I see that my questions was highly ambiguous/unclear. Martyn saw
through it anyway. pdbcur does what I want.
Andreas
On 10/08/2011 5:32, Martyn Winn wrote:
If you mean what I think you mean, then use the SUMMarise option of
pdbcur. That gives output like:
Chain "A" has 505 residues
in 7 spans: 1-305 307-500 711-711 716-716 719-719 721-722 730-730
0 residues have alternative conformations
Composition: ALA 23 ARG 23 ASN 36 ASP 24
CYS 34 CYH 0 GLN 21 GLU 30
GLY 38 HIS 11 ILE 29 LEU 44
LYS 32 MET 8 PHE 17 PRO 21
SER 36 THR 28 TRP 5 TYR 13
VAL 26 HEM 0 WAT 0 SUL 0
END 0 DUM 0 Other 6
HTH
Martyn
On Wed, 2011-08-10 at 17:24 +0100, Andreas Förster wrote:
Dear all,
how do you extract segments from a pdb file, so that from an input pdb
file you get output like this:
10-103, 120-174, 200-240
or, better yet:
A: 10-103, 120-174, 200-240
B: 10-104, 120-174, 199-241
if the N terminus is missing and there are two gaps in the structure.
I tend to open the pdb file with PyMOL and click on the ends, but a
script/command would be much quicker.
Thanks.
Andreas
--
Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk
