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ARMS: Spatial Alignment with the RMS (Root Mean Square) method.

Reference of the RMS numerical algorithm:
[1] M. Petitjean, On the Root Mean Square Quantitative Chirality and
    Quantitative Symmetry Measures, J.Math.Phys. 1999,40[9],4587-4595
    (see appendix of ref. [1])

Reference of the SDM algorithm:
[2] M. Petitjean, Interactive Maximal Common 3D Substructure Searching
    with the Combined SDM/RMS Algorithm, Comput.Chem. 1998,22[6],463-465
 
Author email: petitjean@itodys.jussieu.fr

ARMS reads the cartesian coordinates of two molecules, then optimally
rotates and translates the molecule 2 onto the molecule 1.
A pairwise correspondence between two equal length ranges of atoms
is input. The maximal common 3D motif is computed after alignment,
with the SDM algorithm.

The two input molecules should be concatenated into a single file
prior execution.


Input data and parameters:
-------------------------

INPUT  FORMAT:
  CAS : Reserved for internal purposes
  HIN : Hyperchem-type files
  MDL : Cambridge Crystallographic Model files
  ML2 : SYBYL Mol2 files
  PDB : Protein Data Bank or Nucleic Acid Data Bank files
        (only HEADER, ATOM, ENDMDL and END records are recognized)
  BIO : Biosym (MSI) files
  ISU : Reserved for internal purposes

INPUT  MOLEC FILE NAME: name of the input file containing both molecules

OUTPUT MOLEC FILE NAME: name of the output file containing the optimally
  rotated and translated molecule 2

IMOL1: sequential position number of molecule 1 in the input molecules file

IMOL2: sequential position number of molecule 2 in the input molecules file

IAT1: first atom in molecule 1 to be paired

IAT2: first atom in molecule 2 to be paired

LENGTH: number of atom pairs.
  Atoms IAT1 to IAT1-1+LENGTH are paired with atoms IAT2 to IAT2-1+LENGTH

CUT-OFF DIST:
  This parameter does NOT affect the results. It saves space and time.
  As a rule of thumb, this value should be roughly near a bondlength.
  E.g. about 1.5 to 2 for small inorganic molecules, 0.9 to 1.2 for full
  proteins, 4 to 5 for C-alpha protein backbones).

TRANSL: enter 'N' or 'n' to disable translations.
        Any other input enables translations


Output results:
--------------

The r.m.s. between the input pairs, and the optimal rotation and translation.
The size of the common 3D motif, followed by the recomputed
pairwise correspondence between the atoms in the common motif.

The new coordinates of the optimally rotated and translated molecule 2.


Remarks:
-------

The number of atoms is currently limited to 15000 for each molecule.
The source has to be recompiled to read larger molecules.

Many applications of the method involve protein backbones only,
although most PDB files contain other atoms. Building a PDB file
containing only alpha carbons involve the following steps:
- extract alpha carbons with editor and put them in a separate file.
  For unix/linux systems, it is possible to use the command:
  grep "  CA  " full_pdb_file > backbone_only_pdb_file
- edit the new file and add the adequate HEADER and END records,
  respectively at the beginning and the end of each protein backbone.
- concatenate protein backbones files in a single file.

The initial pairwise correspondence is set by the user.
An automatic search of the best input pairwise correspondence without
sequential numbering assumption is possible with the CSR freeware,
also available from the author (see ref. [2]).

The output optimal translation is splitted in two parts: one before
rotation (to be substracted), and one after rotation (to be added).

The generated file containing the output moved molecule 2 is empty for
CAS, MDL and BIO formats, and the message "EERCO2 = 1" is displayed.

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