WRITE command:
WRITE fitted.pdbIf the first character of the filename is a pipe character (
WRITE |lesswill 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).
CENTRE (or CENTER) command is
given then the centre of geometry of the fitted coordinates will be
located at the origin.
If only two structures are fitted then the WRITE REFERENCE
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
vector.
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.
The 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).
The 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 RATOMS and RZONE commands have
been used, the atoms and zones used for the fitting will be used.
The 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:
RESIDUE |lesswill cause the results to be displayed on the screen using the
less pager program.
If the distance cutoff is set then residues fully outside distance cutoff are flagged with ** and residues partially outside distance cutoff are flagged with * (see Section 8.7)
The command, PAIRDIST prints the pairwise distances between equivalent atom pairs in the reference and mobile structures. PAIRDIST has the same syntax as RESIDUE. If the distance cutoff is set then residues outside the distance cutoff are flagged with *.