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.