CONVERT STRIDE SECONDARY STRUCTURE TO PDB FORMAT

This program reads in a STRIDE output file and converts the secondary structure in it to PDB format. For SHEET, some of the secondary structure is missing. For SHEET, each strand is recorded as being its own beta sheet, without matching it to other strands, and has sheetID = A. This is enough SHEET information for use by the VALPRED program. Please provide a STRIDE file. See format here. Upload the STRIDE file from your computer. Please note that this STRIDE file is not validated, so make sure that it is a valid STRIDE file. or Enter the STRIDE file contents here. Please note that these STRIDE file contents are not validated, so make sure that they are valid STRIDE file contents. (Provide either a file or enter the contents here, not both. If both provided, then contents here will be processed instead of uploaded file.) Display results on screen Write results to output file Here is an example of STRIDE output that is input to this program : REM  -------------------- Secondary structure summary -------------------  ~~~~ REM                                                                        ~~~~ CHN  SDH_HUMAN.pdb A                                                       ~~~~ REM                                                                        ~~~~ REM                .         .         .         .         .               ~~~~ SEQ  1    SAQYPVVDHEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHTV   50          ~~~~ STR       TTTTTEEEEEEEEEEE   HHHHHHHHHHHHH   EEEETTTTGGG GGG               ~~~~ REM                                                                        ~~~~ LOC  AlphaHelix   GLY    71 A      ALA     83 A                            ~~~~ LOC  AlphaHelix   TRP   119 A      SER    130 A                            ~~~~ LOC  AlphaHelix   GLN   136 A      TYR    156 A                            ~~~~ LOC  AlphaHelix   ARG   195 A      ARG    210 A                            ~~~~ LOC  310Helix     VAL   395 A      LYS    397 A                            ~~~~ LOC  310Helix     ASP   545 A      LYS    547 A                            ~~~~ LOC  310Helix     PHE   618 A      GLU    620 A                            ~~~~ LOC  310Helix     LEU    65 B      LYS     67 B                            ~~~~ LOC  Strand       VAL    57 A      VAL     67 A                            ~~~~ LOC  Strand       THR    87 A      VAL     90 A                            ~~~~ LOC  Strand       ILE   107 A      ASN    108 A                            ~~~~ LOC  Strand       GLN   170 A      ARG    171 A                            ~~~~ LOC  TurnIV       SER    52 A      TYR     55 A                            ~~~~ LOC  TurnVIII     ALA    53 A      PRO     56 A                            ~~~~ LOC  TurnVIII     PHE    62 A      VAL     65 A                            ~~~~ LOC  TurnIV       THR    91 A      PHE     94 A                            ~~~~ LOC  TurnIV       GLY   112 A      GLU    115 A                            ~~~~ LOC  TurnI'       SER   130 A      LEU    133 A                            ~~~~ LOC  TurnI        THR   163 A      GLY    166 A                            ~~~~ LOC  GammaInv     GLU   154 B      TYR    156 B                            ~~~~ LOC  GammaInv     LEU   234 B      ASP    236 B                            ~~~~ Here is an example of output from this program that is in PDB format : HELIX    1   1 GLY A   28  ALA A   41  1                                  14 HELIX    2   2 PHE A   52  ALA A   61  5                                  10 HELIX    3   3 ASN A   76  SER A   88  1                                  13 HELIX    4   4 ASP A   93  GLY A  115  1                                  23 HELIX   34  34 CYS D   65  VAL D   92  1                                  28 HELIX   35  35 GLY D   94  HIS D  122  1                                  29 HELIX   36  36 GLY D  125  LYS D  135  1                                  11 SHEET    1   A 1 VAL A  15  GLU A  19  0 SHEET    1   A 1 ILE A 202  ARG A 206  0 SHEET    1   A 1 GLU A 188  CYS A 196  0 SHEET    1   A 1 TYR A 177  GLU A 185  0 SHEET    1   A 1 SER A 172  VAL A 175  0 SHEET    1   A 1 THR A  45  THR A  49  0 SHEET    1   A 1 ALA A  22  VAL A  25  0 SHEET    1   A 1 ASN A 209  VAL A 212  0 SHEET    1   A 1 GLN A 386  ALA A 395  0 SHEET    1   A 1 GLN A 378  VAL A 383  0 SOURCE CODE : STRIDEtoPDBsecondarystruct_pl.txt COPYRIGHT : Copyright © 2010 Emma Rath. All rights reserved. Soon this program will be released under an open source software license such as GNU General Public License or Creative Commons license for Free Software Foundation's GNU General Public License at creativecommons.org