This sounds like a job for SPASM. We used it to find instances of left-handed
helices in the PDB. See:
- SPASM: http://www.ncbi.nlm.nih.gov/pubmed/9917419
- Left-handed helices: http://www.ncbi.nlm.nih.gov/pubmed/15740737
The database for SPASM hasn't been updated for a few years, but it may
Does anyone know a good way to search for a fragment matches(~16 residue
long helix or loop) from pdb?I have a fragment of pdb and want to pull out
all the similar structures from the pdb, any easy way to do that? Thanks a
lot.
On Tue, Oct 30, 2012 at 9:34 AM, David Briggs
CCP4's gesamt should help you here. It can search a collection of PDB/mmCIF
files for a structural match, any mainchain fragment with C-alphas would do.
For searching through an archive, you need to use it off-line, from a terminal
window. Run $CCP4/bin/gesamt without parameters, it will print
