Reading Structures

ProFit reads files in PDB format. If compiled with XMAS support, then XMAS files may also be read, but only PDB files may be written. It uses the concept of a reference structure and a mobile structure. The reference structure remains static in space and the mobile structure is fitted onto it. When the files are specified on the command line, the reference structure is specified first, the mobile structure second.

Once in the program, you may read the reference structure using the REFERENCE command and the mobile structure using the MOBILE command. Using these commands causes the equivalent current structure to be deleted from the program's memory first. However, any zone and atom specifications (see Sections 6 and 7) are not deleted. For example, you can read p3hfl.pdb as a new reference structure using the command:

   REFERENCE p3hfl.pdb

and read p3hfm.pdb as a new mobile structure with:

   MOBILE p3hfm.pdb

If compiled with XMAS support, then the XMAS format is specified by placing the keyword XMAS after the commands REFERENCE or MOBILE:

   REFERENCE XMAS p3hfl.pdb
   MOBILE XMAS p3hfm.pdb

When you read a structure containing insertions, you will receive a warning message to this effect. This dates from when the program was unable to handle residue specifications containing insertion codes, but is still useful to draw your attention to the fact that they are present.

Note that atoms with coordinates of 9999.00, 9999.00, 9999.00 will be ignored during all calculations allowing atoms with undefined coordinates to be handled.

When fitting multiple structures (new in ProFit V2.0), you use the MULTI command to read in the structures. See Section 8.