[ccp4bb] protein segments from pdb
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
Re: [ccp4bb] protein segments from pdb
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 -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603634Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] protein segments from pdb
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
