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ARMS: Spatial Alignment with the RMS (Root Mean Square) method.
Reference of the RMS numerical algorithm:
 M. Petitjean, On the Root Mean Square Quantitative Chirality and
Quantitative Symmetry Measures, J.Math.Phys. 1999,40,4587-4595
(see appendix of ref. )
Reference of the SDM algorithm:
 M. Petitjean, Interactive Maximal Common 3D Substructure Searching
with the Combined SDM/RMS Algorithm, Comput.Chem. 1998,22,463-465
Author email: firstname.lastname@example.org
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
Input data and parameters:
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
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
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.
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. ).
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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