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23 """Module containing the introductory text container."""
24
25
26 import dep_check
27
28
29 if dep_check.ctypes_module:
30 import ctypes
31 if hasattr(ctypes, 'windll'):
32 import ctypes.wintypes
33 else:
34 ctypes = None
35 if dep_check.ctypes_structure_module:
36 from ctypes import Structure
37 else:
38 Structure = object
39 import numpy
40 from os import environ, waitpid
41 import platform
42 PIPE, Popen = None, None
43 if dep_check.subprocess_module:
44 from subprocess import PIPE, Popen
45 import sys
46 from textwrap import wrap
47
48
49 from status import Status; status = Status()
50 from version import revision, url, version, version_full
51
52
54 """A container storing information about relax."""
55
56
57 instance = None
58
60 """Create the program introduction text stings.
61
62 This class generates a container with the following objects:
63 - title: The program title 'relax'
64 - version: For example 'repository checkout' or '1.3.8'.
65 - desc: The short program description.
66 - copyright: A list of copyright statements.
67 - licence: Text pertaining to the licencing.
68 - errors: A list of import errors.
69 """
70
71
72 self.title = "relax"
73 self.version = version
74
75
76 self.website = "http://www.nmr-relax.com"
77
78
79 self.desc = "Molecular dynamics by NMR data analysis"
80
81
82 self.desc_long = "The program relax is designed for the study of the dynamics of proteins or other macromolecules though the analysis of experimental NMR data. It is a community driven project created by NMR spectroscopists for NMR spectroscopists. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, and the Lipari and Szabo model-free analysis."
83
84
85 self.copyright = []
86 self.copyright.append("Copyright (C) 2001-2006 Edward d'Auvergne")
87 self.copyright.append("Copyright (C) 2006-2013 the relax development team")
88
89
90 self.licence = "This is free software which you are welcome to modify and redistribute under the conditions of the GNU General Public License (GPL). This program, including all modules, is licensed under the GPL and comes with absolutely no warranty. For details type 'GPL' within the relax prompt."
91
92
93 self.errors = []
94 if not dep_check.C_module_exp_fn:
95 self.errors.append(dep_check.C_module_exp_fn_mesg)
96
97
98 self._setup_references()
99
100
101 - def __new__(self, *args, **kargs):
102 """Replacement function for implementing the singleton design pattern."""
103
104
105 if self.instance is None:
106 self.instance = object.__new__(self, *args, **kargs)
107
108
109 return self.instance
110
111
131
132
133 - def centre(self, string, width=100):
134 """Format the string to be centred to a certain number of spaces.
135
136 @param string: The string to centre.
137 @type string: str
138 @keyword width: The number of characters to centre to.
139 @type width: int
140 @return: The centred string with leading whitespace added.
141 @rtype: str
142 """
143
144
145 spaces = int((width - len(string)) / 2)
146
147
148 string = spaces * ' ' + string
149
150
151 return string
152
153
155 """Return a string representation of the file type.
156
157 @param path: The full path of the file to return information about.
158 @type path: str
159 @return: The single line file type information string.
160 @rtype: str
161 """
162
163
164 if Popen == None:
165 return ''
166
167
168 if hasattr(ctypes, 'windll'):
169 return ''
170
171
172 cmd = "file -b '%s'" % path
173
174
175 pipe = Popen(cmd, shell=True, stdout=PIPE, close_fds=False)
176 waitpid(pipe.pid, 0)
177
178
179 data = pipe.stdout.readlines()
180
181
182 if data[0][:-1] == 'Mach-O universal binary with 3 architectures':
183
184 arch = [None, None, None]
185 for i in range(3):
186 row = data[i+1].split('\t')
187 arch[i] = row[1][:-1]
188 arch.sort()
189
190
191 if arch == ['Mach-O 64-bit executable x86_64', 'Mach-O executable i386', 'Mach-O executable ppc']:
192 file_type = '3-way exec (i386, ppc, x86_64)'
193 elif arch == ['Mach-O 64-bit bundle x86_64', 'Mach-O bundle i386', 'Mach-O bundle ppc']:
194 file_type = '3-way bundle (i386, ppc, x86_64)'
195 elif arch == ['Mach-O 64-bit dynamically linked shared library x86_64', 'Mach-O dynamically linked shared library i386', 'Mach-O dynamically linked shared library ppc']:
196 file_type = '3-way lib (i386, ppc, x86_64)'
197 elif arch == ['Mach-O 64-bit object x86_64', 'Mach-O object i386', 'Mach-O object ppc']:
198 file_type = '3-way obj (i386, ppc, x86_64)'
199 else:
200 file_type = '3-way %s' % arch
201
202
203 elif data[0][:-1] == 'Mach-O universal binary with 2 architectures':
204
205 arch = [None, None]
206 for i in range(2):
207 row = data[i+1].split('\t')
208 arch[i] = row[1][:-1]
209 arch.sort()
210
211
212 if arch == ['Mach-O executable i386', 'Mach-O executable ppc']:
213 file_type = '2-way exec (i386, ppc)'
214 elif arch == ['Mach-O bundle i386', 'Mach-O bundle ppc']:
215 file_type = '2-way bundle (i386, ppc)'
216 elif arch == ['Mach-O dynamically linked shared library i386', 'Mach-O dynamically linked shared library ppc']:
217 file_type = '2-way lib (i386, ppc)'
218 elif arch == ['Mach-O object i386', 'Mach-O object ppc']:
219 file_type = '2-way obj (i386, ppc)'
220 else:
221 file_type = '2-way %s' % arch
222
223
224 else:
225 file_type = data[0][:-1]
226 for i in range(1, len(data)):
227 row = data[i].split('\t')
228 arch[i] = row[1][:-1]
229 file_type += " %s" % arch
230
231
232 return file_type
233
234
258
259
260 - def intro_text(self):
261 """Create the introductory string for STDOUT printing.
262
263 This text is word-wrapped to a fixed width of 100 characters (or 80 on MS Windows).
264
265
266 @return: The introductory string.
267 @rtype: str
268 """
269
270
271 intro_string = '\n\n\n'
272
273
274 if version == 'repository checkout':
275 text = "%s %s r%s" % (self.title, self.version, revision())
276 text2 = "%s" % (url())
277 intro_string = intro_string + self.centre(text, status.text_width) + '\n' + self.centre(text2, status.text_width) + '\n\n'
278
279
280 else:
281 text = "%s %s" % (self.title, self.version)
282 intro_string = intro_string + self.centre(text, status.text_width) + '\n\n'
283
284
285 intro_string = intro_string + self.centre(self.desc, status.text_width) + '\n\n'
286
287
288 for i in range(len(self.copyright)):
289 intro_string = intro_string + self.centre(self.copyright[i], status.text_width) + '\n'
290 intro_string = intro_string + '\n'
291
292
293 for line in wrap(self.licence, status.text_width):
294 intro_string = intro_string + line + '\n'
295 intro_string = intro_string + '\n'
296
297
298 help = "Assistance in using the relax prompt and scripting interface can be accessed by typing 'help' within the prompt."
299 for line in wrap(help, status.text_width):
300 intro_string = intro_string + line + '\n'
301
302
303 for i in range(len(self.errors)):
304 intro_string = intro_string + '\n' + self.errors[i] + '\n'
305 intro_string = intro_string + '\n'
306
307
308 if hasattr(self, 'multi_processor_string'):
309 for line in wrap('Processor fabric: %s\n' % self.multi_processor_string, status.text_width):
310 intro_string = intro_string + line + '\n'
311
312
313 return intro_string
314
315
504
505
506
507 - def ram_info(self, format=" %-25s%s\n"):
508 """Return a string for printing to STDOUT with info from the Python packages used by relax.
509
510 @keyword format: The formatting string.
511 @type format: str
512 @return: The info string.
513 @rtype: str
514 """
515
516
517 if Popen == None:
518 return ''
519
520
521 text = ''
522
523
524 pipe = Popen('free -m', shell=True, stdin=PIPE, stdout=PIPE, stderr=PIPE, close_fds=False)
525 free_lines = pipe.stdout.readlines()
526 if free_lines:
527
528 for line in free_lines:
529
530 row = line.split()
531
532
533 if row[0] == 'Mem:':
534 text += format % ("Total RAM size: ", row[1], "Mb")
535
536
537 if row[0] == 'Swap:':
538 text += format % ("Total swap size: ", row[1], "Mb")
539
540
541 if not text and hasattr(ctypes, 'windll'):
542
543 mem = MemoryStatusEx()
544
545
546 text += format % ("Total RAM size: ", mem.ullTotalPhys / 1024.**2, "Mb")
547
548
549 text += format % ("Total swap size: ", mem.ullTotalVirtual / 1024.**2, "Mb")
550
551
552 if not text:
553 text += format % ("Total RAM size: ", "?", "Mb")
554 text += format % ("Total swap size: ", "?", "Mb")
555
556
557 return text
558
559
609
610
612 """Return a string for printing to STDOUT with info about the current relax instance.
613
614 @return: The info string.
615 @rtype: str
616 """
617
618
619 text = ''
620
621
622 format = " %-25s%s\n"
623 format2 = " %-25s%s %s\n"
624
625
626 text = text + ("\nHardware information:\n")
627 if hasattr(platform, 'machine'):
628 text = text + (format % ("Machine: ", platform.machine()))
629 if hasattr(platform, 'processor'):
630 text = text + (format % ("Processor: ", platform.processor()))
631 text = text + (format % ("Endianness: ", sys.byteorder))
632 text = text + self.ram_info(format=format2)
633
634
635 text = text + ("\nOperating system information:\n")
636 if hasattr(platform, 'system'):
637 text = text + (format % ("System: ", platform.system()))
638 if hasattr(platform, 'release'):
639 text = text + (format % ("Release: ", platform.release()))
640 if hasattr(platform, 'version'):
641 text = text + (format % ("Version: ", platform.version()))
642 if hasattr(platform, 'win32_ver') and platform.win32_ver()[0]:
643 text = text + (format % ("Win32 version: ", (platform.win32_ver()[0] + " " + platform.win32_ver()[1] + " " + platform.win32_ver()[2] + " " + platform.win32_ver()[3])))
644 if hasattr(platform, 'linux_distribution') and platform.linux_distribution()[0]:
645 text = text + (format % ("GNU/Linux version: ", (platform.linux_distribution()[0] + " " + platform.linux_distribution()[1] + " " + platform.linux_distribution()[2])))
646 if hasattr(platform, 'mac_ver') and platform.mac_ver()[0]:
647 text = text + (format % ("Mac version: ", (platform.mac_ver()[0] + " (" + platform.mac_ver()[1][0] + ", " + platform.mac_ver()[1][1] + ", " + platform.mac_ver()[1][2] + ") " + platform.mac_ver()[2])))
648 if hasattr(platform, 'dist'):
649 text = text + (format % ("Distribution: ", (platform.dist()[0] + " " + platform.dist()[1] + " " + platform.dist()[2])))
650 if hasattr(platform, 'platform'):
651 text = text + (format % ("Full platform string: ", (platform.platform())))
652 if hasattr(ctypes, 'windll'):
653 text = text + (format % ("Windows architecture: ", (self.win_arch())))
654
655
656 text = text + ("\nPython information:\n")
657 if hasattr(platform, 'architecture'):
658 text = text + (format % ("Architecture: ", (platform.architecture()[0] + " " + platform.architecture()[1])))
659 if hasattr(platform, 'python_version'):
660 text = text + (format % ("Python version: ", platform.python_version()))
661 if hasattr(platform, 'python_branch'):
662 text = text + (format % ("Python branch: ", platform.python_branch()))
663 if hasattr(platform, 'python_build'):
664 text = text + ((format[:-1]+', %s\n') % ("Python build: ", platform.python_build()[0], platform.python_build()[1]))
665 if hasattr(platform, 'python_compiler'):
666 text = text + (format % ("Python compiler: ", platform.python_compiler()))
667 if hasattr(platform, 'libc_ver'):
668 text = text + (format % ("Libc version: ", (platform.libc_ver()[0] + " " + platform.libc_ver()[1])))
669 if hasattr(platform, 'python_implementation'):
670 text = text + (format % ("Python implementation: ", platform.python_implementation()))
671 if hasattr(platform, 'python_revision'):
672 text = text + (format % ("Python revision: ", platform.python_revision()))
673 if sys.executable:
674 text = text + (format % ("Python executable: ", sys.executable))
675 if hasattr(sys, 'flags'):
676 text = text + (format % ("Python flags: ", sys.flags))
677 if hasattr(sys, 'float_info'):
678 text = text + (format % ("Python float info: ", sys.float_info))
679 text = text + (format % ("Python module path: ", sys.path))
680
681
682 text = text + self.package_info()
683
684
685 text = text + "\nrelax information:\n"
686 text = text + (format % ("Version: ", version_full()))
687 if hasattr(self, "multi_processor_string"):
688 text += format % ("Processor fabric: ", self.multi_processor_string)
689
690
691 text = text + self.relax_module_info()
692
693
694 text = text + ("\n")
695
696
697 return text
698
699
701 """Determine the MS Windows architecture.
702
703 @return: The architecture string.
704 @rtype: str
705 """
706
707
708 if 'PROCESSOR_ARCHITEW6432' in environ:
709 arch = environ['PROCESSOR_ARCHITEW6432']
710
711
712 else:
713 arch = environ['PROCESSOR_ARCHITECTURE']
714
715
716 return arch
717
718
719
721 """Special object for obtaining hardware info in MS Windows."""
722
723 if hasattr(ctypes, 'windll'):
724 _fields_ = [
725 ('dwLength', ctypes.wintypes.DWORD),
726 ('dwMemoryLoad', ctypes.wintypes.DWORD),
727 ('ullTotalPhys', ctypes.c_ulonglong),
728 ('ullAvailPhys', ctypes.c_ulonglong),
729 ('ullTotalPageFile', ctypes.c_ulonglong),
730 ('ullAvailPageFile', ctypes.c_ulonglong),
731 ('ullTotalVirtual', ctypes.c_ulonglong),
732 ('ullAvailVirtual', ctypes.c_ulonglong),
733 ('ullExtendedVirtual', ctypes.c_ulonglong),
734 ]
735
737 """Set up the information and handle non MS Windows systems."""
738
739
740 if hasattr(ctypes, 'windll'):
741 self.dwLength = ctypes.sizeof(self)
742 ctypes.windll.kernel32.GlobalMemoryStatusEx(ctypes.byref(self))
743
744
745
747 """Reference base class."""
748
749
750 type = None
751 author = None
752 author2 = None
753 title = None
754 status = None
755 journal = None
756 journal_full = None
757 volume = None
758 number = None
759 doi = None
760 pubmed_id = None
761 url = None
762 pages = None
763 year = None
764
765
767 """Generate some variables on the fly.
768
769 This is only called for objects not found in the class.
770
771 @param name: The name of the object.
772 @type name: str
773 @raises AttributeError: If the object cannot be created.
774 @returns: The generated object.
775 @rtype: anything
776 """
777
778
779 if name in ['page_first', 'page_last']:
780
781 if not self.pages:
782 return None
783
784
785 vals = self.pages.split('-')
786
787
788 if len(vals) == 1:
789 return vals[0]
790
791
792 if name == 'page_first':
793 return vals[0]
794
795
796 if name == 'page_last':
797 return vals[1]
798
799 raise AttributeError(name)
800
801
802 - def cite_short(self, author=True, title=True, journal=True, volume=True, number=True, pages=True, year=True, doi=True, url=True, status=True):
803 """Compile a short citation.
804
805 The returned text will have the form of:
806
807 - d'Auvergne, E.J. and Gooley, P.R. (2008). Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-119.
808
809
810 @keyword author: The author flag.
811 @type author: bool
812 @keyword title: The title flag.
813 @type title: bool
814 @keyword journal: The journal flag.
815 @type journal: bool
816 @keyword volume: The volume flag.
817 @type volume: bool
818 @keyword number: The number flag.
819 @type number: bool
820 @keyword pages: The pages flag.
821 @type pages: bool
822 @keyword year: The year flag.
823 @type year: bool
824 @keyword doi: The doi flag.
825 @type doi: bool
826 @keyword url: The url flag.
827 @type url: bool
828 @keyword status: The status flag. This will only be shown if not 'published'.
829 @type status: bool
830 @return: The full citation.
831 @rtype: str
832 """
833
834
835 cite = ''
836 if author and self.author and hasattr(self, 'author'):
837 cite = cite + self.author
838 if year and self.year and hasattr(self, 'year'):
839 cite = cite + ' (' + repr(self.year) + ').'
840 if title and self.title and hasattr(self, 'title'):
841 cite = cite + ' ' + self.title
842 if journal and self.journal and hasattr(self, 'journal'):
843 cite = cite + ' ' + self.journal + ','
844 if volume and self.volume and hasattr(self, 'volume'):
845 cite = cite + ' ' + self.volume
846 if number and self.number and hasattr(self, 'number'):
847 cite = cite + '(' + self.number + '),'
848 if pages and self.pages and hasattr(self, 'pages'):
849 cite = cite + ' ' + self.pages
850 if doi and self.doi and hasattr(self, 'doi'):
851 cite = cite + ' (http://dx.doi.org/'+self.doi + ')'
852 if url and self.url and hasattr(self, 'url'):
853 cite = cite + ' (' + self.url + ')'
854 if status and hasattr(self, 'status') and self.status != 'published':
855 cite = cite + ' (' + self.status + ')'
856
857
858 if cite[-1] != '.':
859 cite = cite + '.'
860
861
862 return cite
863
864
865 - def cite_html(self, author=True, title=True, journal=True, volume=True, number=True, pages=True, year=True, doi=True, url=True, status=True):
866 """Compile a citation for HTML display.
867
868 @keyword author: The author flag.
869 @type author: bool
870 @keyword title: The title flag.
871 @type title: bool
872 @keyword journal: The journal flag.
873 @type journal: bool
874 @keyword volume: The volume flag.
875 @type volume: bool
876 @keyword number: The number flag.
877 @type number: bool
878 @keyword pages: The pages flag.
879 @type pages: bool
880 @keyword year: The year flag.
881 @type year: bool
882 @keyword doi: The doi flag.
883 @type doi: bool
884 @keyword url: The url flag.
885 @type url: bool
886 @keyword status: The status flag. This will only be shown if not 'published'.
887 @type status: bool
888 @return: The full citation.
889 @rtype: str
890 """
891
892
893 cite = ''
894 if author and hasattr(self, 'author') and self.author:
895 cite = cite + self.author
896 if year and hasattr(self, 'year') and self.year:
897 cite = cite + ' (' + repr(self.year) + ').'
898 if title and hasattr(self, 'title') and self.title:
899 cite = cite + ' ' + self.title
900 if journal and hasattr(self, 'journal') and self.journal:
901 cite = cite + ' <em>' + self.journal + '</em>,'
902 if volume and hasattr(self, 'volume') and self.volume:
903 cite = cite + ' <strong>' + self.volume + '</strong>'
904 if number and hasattr(self, 'number') and self.number:
905 cite = cite + '(' + self.number + '),'
906 if pages and hasattr(self, 'pages') and self.pages:
907 cite = cite + ' ' + self.pages
908 if doi and hasattr(self, 'doi') and self.doi:
909 cite = cite + ' (<a href="http://dx.doi.org/%s">abstract</a>)' % self.doi
910 if url and hasattr(self, 'url') and self.url:
911 cite = cite + ' (<a href="%s">url</a>)' % self.url
912 if status and hasattr(self, 'status') and self.status != 'published':
913 cite = cite + ' (<i>%s</i>)' % self.status
914
915
916 if cite[-1] != '.':
917 cite = cite + '.'
918
919
920 return cite
921
922
923
925 """Bibliography container."""
926
927 type = "journal"
928 author = "Bieri, M., d'Auvergne, E. J. and Gooley, P. R."
929 author2 = [["Michael", "Bieri", "M.", ""], ["Edward", "d'Auvergne", "E.", "J."], ["Paul", "Gooley", "P.", "R."]]
930 title = "relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and micro-s motion of proteins"
931 journal = "J. Biomol. NMR"
932 journal_full = "Journal of Biomolecular NMR"
933 abstract = "Investigation of protein dynamics on the ps-ns and mus-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was developed for fast and simple model-free analysis and is fully integrated into the software package relax. It is written in Python and uses wxPython to build the graphical user interface (GUI) for maximum performance and multi-platform use. This software allows the analysis of NMR relaxation data with ease and the generation of publication quality graphs as well as color coded images of molecular structures. The interface is designed for simple data analysis and management. The software was tested and validated against the command line version of relax."
934 authoraddress = "Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria 3010, Australia."
935 doi = "10.1007/s10858-011-9509-1"
936 pubmed_id = 21618018
937 status = "published"
938 year = 2011
939
940
941
943 """Bibliography container."""
944
945 type = "journal"
946 author = "Clore, G. M. and Szabo, A. and Bax, A. and Kay, L. E. and Driscoll, P. C. and Gronenborn, A. M."
947 title = "Deviations from the simple 2-parameter model-free approach to the interpretation of N-15 nuclear magnetic-relaxation of proteins"
948 journal = "J. Am. Chem. Soc."
949 journal_full = "Journal of the American Chemical Society"
950 volume = "112"
951 number = "12"
952 pages = "4989-4991"
953 address = "1155 16th St, NW, Washington, DC 20036"
954 sourceid = "ISI:A1990DH27700070"
955 status = "published"
956 year = 1990
957
958
959
961 """Bibliography container."""
962
963 type = "thesis"
964 author = "d'Auvergne, E. J."
965 author2 = [["Edward", "d'Auvergne", "E.", "J."]]
966 title = "Protein dynamics: a study of the model-free analysis of NMR relaxation data."
967 school = "Biochemistry and Molecular Biology, University of Melbourne."
968 url = "http://eprints.infodiv.unimelb.edu.au/archive/00002799/"
969 status = "published"
970 year = 2006
971
972
973
975 """Bibliography container."""
976
977 type = "journal"
978 author = "d'Auvergne, E. J. and Gooley, P. R."
979 author2 = [["Edward", "d'Auvergne", "E.", "J."], ["Paul", "Gooley", "P.", "R."]]
980 title = "The use of model selection in the model-free analysis of protein dynamics."
981 journal = "J. Biomol. NMR"
982 journal_full = "Journal of Biomolecular NMR"
983 volume = "25"
984 number = "1"
985 pages = "25-39"
986 abstract = "Model-free analysis of NMR relaxation data, which is widely used for the study of protein dynamics, consists of the separation of the global rotational diffusion from internal motions relative to the diffusion frame and the description of these internal motions by amplitude and timescale. Five model-free models exist, each of which describes a different type of motion. Model-free analysis requires the selection of the model which best describes the dynamics of the NH bond. It will be demonstrated that the model selection technique currently used has two significant flaws, under-fitting, and not selecting a model when one ought to be selected. Under-fitting breaks the principle of parsimony causing bias in the final model-free results, visible as an overestimation of S2 and an underestimation of taue and Rex. As a consequence the protein falsely appears to be more rigid than it actually is. Model selection has been extensively developed in other fields. The techniques known as Akaike's Information Criteria (AIC), small sample size corrected AIC (AICc), Bayesian Information Criteria (BIC), bootstrap methods, and cross-validation will be compared to the currently used technique. To analyse the variety of techniques, synthetic noisy data covering all model-free motions was created. The data consists of two types of three-dimensional grid, the Rex grids covering single motions with chemical exchange [S2,taue,Rex], and the Double Motion grids covering two internal motions [S f 2,S s 2,tau s ]. The conclusion of the comparison is that for accurate model-free results, AIC model selection is essential. As the method neither under, nor over-fits, AIC is the best tool for applying Occam's razor and has the additional benefits of simplifying and speeding up model-free analysis."
987 authoraddress = "Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria 3010, Australia."
988 keywords = "Amines ; Diffusion ; *Models, Molecular ; Motion ; Nuclear Magnetic Resonance, Biomolecular/*methods ; Proteins/*chemistry ; Research Support, Non-U.S. Gov't ; Rotation"
989 doi = "10.1023/A:1021902006114"
990 pubmed_id = 12566997
991 status = "published"
992 year = 2003
993
994
995
997 """Bibliography container."""
998
999 type = "journal"
1000 author = "d'Auvergne, E. J. and Gooley, P. R."
1001 author2 = [["Edward", "d'Auvergne", "E.", "J."], ["Paul", "Gooley", "P.", "R."]]
1002 title = "Model-free model elimination: A new step in the model-free dynamic analysis of NMR relaxation data."
1003 journal = "J. Biomol. NMR"
1004 journal_full = "Journal of Biomolecular NMR"
1005 volume = "35"
1006 number = "2"
1007 pages = "117-135"
1008 abstract = "Model-free analysis is a technique commonly used within the field of NMR spectroscopy to extract atomic resolution, interpretable dynamic information on multiple timescales from the R (1), R (2), and steady state NOE. Model-free approaches employ two disparate areas of data analysis, the discipline of mathematical optimisation, specifically the minimisation of a chi(2) function, and the statistical field of model selection. By searching through a large number of model-free minimisations, which were setup using synthetic relaxation data whereby the true underlying dynamics is known, certain model-free models have been identified to, at times, fail. This has been characterised as either the internal correlation times, tau( e ), tau( f ), or tau( s ), or the global correlation time parameter, local tau( m ), heading towards infinity, the result being that the final parameter values are far from the true values. In a number of cases the minimised chi(2) value of the failed model is significantly lower than that of all other models and, hence, will be the model which is chosen by model selection techniques. If these models are not removed prior to model selection the final model-free results could be far from the truth. By implementing a series of empirical rules involving inequalities these models can be specifically isolated and removed. Model-free analysis should therefore consist of three distinct steps: model-free minimisation, model-free model elimination, and finally model-free model selection. Failure has also been identified to affect the individual Monte Carlo simulations used within error analysis. Each simulation involves an independent randomised relaxation data set and model-free minimisation, thus simulations suffer from exactly the same types of failure as model-free models. Therefore, to prevent these outliers from causing a significant overestimation of the errors the failed Monte Carlo simulations need to be culled prior to calculating the parameter standard deviations."
1009 authoraddress = "Department of Biochemistry and Molecular Biology, Bio21 Institute of Biotechnology and Molecular Science, University of Melbourne, Parkville, Victoria, 3010, Australia"
1010 doi = "10.1007/s10858-006-9007-z"
1011 pubmed_id = 16791734
1012 status = "published"
1013 year = 2006
1014
1015
1016
1018 """Bibliography container."""
1019
1020 type = "journal"
1021 author = "d'Auvergne, E. J. and Gooley, P. R."
1022 author2 = [["Edward", "d'Auvergne", "E.", "J."], ["Paul", "Gooley", "P.", "R."]]
1023 title = "Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm."
1024 journal = "Mol. Biosys."
1025 journal_full = "Molecular BioSystems"
1026 volume = "3"
1027 number = "7"
1028 pages = "483-494"
1029 abstract = "Model-free analysis of NMR relaxation data, which describes the motion of individual atoms, is a problem intricately linked to the Brownian rotational diffusion of the macromolecule. The diffusion tensor parameters strongly influence the optimisation of the various model-free models and the subsequent model selection between them. Finding the optimal model of the dynamics of the system among the numerous diffusion and model-free models is hence quite complex. Using set theory, the entirety of this global problem has been encapsulated by the universal set Ll, and its resolution mathematically formulated as the universal solution Ll. Ever since the original Lipari and Szabo papers the model-free dynamics of a molecule has most often been solved by initially estimating the diffusion tensor. The model-free models which depend on the diffusion parameter values are then optimised and the best model is chosen to represent the dynamics of the residue. Finally, the global model of all diffusion and model-free parameters is optimised. These steps are repeated until convergence. For simplicity this approach to Ll will be labelled the diffusion seeded model-free paradigm. Although this technique suffers from a number of problems many have been solved. All aspects of the diffusion seeded paradigm and its consequences, together with a few alternatives to the paradigm, will be reviewed through the use of set notation."
1030 authoraddress = "Department of Biochemistry and Molecular Biology, Bio21 Institute of Biotechnology and Molecular Science, University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia."
1031 keywords = "Magnetic Resonance Spectroscopy/*methods ; *Models, Theoretical ; Proteins/chemistry ; Thermodynamics"
1032 doi = "10.1039/b702202f"
1033 pubmed_id = 17579774
1034 status = "published"
1035 year = 2007
1036
1037
1038
1040 """Bibliography container."""
1041
1042 type = "journal"
1043 author = "d'Auvergne, E. J. and Gooley, P. R."
1044 author2 = [["Edward", "d'Auvergne", "E.", "J."], ["Paul", "Gooley", "P.", "R."]]
1045 title = "Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces."
1046 journal = "J. Biomol. NMR"
1047 journal_full = "Journal of Biomolecular NMR"
1048 volume = "40"
1049 number = "2"
1050 pages = "107-119"
1051 abstract = "The key to obtaining the model-free description of the dynamics of a macromolecule is the optimisation of the model-free and Brownian rotational diffusion parameters using the collected R (1), R (2) and steady-state NOE relaxation data. The problem of optimising the chi-squared value is often assumed to be trivial, however, the long chain of dependencies required for its calculation complicates the model-free chi-squared space. Convolutions are induced by the Lorentzian form of the spectral density functions, the linear recombinations of certain spectral density values to obtain the relaxation rates, the calculation of the NOE using the ratio of two of these rates, and finally the quadratic form of the chi-squared equation itself. Two major topological features of the model-free space complicate optimisation. The first is a long, shallow valley which commences at infinite correlation times and gradually approaches the minimum. The most severe convolution occurs for motions on two timescales in which the minimum is often located at the end of a long, deep, curved tunnel or multidimensional valley through the space. A large number of optimisation algorithms will be investigated and their performance compared to determine which techniques are suitable for use in model-free analysis. Local optimisation algorithms will be shown to be sufficient for minimisation not only within the model-free space but also for the minimisation of the Brownian rotational diffusion tensor. In addition the performance of the programs Modelfree and Dasha are investigated. A number of model-free optimisation failures were identified: the inability to slide along the limits, the singular matrix failure of the Levenberg-Marquardt minimisation algorithm, the low precision of both programs, and a bug in Modelfree. Significantly, the singular matrix failure of the Levenberg-Marquardt algorithm occurs when internal correlation times are undefined and is greatly amplified in model-free analysis by both the grid search and constraint algorithms. The program relax ( http://www.nmr-relax.com ) is also presented as a new software package designed for the analysis of macromolecular dynamics through the use of NMR relaxation data and which alleviates all of the problems inherent within model-free analysis."
1052 authoraddress = "Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077, Goettingen, Germany"
1053 keywords = "*Algorithms ; Cytochromes c2/chemistry ; Diffusion ; *Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular/*methods ; Rhodobacter capsulatus/chemistry ; *Rotation"
1054 doi = "10.1007/s10858-007-9214-2"
1055 pubmed_id = 18085410
1056 status = "published"
1057 year = 2008
1058
1059
1060
1062 """Bibliography container."""
1063
1064 type = "journal"
1065 author = "d'Auvergne, E. J. and Gooley, P. R."
1066 author2 = [["Edward", "d'Auvergne", "E.", "J."], ["Paul", "Gooley", "P.", "R."]]
1067 title = "Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor."
1068 journal = "J. Biomol. NMR"
1069 journal_full = "Journal of Biomolecular NMR"
1070 volume = "40"
1071 number = "2"
1072 pages = "121-133"
1073 abstract = "Finding the dynamics of an entire macromolecule is a complex problem as the model-free parameter values are intricately linked to the Brownian rotational diffusion of the molecule, mathematically through the autocorrelation function of the motion and statistically through model selection. The solution to this problem was formulated using set theory as an element of the universal set [formula: see text]-the union of all model-free spaces (d'Auvergne EJ and Gooley PR (2007) Mol. BioSyst. 3(7), 483-494). The current procedure commonly used to find the universal solution is to initially estimate the diffusion tensor parameters, to optimise the model-free parameters of numerous models, and then to choose the best model via model selection. The global model is then optimised and the procedure repeated until convergence. In this paper a new methodology is presented which takes a different approach to this diffusion seeded model-free paradigm. Rather than starting with the diffusion tensor this iterative protocol begins by optimising the model-free parameters in the absence of any global model parameters, selecting between all the model-free models, and finally optimising the diffusion tensor. The new model-free optimisation protocol will be validated using synthetic data from Schurr JM et al. (1994) J. Magn. Reson. B 105(3), 211-224 and the relaxation data of the bacteriorhodopsin (1-36)BR fragment from Orekhov VY (1999) J. Biomol. NMR 14(4), 345-356. To demonstrate the importance of this new procedure the NMR relaxation data of the Olfactory Marker Protein (OMP) of Gitti R et al. (2005) Biochem. 44(28), 9673-9679 is reanalysed. The result is that the dynamics for certain secondary structural elements is very different from those originally reported."
1074 authoraddress = "Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen, D-37077, Germany"
1075 keywords = "Algorithms ; Amides/chemistry ; Bacteriorhodopsins/chemistry ; Crystallography, X-Ray ; Diffusion ; *Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular/*methods ; Olfactory Marker Protein/chemistry ; Peptide Fragments/chemistry ; Protein Structure, Secondary ; *Rotation"
1076 language = "eng"
1077 doi = "10.1007/s10858-007-9213-3"
1078 pubmed_id = 18085411
1079 status = "published"
1080 year = 2008
1081
1082
1083
1085 """Bibliography container."""
1086
1087 type = "journal"
1088 author = "Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J. and Bax, A."
1089 author2 = [["Frank", "Delaglio", "F.", None], ["Stephan", "Grzesiek", "S.", None], ["Geerten", "Vuister", "G.", "W."], ["Guang", "Zhu", "G.", None], ["John", "Pfeifer", "J.", None], ["Ad", "Bax", "A.", None]]
1090 title = "NMRPipe: a multidimensional spectral processing system based on UNIX pipes."
1091 journal = "J. Biomol. NMR"
1092 journal_full = "Journal of Biomolecular NMR"
1093 volume = "6"
1094 number = "3"
1095 pages = "277-293"
1096 abstract = "The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks."
1097 authoraddress = "Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA."
1098 keywords = "Magnetic Resonance Spectroscopy/*instrumentation ; *Software"
1099 language = "eng"
1100 doi = "10.1007/BF00197809"
1101 pubmed_id = 8520220
1102 status = "published"
1103 year = 1995
1104
1105
1106
1108 """Bibliography container."""
1109
1110 author = "Goddard, T.D. and Kneller, D.G."
1111 author2 = [["Tom", "Goddard", "T.", "D."], ["Donald", "Kneller", "D.", "G."]]
1112 journal = "University of California, San Francisco."
1113 title = "Sparky 3."
1114 status = "unpublished"
1115 type = "internet"
1116
1117
1118
1120 """Bibliography container."""
1121
1122 type = "journal"
1123 author = "Lipari, G. and Szabo, A."
1124 title = "Model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules I. Theory and range of validity"
1125 journal = "J. Am. Chem. Soc."
1126 journal_full = "Journal of the American Chemical Society"
1127 volume = "104"
1128 number = "17"
1129 pages = "4546-4559"
1130 authoraddress = "NIADDKD,Chem Phys Lab,Bethesda,MD 20205."
1131 sourceid = "ISI:A1982PC82900009"
1132 status = "published"
1133 year = 1982
1134
1135
1136
1138 """Bibliography container."""
1139
1140 type = "journal"
1141 author = "Lipari, G. and Szabo, A."
1142 title = "Model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules II. Analysis of experimental results"
1143 journal = "J. Am. Chem. Soc."
1144 journal_full = "Journal of the American Chemical Society"
1145 volume = "104"
1146 number = "17"
1147 pages = "4559-4570"
1148 abstract = "For pt.I see ibid., vol.104, p.4546 (1982). In the preceding paper it has been shown that the unique dynamic information on fast internal motions in an NMR relaxation experiment on macromolecules in solution is specified by a generalized order parameter, S , and an effective correlation time, tau /sub e/. The authors now deal with the extraction and interpretation of this information. The procedure used to obtain S /sup 2/ and tau /sub e/ from experimental data by using a least-squares method and, in certain favorable circumstances, by using an analytical formula is described. A variety of experiments are then analyzed to yield information on the time scale and spatial restriction of internal motions of isoleucines in myoglobin, methionines in dihydrofolate reductase and myoglobin, a number of aliphatic residues in basic pancreatic trypsin inhibitor, and ethyl isocyanide bound to myoglobin, hemoglobin, and aliphatic side chains in three random-coil polymers. The numerical values of S /sup 2/ and tau /sub e / can be readily interpreted within the framework of a variety of models."
1149 authoraddress = "NIADDKD,Chem Phys Lab,Bethesda,MD 20205."
1150 sourceid = "ISI:A1982PC82900010"
1151 status = "published"
1152 year = 1982
1153