Index

2.Copyright notice

1. About the Program

This computer program has many uses. Its primary use is to optimize the fit of a subset of atomic coordinates from one structure (Working Structure) to the same subset of another structure (Reference Structure). The centroid of the working subset is first moved to that of the reference set and then a rotation matrix is derived using a method suggested by Kabsch. The rotation matrix gives vector w' = [R] w. The matrix [R] is defined relative to an orthogonal coordinate systems. The whole of the working coordinate set can be transformed and output in an orientation matching that of the reference set.The subset can be defined either by residue numbers with options for main chain only,side chain only or Ca's, or by the position of the atoms in the file.The program can also give the same statistics of fit (eg rms differences between atom pairs,etc) without any transformation of the working coordinates.

This package consists of 3 modules. The main program, that performes the calculation and optimizes the fit of the two structures, is written using Fortran 77. The output is made by two modules written utilising C++ where as the graphical representation is made by the Chemscape Chime 2.0.2 Java pugin developed by MDL Inc.( download here). The Input page is written in HTML 4.0, whereas the the input of the files can be made by either retrieving from PDB or uploading from the user's computer (both scripts were written utilising Perl 5.005).

The calculation is executed on a web server located at the Departement of Biology of the University of Athens. The machine is an o2 SGI with a 180 MHz R5000 processor and 192 Mbytes of main memory.

The results are displayed either in text or in text/graphics mode(the Chemscape Chime 2.0.2 is necessary to be installed).