---
name: "superpose"
section: "1"
platform: "linux"
package: "libssm-bin"
version: "1.4.0-2+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/superpose"
---

# superpose(1)

Protein Structure Superposition

## 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