The fitted mobile structure may be written to a file in PDB format
If the first character of the filename is a pipe character (), then the results will be piped into the specified program. For example:
will cause the coordinates to be displayed on the screen using the
less pager program.
The reference set may also be written:
WRITE REFERENCE ref_fitted.pdb
(only the three letters `REF' of the REFERENCE parameter are required). This is only useful if the CENTRE command has been used (see below).
By default, the mobile structure is moved to the coordinate frame of
the reference set. If the
CENTER) command is
given then the centre of geometry of the fitted coordinates will be
located at the origin.
If a residue has been set as the centre of fitting using
(see Section 9.6) then that residue will be moved to the
origin when the
CENTRE command is used.
If only two structures are fitted then the
command must be used to write the reference set in the origin-centred
coordinate frame. If multiple structures are fitted and written using
MWRITE then the reference set will be written automatically.
More details about the fitting may be obtained by using the
MATRIX command. This displays the centres of geometry, the
rotation matrix and the translation vector which is the vector between
the centres of geometry. Thus to superimpose the mobile structure onto
the reference structure using these data, you should translate the
mobile set to the origin, apply the rotation matrix, translate back to
the original centre of geometry and finally apply the translation
Note that the rotation matrix is not orthogonal and cannot therefore be used to extract Euler angles. This is a result of the fitting method used.
NFITTED command displays the number of atom pairs which
were fitted in the last fitting operation. Note that this will not
be the number of residues fitted unless you are only fitting one
atom type per residue (typically C atoms).
RESIDUE command is used to obtain a by-residue RMS
deviation on the currently specified RMS atoms in the currently
specified RMS zone. If no
RZONE commands have
been used, the atoms and zones used for the fitting will be used.
RESIDUE command may be followed by an optional filename
parameter in which case 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 first character of the filename is a
pipe character (), then the results will be piped into the
specified program. For example:
will cause the results to be displayed on the screen using the
less pager program.
If the distance cutoff is set then residues fully outside the distance cutoff
are flagged with
** and residues partially outside the distance cutoff
are flagged with
* (see Section 9.7)
The related command,
PAIRDIST prints the pairwise distances between
equivalent atom pairs in the reference and mobile structures.
has the same syntax as
RESIDUE. If the distance cutoff is set then
residues outside the distance cutoff are flagged with
As of ProFit V3.0, it is possible to output the equivalenced regions
found by iterative fitting as an alignment using the
command. 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
parameters set the printout to (machine-friendly) FASTA or PIR
formatting for the chain names and sequences.
Alignments can be exported to a text file using the
command. ProFit V3.0 can read PIR formatted files for assigning zones.
Note: For a set of fit zones to be converted into an alignment, the fitting zones must occur sequentially along the protein chain. Additionally, the fit zones cannot overlap. In other words, to obtain a sequence alignment the fitting zones must be in sequence.