

   Fits multiple structures. 'filename' contains a list of structure 
   files to be fitted.

   MULTI causes a set of structure files to be read in. The filenames
   are given within the file specified in the command. The first
   structure file is used as a reference set for the first fitting
   stage but the coordinates are averaged after each fitting stage
   to derive an averaged template used for subsequent fitting.

   i.e. Given N files to fit, file 2 is fitted to file 1 and an
   averaged structure, A, is calculated, file 3 is then fitted to A
   and a new average, A' is calculated. This continues until all N
   structures have been fitted. The whole procedure iterates until
   convergence (typically 3 or 4 cycles).

   The resulting fitted files are written with the MWRITE command.
   Note that there is no "reference" set in the sense used for
   2-structure fitting; fitted versions of all N files will be written
   since the reference set is actually an averaged template.

   Progress and RMSDs are reported at each iteration unless the QUIET
   command is used.
#QUIET


   QUIET [OFF]

   Switches off all warning and informational messages
#MWRITE


   MWRITE [ext]

   Writes multiple fitting results.

   The filenames are the same as the input file but with the extension
   replaced by that specified in the command. If no extension is
   specified then '.fit' will be used. If the input file contained no
   extension, then the extension specified will be appended to the
   filename.

   Note that since only the extension is changed when writing back the
   fitted files, you must have permission to write to the directory
   from which the original files were read.
#LIMIT


   LIMIT (start stop | OFF)

   When obtaining fit zones from a sequence alignment, either from
   ALIGN or from READALIGNMENT, limit the zones to use residues
   between the specified positions in the alignment.

   For example, if the alignment were:

                          1         2         3
                 123456789012345678901234567890123
                 ASAHSTGEHNM--PLELLGHISLAM---NPRTY
                 ---HSTADHNLRTPLEVLG--SLAMEDRQPRTY

   the zones would normally be taken from the following positions
   in the alignment:
         4-11, 14-19, 22-25, 29-33

   By using the command:
         LIMIT 20 28
   only the zone from 22-25 would be included.

   This is particularly useful in conjunction with the ITERATE command
   and fitting of multiple structures.
#CENTRE


   CENTRE [OFF]

   Causes coordinates to be written centred about the centre of 
   geometry of the fitted region rather than translated back to the 
   reference set's location. If only fitting 2 structures, the 
   WRITE REFERENCE command is required to write the reference set
   in the same coordinate frame. (With multiple structure, MWRITE
   will write the reference set in any case.)
#CENTER


   CENTER [OFF]

   See CENTRE