focal (1) superpose.1.gz

NAME

       superpose - Protein Structure Superposition

USAGE

              superpose q.pdb [-s CIDQ] t1.pdb [-s CID1] ... tN.pdb [-s CIDN] [-o foo_out.pdb]

       where  q.pdb  is  the  Query  structure  to  which transformation applied, ti.pdb is the ith fixed Target
       structure, [-s CIDi] are optional selection strings in MMDB convention, and [-o foo_out.pdb] is  optional
       output file specification.

       If more than one target is specified, multiple structure alignment is calculated.

       Instead of using asterisks '*' for selecting all atoms, '-all'

       may be used, such that

              superpose q.pdb -s * t.pdb -s * foo_out.pdb

       and

              superpose q.pdb -s -all t.pdb -s -all foo_out.pdb

       are equivalent.

REFERENCES

       Collaborative  Computational  Project,  Number  4.  2011.   "Overview  of  the  CCP4  suite  and  current
       developments". Acta Cryst. D67, 235-242.  as well as any specific reference in the program write-up.

       E. Krissinel and K. Henrick (2004). Secondary-structure matching (SSM),  a  new  tool  for  fast  protein
       structure      alignment      in      three      dimensions.      Acta     Cryst.     D60,     2256-2268.
       http://www.ebi.ac.uk/msd-srv/ssm/papers/ssm_reprint.pdf