| expdbins.exe |
|
Exchange format: PDB → SHELX or SHEL X→ PDB
2022.3.30
Program: expdbins15.exe.zip (Windows) /
expdbins15.zip (macOS10 High Sierra) Input fileFtest1b.ins (SHELX format) Output file: test1b_1.pdb (PDB format)
*Download each file by right-click. *2019.3.29: Additional comments lines are put in res file after TITL line in SHELXL2016. This causes an error in running, and then the file format is judged by the file extension (res, ins, pdb). Moreover, the output file is numbering by addition number of _1, _2, _3 ... _0. Exsample: xxxx.res → xxxx_1.pdb, xxxx_1.pdb → xxxx_2.res SHELX ins or res file
TITL Tyrocidine-B(Z) P212121 REM c[Val-Orn-Leu-D-Phe-Pro-Tyr-Gln-Asn-D-Phe-Trp] CELL 0.836 34.1331 9.5394 30.2385 90.000 90.000 90.000 ZERR 4.00 0.0068 0.0019 0.0060 0.000 0.000 0.000 LATT -1 SYMM 0.5-X,-Y,0.5+Z SYMM 0.5+X,0.5-Y,-Z SYMM -X,0.5+Y,0.5-Z SFAC C H N O UNIT 272 352 56 52 RESI 1 TTY © residue number and name C018 1 0.50674 1.07911 0.50833 11.00 0.05000 1 C021 1 0.52722 1.14772 0.53826 11.00 0.05000 1 C010 1 0.49905 1.12708 0.46133 11.00 0.05000 1 C003 1 0.53326 1.09592 0.58496 11.00 0.05000 1 C035 1 0.54418 1.26727 0.52441 11.00 0.05000 1 ... USAGE
Save program and data in the same directoy. Double click expdbins.exe and command line is coming up. Red fonts are inputs on the window. ---
Exchange Format between PDB and INS files
This is an expart namer for oligopeptide
Input PDB/INS file: test1b.ins
INPUT> File format was SHELXS/L
Put Uij (ANISOU) into PDB [Y/*N]: [return]
SHELX= Tyrocidine-B(Z) P212121 ←judged as input is a SHELX file
SHELX= REM c[Val-Orn-Leu-D-Phe-Pro-Tyr-Gln-Asn-D-Phe-Trp]
SHELX= CELL 0.836 34.1331 9.5394 30.2385 90.000 90.000 90.000
SHELX= ZERR 4.00 0.0068 0.0019 0.0060 0.000 0.000 0.000
SHELX= LATT -1
SHELX= SYMM 0.5-X,-Y,0.5+Z
SHELX= SYMM 0.5+X,0.5-Y,-Z
SHELX= SYMM -X,0.5+Y,0.5-Z
SHELX= SFAC C H N O
SHELX= UNIT 272 352 56 52
NATOM> Read 97 atoms
REMA> TITL Tyrocidine-B(Z) P212121|REM c[Val-Orn-Leu-D-Phe-Pro-Tyr-Gln-Asn-
REMA> D-Phe-Trp]|CELL 0.836 34.1331 9.5394 30.2385 90.000 90.000 90.0
REMA> 00|ZERR 4.00 0.0068 0.0019 0.0060 0.000 0.000 0.000|LATT
REMA> -1|SYMM 0.5-X,-Y,0.5+Z|SYMM 0.5+X,0.5-Y,-Z|SYMM -X,0.5+Y,0.5-Z|S
REMA> FAC C H N O|UNIT 272 352 56 52
CELL> 34.133 9.539 30.239 90.000 90.000 90.000
Remove hydrogens [Y/*N]: [return]
SPACE GROUP: [return]
Put CONECT informations to PDB [y/*n]: [return]
Output file name: test1b_1.pdb ← File extension was changed and file number was added.
Job finshed. OK? [return]
---
test1b_1.pdb
HEADER File converted at Input SHELXS/L INS file: test1b.pdb EXPDTA X-Ray diffraction REMA TITL Tyrocidine-B(Z) P212121 REMA REM c[Val-Orn-Leu-D-Phe-Pro-Tyr-Gln-Asn-D-Phe-Trp] REMA CELL 0.836 34.1331 9.5394 30.2385 90.000 90.000 90.000 REMA ZERR 4.00 0.0068 0.0019 0.0060 0.000 0.000 0.000 REMA LATT -1 REMA SYMM 0.5-X,-Y,0.5+Z REMA SYMM 0.5+X,0.5-Y,-Z REMA SYMM -X,0.5+Y,0.5-Z REMA SFAC C H N O REMA UNIT 272 352 56 52 REMA ↑ SHELX data were stored at the header region. CRYST1 34.133 9.539 30.239 90.00 90.00 90.00 P 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.029297 0.000000 0.000000 0.00000 SCALE2 -0.000000 0.104828 0.000000 0.00000 SCALE3 0.000000 -0.000000 0.033070 0.00000 ATOM 1 C018 TTY 1 17.297 10.294 15.371 1.00 3.95 ATOM 2 C021 TTY 1 17.996 10.949 16.276 1.00 3.95 ATOM 3 C010 TTY 1 17.034 10.752 13.950 1.00 3.95 ATOM 4 C003 TTY 1 18.202 10.454 17.688 1.00 3.95 ATOM 5 C035 TTY 1 18.575 12.089 15.857 1.00 3.95 ATOM 6 C016 TTY 1 15.815 10.121 13.485 1.00 3.95 ATOM 7 C033 TTY 1 18.269 10.415 12.935 1.00 3.95 ...□ □ □ |