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2    
3     PROCHECK - Stereochemical Quality of Protein Structures
4     -------------------------------------------------------
5     and AQUA for PROCHECK-NMR
6     -------------------------
7    
8     CONFIDENTIALITY AGREEMENT
9     -------------------------
10    
11    
12    
13     In regard to the PROCHECK suite of programs, specified in Appendix 1
14     herewith and the AQUA suite of programs specified in Appendix 2 herewith
15     (the Software) supplied to us, the copyright and other intellectual
16     property rights to which belong to the authors, we
17    
18     __________________________________________________________________
19    
20     undertake to the authors that we shall be bound by the following terms and
21     conditions:-
22    
23     1. We will receive the Software and any related documentation in confidence
24     and will not use the same except for the purpose of the department's own
25     research. The Software will be used only by such of our officers or
26     employees to whom it must reasonably be communicated to enable us to
27     undertake our research and who agree to be bound by the same confidence.
28     The department shall procure and enforce such agreement from its staff for
29     the benefit of the authors.
30    
31     2. The publication of research using the Software must reference
32    
33     "Laskowski R A, MacArthur M W, Moss D S & Thornton J M (1993). PROCHECK:
34     a program to check the stereochemical quality of protein
35     structures. J. Appl. Cryst., 26, 283-291."
36    
37     and
38    
39     "Rullmann J A C (1996). AQUA, Computer Program, Department of NMR
40     Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht
41     University, The Netherlands."
42    
43    
44     3. Research shall take place solely at the department's premises at
45    
46     __________________________________________________________________
47    
48     4. All forms of the Software will be kept in a reasonably secure place to
49     prevent unauthorised access.
50    
51     5. Each copy of the Software or, if not practicable then, any package
52     associated therewith shall be suitably marked (and such marking maintained)
53     with the following copyright notice: " Copyright 1992 M W MacArthur, R A
54     Laskowski, D S Moss, J A C Rullmann & J M Thornton All Rights Reserved".
55    
56     6. The Software may be modified but any changes made shall be made
57     available to the authors.
58    
59     7. The Software shall be used exclusively for academic teaching and
60     research. The Software will not be used for any commercial research or
61     research associated with an industrial company.
62    
63     8. The confidentiality obligation in paragraph one shall not apply:
64    
65     (i) to information and data known to the department at the time of
66     receipt hereunder (as evidenced by its written records);
67    
68     (ii) to information and data which was at the time of receipt in the
69     public domain or thereafter becomes so through no wrongful act of
70     the department;
71    
72     (iii) to information and data which the department receives from a third
73     party not in breach of any obligation of confidentiality owed to
74     the authors.
75    
76    
77    
78     Please sign this Undertaking and return a copy of it to indicate that you
79     have read, understood and accepted the above terms.
80    
81    
82    
83     For and on behalf of _____________________________
84    
85     _________________________________________________
86    
87     ..................................................
88    
89     Dated ............................................
90    
91    
92    
93    
94     APPENDIX 1 - DETAILS OF THE PROCHECK SUITE OF PROGRAMS PROVIDED (v.3.4.3)
95     ---------------------------------------------------------------
96    
97     Files to be included
98     --------------------
99    
100     1. anglen.f }
101     2. anglen.inc }
102     3. bplot.f }
103     4. bplot.inc }
104     5. brkcln.par }
105     6. clean.f }
106     7. gfac2pdb.f }
107     8. gfac2pdb.inc }
108     9. mplot.f }
109     10. mplot.inc } Source program files
110     11. nb.c }
111     12. pplot.f }
112     13. pplot.inc }
113     14. ps.f }
114     15. rmsdev.f }
115     16. rmsdev.inc }
116     17. secstr.f }
117     18. sstruc.par }
118     19. tplot.f }
119     20. tplot.inc }
120     21. viol2pdb.f }
121     22. viol2pdb.inc }
122     23. vplot.f }
123     24. vplot.inc }
124     25. gfac2pdb.scr }
125     26. procheck.com }
126     27. procheck.scr }
127     28. procheck_comp.com }
128     29. procheck_comp.scr }
129     30. procheck_nmr.scr }
130     31. proplot.com }
131     32. proplot.scr } Script files
132     33. proplot_comp.scr }
133     34. proplot_nmr.scr }
134     35. proplot_comp.com }
135     36. prosub.com }
136     37. setup.com }
137     38. setup.scr }
138     39. viol2pdb.scr }
139     40. convax.for }
140     41. procomp.com } Installation files
141     42. procomp.scr }
142     43. maninst.ps }
143     44. manual.tar.Z } Documentation files
144     45. nmr_manual.tar.Z }
145     46. procheck.dat }
146     47. procheck.prm } Data
147     48. procheck_comp.prm } files
148     49. procheck_nmr.prm }
149    
150    
151     APPENDIX 2 - DETAILS OF THE AQUA SUITE OF PROGRAMS PROVIDED (v.0.40)
152     -----------------------------------------------------------
153    
154     Files to be included
155     --------------------
156    
157     Source files:-
158     ------------
159    
160     AquaCalc.c AquaCalc.h
161     AquaData.h
162     AquaDist.c AquaDist.h
163     AquaFiles.c AquaFiles.h
164     AquaFuncts.c AquaFuncts.h
165     AquaFuncts_biosym.c AquaFuncts_biosym.h
166     AquaFuncts_cv.c AquaFuncts_cv.h
167     AquaFuncts_io.c AquaFuncts_io.h
168     AquaFuncts_pdb.c AquaFuncts_pdb.h
169     AquaFuncts_pdbmr.c AquaFuncts_pdbmr.h
170     AquaHow.c AquaHow.h
171     AquaMacros.h
172     AquaPseudo.c AquaPseudo.h
173     AquaStrucset.c AquaStrucset.h
174     AquaTypes.h
175     AquaWhat.c AquaWhat.h
176     Qext.c Qext.h
177     Range.c Range.h
178     cv_subs.h
179    
180     Script files:-
181     ------------
182     ReadNrv.pm* convDIANAtorsrestr qdbext*
183     aqdrst* convDISGEOdistrestr qguessc*
184     aqpc* convDISGEOtorsrestr qguessr*
185     aqpcsel convMRTABLE qhelp*
186     aquanal.pl* convXPLORdistrestr qmodr*
187     clean0* convXPLORtorsrestr qsplitr*
188     convBIOSYMdistrestr makecmm* qsumm*
189     convBIOSYMtorsrestr qconvert* qsumm_aux1*
190     convDIANAdistrestr qconvr* qsumm_aux2*
191    
192     Documentation:-
193     -------------
194     README models.txt qconvr.txt
195     aqpc.txt mr.txt qdbext.txt
196     aqua_setup.txt names.txt qext.txt
197     biosym.txt overview.txt qhelp.txt
198     chains.txt perl.txt qsumm.txt
199     conversion.txt procheck.txt restraint_format.txt
200     dbas.txt qanal.txt setup.txt
201     intro.txt qclean.txt torsion.txt
202     log.txt qconvert.txt xplor.txt
203    
204     Extras:-
205     ------
206     joinpdb* splitpdb*
207    
208    
209    
210     Please complete the above form, sign it, and then send or fax to:-
211    
212    
213     Roman Laskowski
214     European Bioinformatics Institute,
215     Wellcome Trust Genome Campus,
216     Hinxton,
217     Cambridge, CB10 1SD,
218     United Kingdom
219    
220     Fax:- +44 (0)1223 494 468
221    
222     If you have any problems either installing the software or running it,
223     please e-mail your problems to:-
224    
225     roman@ebi.ac.uk
226    
227     Questions about AQUA should be directed to Ton Rullmann at
228    
229     rull@nmr.chem.ruu.nl

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