1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
|
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
|
