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
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