Hi, I currently have an implementation of DSSP in C++ with lots of improvements such as correctly identifying Pi-helices.
The output of the program is pseudo-PDB, so you could paste it to the top of your PDB file and most programs, including PyMol would read it accurately. The output additionally includes geometrical parameters for each helix, and direction vectors as well as chirality to distinguish right from left handed helices. --sample output start -- REMARK ----------------------------------------------------------------------- REMARK Secondary Structure Definition program - (c) Michel N. Fodje, 2001-02 REMARK Based on method described in: REMARK Fodje and Al-Karadaghi (2002) REMARK Protein Engineering vol.15 no.5 pp.335-358 REMARK ----------------------------------------------------------------------- HEADER LYASE 22-DEC-99 1DOZ REMARK PDB helix K&S REMARK from to class geometry axis dir Chiral length REMARK HLX-# |-resid -| |-resid -| | r d n x y z | HELIX 1 1 ILE A 22 ILE A 29 1 2.3 1.5 3.7 0.4 0.4 -0.8 H+ 8 HELIX 2 2 PRO A 37 ALA A 49 1 2.3 1.5 3.6 0.6 -0.1 0.8 H+ 13 HELIX 3 3 PRO A 55 ILE A 74 1 2.3 1.5 3.7 0.6 0.7 0.3 H+ 20 HELIX 4 4 ILE A 93 LYS A 102 1 2.3 1.5 3.6 0.0 0.8 0.6 H+ 10 HELIX 5 5 VAL A 122 LEU A 136 1 2.3 1.5 3.7 -0.5 0.8 0.2 H+ 15 HELIX 6 6 PRO A 151 SER A 167 1 2.3 1.5 3.6 0.1 -1.0 0.2 H+ 17 HELIX 7 7 GLU A 170 ARG A 173 1 2.2 1.6 3.6 0.1 0.6 -0.8 H+ 4 HELIX 8 8 TYR A 196 GLY A 210 1 2.3 1.5 3.7 0.6 -0.4 0.7 H+ 15 HELIX 9 9 VAL A 235 LYS A 246 1 2.4 1.4 3.8 0.7 -0.7 -0.1 H+ 12 HELIX 10 10 LEU A 263 LEU A 266 1 2.4 1.5 3.9 0.4 -0.9 -0.2 H+ 4 HELIX 11 11 GLU A 272 ASP A 279 1 2.3 1.5 3.6 0.4 -0.9 -0.2 H+ 8 HELIX 12 12 PRO A 294 LYS A 307 1 2.3 1.5 3.6 0.2 0.9 -0.5 H+ 14 HELIX 13 13 LEU A 266 CYS A 273 3 2.7 1.2 4.2 0.4 -0.9 -0.3 I+ 8 HELIX 14 14 GLU A 19 ASP A 21 5 2.1 1.8 3.4 -0.1 0.2 -1.0 G+ 3 HELIX 15 15 ILE A 29 GLY A 32 5 2.2 1.8 3.5 0.9 0.1 0.3 G+ 4 HELIX 16 16 GLU A 187 PHE A 192 5 2.1 1.8 3.2 0.6 0.8 -0.2 G+ 6 SHEET 1 A 4 LYS A 4 ALA A 12 -1 SHEET 2 A 4 ILE A 78 LEU A 86 -1 SHEET 3 A 4 GLU A 107 VAL A 112 -1 SHEET 4 A 4 THR A 140 SER A 143 -1 SHEET 1 B 4 MET A 177 HIS A 183 -1 SHEET 2 B 4 TYR A 216 GLN A 221 -1 SHEET 3 B 4 ALA A 250 VAL A 254 -1 SHEET 4 B 4 SER A 283 TYR A 285 -1 --sample output end -- You can currently access it from the web at: http://www.mbfys.lu.se/Services/SecStr/ The source code should be available at the same site in the near future when the documentation is complete. My pythonese is not up to notch, otherwise I would really like to contribute code to this fine project. /Michel On Tue, 2002-09-10 at 15:48, Gareth Stockwell wrote: > David, > > Have a look at the rTools package on Kristian Rother's page > > http://www.rubor.de/bioinf/ > > (I haven't used this myself, and it appears to have some external > dependencies - notably Java, but it may be what you want) > > Gareth > > > On Tue, 2002-09-10 at 14:11, David Guerra Aragao wrote: > > Hello to all, > > > > I would like to use DSSP secondary structure assignments but I don't > > know how to incorporate DSSP output in pdb format for PyMOL. > > > > I have found plenty of information arround but none about this issue. > > > > Can i get some help ? > > > > David > > > > -- > > David Aragao > > Linux User nº 237333 on http://counter.li.org/ > > "You will pay for your sins. If you have already paid, please disregard > > this message." > > > > > > > > > > > > ------------------------------------------------------- > > This sf.net email is sponsored by: OSDN - Tired of that same old > > cell phone? Get a new here for FREE! > > https://www.inphonic.com/r.asp?r_______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- > ----------------------------------------------------------------------------- > Gareth Stockwell > EMBL - European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > gar...@ebi.ac.uk > Tel 01223 492548 Personal homepage: > http://www.ebi.ac.uk/~gareth > > > > > ------------------------------------------------------- > This sf.net email is sponsored by: OSDN - Tired of that same old > cell phone? Get a new here for FREE! > https://www.inphonic.com/r.asp?r=sourceforge1&refcode1=vs3390 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users _______________________ Michel N. Fodje Molecular Biophysics, Lund University, Sweden phone: +46 46 222 45 13 email: michel.fo...@mbfys.lu.se web: http://www.mbfys.lu.se _______________________
