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CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules.


M. Petitjean, Interactive Maximal Common 3D Substructure Searching
with the Combined SDM/RMS Algorithm, Comput. Chem. 1998,22[6],463-465).

Author email:

CSR reads the cartesian coordinates of two molecules, then optimally rotates and
translates the molecule 2 onto the molecule 1 to find the maximal common 3D motif.

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

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

ITERMX: maximum number of iterations; recommended value: about 200 for
  small molecules (<100at.), about 2000 for a hundred to a thousand atoms,
  and 20000 for larger molecules

  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).

Output results:

The size N of the common 3D motif, and the r.m.s. between the N pairs
of atoms, followed by the one-to-one correspondence between the N atoms
of molecule 1 and the N atoms of molecule 2.

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.

To operate on C-alpha protein backbones, the other atoms should be
removed prior execution.

The computing time is roughly proportional to the product n1*n2 of
the number of atoms of the two molecules, and proportional to the
number of iterations (reading and writing files not included).

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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Modified: Sat Jan 4 06:14:14 2003 GMT
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