Multiple Structure Fitting

The MULTI command allows a multiple set of structures to be read in for fitting. The filename specified for MULTI is a `file of files' i.e. it contains a list of filenames which will be read.

MULTI is used in place of REFERENCE and MOBILE to read in a set of structure files. 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).

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

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

When the MWRITE command is used, the output filenames are the same as the input files, but with the extension replaced by that specified in the MWRITE command. If no extension is specified, then `.fit' will be used. If the input structure files contained no extension, then the extension specified will be appended to the filenames.

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.

Multiple-structure fitting is particularly effective in combination with the ITERATE command (see Section 8.4) which refines the fitting zones iteratively. This can lead to extremely good multiple structures fits.

Note that multiple structure fitting and zone iteration can be very slow as these have been added to the earlier pair-wise fitting engine. An increase in speed needs a complete re-design of the code.

Specifying Zones With Multiple Structure Fitting

Currently, the ZONE command may only be used with multiple structure fitting when the same zone specification may be applied to every structure. i.e. You cannot specify a zone for each structure separating the zones with a colon (:)

Thus, the following are legal zones:

  ZONE 20-30
  ZONE C,3

while the following are not:

  ZONE 24-34:25-35
  ZONE CAR:VNS
  ZONE 24-34:EIR,11

For normal use, it is recommended that the ALIGN and READALIGNMENT commands (possibly in conjunction with the LIMIT command) are used for specifying zones when fitting multiple structures.

Note however, that when using READALIGNMENT 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.

Note that a bug in using the READALIGNMENT with multiple structure fitting was fixed in V2.3. (The bug caused the program to crash if a deletion appeared in the same place in two or more of the sequences.)