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