PROCHECK - Stereochemical Quality of Protein Structures ------------------------------------------------------- and AQUA for PROCHECK-NMR ------------------------- CONFIDENTIALITY AGREEMENT ------------------------- In regard to the PROCHECK suite of programs, specified in Appendix 1 herewith and the AQUA suite of programs specified in Appendix 2 herewith (the Software) supplied to us, the copyright and other intellectual property rights to which belong to the authors, we __________________________________________________________________ undertake to the authors that we shall be bound by the following terms and conditions:- 1. We will receive the Software and any related documentation in confidence and will not use the same except for the purpose of the department's own research. The Software will be used only by such of our officers or employees to whom it must reasonably be communicated to enable us to undertake our research and who agree to be bound by the same confidence. The department shall procure and enforce such agreement from its staff for the benefit of the authors. 2. The publication of research using the Software must reference "Laskowski R A, MacArthur M W, Moss D S & Thornton J M (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst., 26, 283-291." and "Rullmann J A C (1996). AQUA, Computer Program, Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands." 3. Research shall take place solely at the department's premises at __________________________________________________________________ 4. All forms of the Software will be kept in a reasonably secure place to prevent unauthorised access. 5. Each copy of the Software or, if not practicable then, any package associated therewith shall be suitably marked (and such marking maintained) with the following copyright notice: " Copyright 1992 M W MacArthur, R A Laskowski, D S Moss, J A C Rullmann & J M Thornton All Rights Reserved". 6. The Software may be modified but any changes made shall be made available to the authors. 7. The Software shall be used exclusively for academic teaching and research. The Software will not be used for any commercial research or research associated with an industrial company. 8. The confidentiality obligation in paragraph one shall not apply: (i) to information and data known to the department at the time of receipt hereunder (as evidenced by its written records); (ii) to information and data which was at the time of receipt in the public domain or thereafter becomes so through no wrongful act of the department; (iii) to information and data which the department receives from a third party not in breach of any obligation of confidentiality owed to the authors. Please sign this Undertaking and return a copy of it to indicate that you have read, understood and accepted the above terms. For and on behalf of _____________________________ _________________________________________________ .................................................. Dated ............................................ APPENDIX 1 - DETAILS OF THE PROCHECK SUITE OF PROGRAMS PROVIDED (v.3.4.3) --------------------------------------------------------------- Files to be included -------------------- 1. anglen.f } 2. anglen.inc } 3. bplot.f } 4. bplot.inc } 5. brkcln.par } 6. clean.f } 7. gfac2pdb.f } 8. gfac2pdb.inc } 9. mplot.f } 10. mplot.inc } Source program files 11. nb.c } 12. pplot.f } 13. pplot.inc } 14. ps.f } 15. rmsdev.f } 16. rmsdev.inc } 17. secstr.f } 18. sstruc.par } 19. tplot.f } 20. tplot.inc } 21. viol2pdb.f } 22. viol2pdb.inc } 23. vplot.f } 24. vplot.inc } 25. gfac2pdb.scr } 26. procheck.com } 27. procheck.scr } 28. procheck_comp.com } 29. procheck_comp.scr } 30. procheck_nmr.scr } 31. proplot.com } 32. proplot.scr } Script files 33. proplot_comp.scr } 34. proplot_nmr.scr } 35. proplot_comp.com } 36. prosub.com } 37. setup.com } 38. setup.scr } 39. viol2pdb.scr } 40. convax.for } 41. procomp.com } Installation files 42. procomp.scr } 43. maninst.ps } 44. manual.tar.Z } Documentation files 45. nmr_manual.tar.Z } 46. procheck.dat } 47. procheck.prm } Data 48. procheck_comp.prm } files 49. procheck_nmr.prm } APPENDIX 2 - DETAILS OF THE AQUA SUITE OF PROGRAMS PROVIDED (v.0.40) ----------------------------------------------------------- Files to be included -------------------- Source files:- ------------ AquaCalc.c AquaCalc.h AquaData.h AquaDist.c AquaDist.h AquaFiles.c AquaFiles.h AquaFuncts.c AquaFuncts.h AquaFuncts_biosym.c AquaFuncts_biosym.h AquaFuncts_cv.c AquaFuncts_cv.h AquaFuncts_io.c AquaFuncts_io.h AquaFuncts_pdb.c AquaFuncts_pdb.h AquaFuncts_pdbmr.c AquaFuncts_pdbmr.h AquaHow.c AquaHow.h AquaMacros.h AquaPseudo.c AquaPseudo.h AquaStrucset.c AquaStrucset.h AquaTypes.h AquaWhat.c AquaWhat.h Qext.c Qext.h Range.c Range.h cv_subs.h Script files:- ------------ ReadNrv.pm* convDIANAtorsrestr qdbext* aqdrst* convDISGEOdistrestr qguessc* aqpc* convDISGEOtorsrestr qguessr* aqpcsel convMRTABLE qhelp* aquanal.pl* convXPLORdistrestr qmodr* clean0* convXPLORtorsrestr qsplitr* convBIOSYMdistrestr makecmm* qsumm* convBIOSYMtorsrestr qconvert* qsumm_aux1* convDIANAdistrestr qconvr* qsumm_aux2* Documentation:- ------------- README models.txt qconvr.txt aqpc.txt mr.txt qdbext.txt aqua_setup.txt names.txt qext.txt biosym.txt overview.txt qhelp.txt chains.txt perl.txt qsumm.txt conversion.txt procheck.txt restraint_format.txt dbas.txt qanal.txt setup.txt intro.txt qclean.txt torsion.txt log.txt qconvert.txt xplor.txt Extras:- ------ joinpdb* splitpdb* Please complete the above form, sign it, and then send or fax to:- Roman Laskowski European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom Fax:- +44 (0)1223 494 468 If you have any problems either installing the software or running it, please e-mail your problems to:- roman@ebi.ac.uk Questions about AQUA should be directed to Ton Rullmann at rull@nmr.chem.ruu.nl