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Revision 1.1 - (show annotations) (download)
Sun Jul 18 18:16:05 2010 UTC (3 years, 9 months ago) by jlec
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procheck license added

1
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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