Uppsala Software Factory - GETSSE Manual

• 1 GETSSE - GENERAL INFORMATION

• 2 REFERENCES

• 3 VERSION HISTORY

• 4 INTRODUCTION

• 5 KNOWN BUGS

Program : GETSSE
Version : 041001
Author : Gerard J. Kleywegt, Dept. of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : generating a DEJAVU-style SSE file from a PDB file
Package : DEJAVU

Reference(s) for this program:

* 1 * G.J. Kleywegt & T.A. Jones (1994). Halloween ... Masks and Bones. In "From First Map to Final Model", edited by S. Bailey, R. Hubbard and D. Waller. SERC Daresbury Laboratory, Warrington, pp. 59-66. [http://xray.bmc.uu.se/gerard/papers/halloween.html]

* 2 * G.J. Kleywegt & T.A. Jones (1997). Detecting folding motifs and similarities in protein structures. Methods in Enzymology 277, 525-545.

* 3 * D. Madsen & G.J. Kleywegt (2002). Interactive motif and fold recognition in protein structures. J. Appl. Cryst. 35, 137-139. [http://scripts.iucr.org/cgi-bin/paper?wt0007]

* 4 * M. Novotny, D. Madsen & G.J. Kleywegt (2004). An evaluation of protein-fold-comparison servers. Proteins, 54, 260-270 (2004). [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=14696188&dopt=Citation]

* 5 * Kleywegt, G.J., Zou, J.Y., Kjeldgaard, M. & Jones, T.A. (2001). Around O. In: "International Tables for Crystallography, Vol. F. Crystallography of Biological Macromolecules" (Rossmann, M.G. & Arnold, E., Editors). Chapter 17.1, pp. 353-356, 366-367. Dordrecht: Kluwer Academic Publishers, The Netherlands.

991213 - 0.1 - first version
991220 - 0.2 - minor changes
041001 - 0.3 - replaced Kabsch' routine U3BEST by quaternion-based routine (U3QION) to do least-squares superpositioning

This program can be used to generated an SSE file for DEJAVU from a PDB file of a protein (SSE = Secondary Structure Element(s)). GETSSE replaces the old "make_sse" script and the programs PRO1 and PRO2. Operation should be trivial:

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 % 575 gerard sarek 21:22:46 progs/secs > GETSSE
   
 *** GETSSE *** GETSSE *** GETSSE *** GETSSE *** GETSSE *** GETSSE ***
   
 Version  - 991213/0.1
 (C) 1992-1999 Gerard J. Kleywegt, Dept. Cell Mol. Biol., Uppsala (S)
 User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL)
 Others   - T.A. Jones, G. Bricogne, Rams, W.A. Hendrickson
 Others   - W. Kabsch, CCP4, PROTEIN, E. Dodson, etc. etc.
   
 Started  - Mon Dec 13 21:25:22 1999
 User     - gerard
 Mode     - interactive
 Host     - sarek
 ProcID   - 24871
 Tty      - /dev/ttyq15
   
 *** GETSSE *** GETSSE *** GETSSE *** GETSSE *** GETSSE *** GETSSE ***
   
 Reference(s) for this program:
   
 *  1 * G.J. Kleywegt (1992-1999).
        Uppsala University, Uppsala, Sweden.
        Unpublished program.
   
 *  2 * G.J. Kleywegt, J.Y. Zou, M. Kjeldgaard & T.A. Jones (2000).
        Chapter 17.1.  Around O. Int. Tables for Crystallography,
        Volume F. Submitted.
   
 ==> For manuals and up-to-date references, visit:
 ==> http://xray.bmc.uu.se/usf
   
 *** GETSSE *** GETSSE *** GETSSE *** GETSSE *** GETSSE *** GETSSE ***
   
 4-Character molecule name or ID ? (QQQQ) 0CBS
   
 Description of molecule         ? (...) crabp II
   
 Full pathname of input PDB file ? (qqqq.pdb) 1cbs.pdb
   
 Name of output SSE file         ? (qqqq.sse) 1cbs.sse
 ==> Found file in GKPATH : (/nfs/pdb/full/1cbs.pdb)
   
 Reading PDB file ...
   
 Nr of residues read : (        137)
   
 Doing YASSPA ...
 Nr of ALPHA residues : (         19)
 Nr of BETA  residues : (         69)
   
 Writing SSE file ...
 Nr of ALPHA helices : (          2)
 Nr of BETA  strands : (         11)
   
 *** GETSSE *** GETSSE *** GETSSE *** GETSSE *** GETSSE *** GETSSE ***
   
 Version - 991213/0.1
 Started - Mon Dec 13 21:25:22 1999
 Stopped - Mon Dec 13 21:25:41 1999
   
 CPU-time taken :
 User    -      0.1 Sys    -      0.0 Total   -      0.1
   
 *** GETSSE *** GETSSE *** GETSSE *** GETSSE *** GETSSE *** GETSSE ***
   
 >>>>>>>>>>>>>> USF .... Uppsala Software Factory <<<<<<<<<<<<<<
 >>>>>>>>>> This program: (C) 1992-1999, G J Kleywegt <<<<<<<<<<
 >>>>>>>>>>>>>>>> E-mail: gerard@xray.bmc.uu.se <<<<<<<<<<<<<<<<
 >>>>>>>>>>>>>>>>>> http://xray.bmc.uu.se/usf <<<<<<<<<<<<<<<<<<
   
 *** GETSSE *** GETSSE *** GETSSE *** GETSSE *** GETSSE *** GETSSE ***
   
STOP ... Toodle pip ... statement executed
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
   

Your SSE file should look as follows:

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
!
! ===  0CBS
!
MOL    0CBS
NOTE   crabp II
PDB    1cbs.pdb
!
BETA  'B1' '6' '8' 3 28.80 22.68 37.21 30.80 19.42 31.45
BETA  'B2' '11' '13' 3 29.01 12.74 24.85 24.59 12.26 19.77
ALPHA 'A1' '15' '22' 8 22.39 17.20 17.68 13.43 21.94 13.57
ALPHA 'A2' '26' '36' 11 22.75 24.44 6.74 27.25 23.42 21.31
BETA  'B3' '39' '46' 8 28.85 24.20 26.75 16.44 23.72 46.06
BETA  'B4' '49' '56' 8 12.87 24.55 42.35 27.98 28.83 24.68
BETA  'B5' '59' '65' 7 23.78 31.66 22.88 11.06 26.64 37.13
BETA  'B6' '70' '72' 3 3.91 26.10 34.06 7.83 30.06 29.64
BETA  'B7' '82' '86' 5 4.99 27.20 27.49 6.95 16.62 35.94
BETA  'B8' '92' '99' 8 14.02 11.84 35.98 4.36 26.72 21.04
BETA  'B9' '106' '113' 8 6.26 18.45 18.87 20.63 11.50 37.09
BETA  'B10' '118' '125' 8 26.24 11.41 35.46 11.63 16.96 17.92
BETA  'B11' '128' '135' 8 14.29 12.49 16.41 29.70 14.76 34.39
ENDMOL
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
   

None, at present.