Hi, I've actually found an easier way to obtain copies of the relax manual as I make changes. I've uploaded the file to http://download.gna.org/relax/manual/. The most recent copy is relax_17348.pdf (the number is the repository revision number the manual was created from). Thank you for the suggestions.
Cheers, Edward On 27 August 2012 19:01, Edward d'Auvergne <[email protected]> wrote: > Hi Nick, > > The problem appears to be in the intensity files with the RelaxWarnings: > > RelaxWarning: The sequence data in the line ['R1', '0.9262', '0.0013'] > is invalid, the residue number data '0.9262' is invalid. > > This tells me that the file contains a column with the 1 letter > residue code fused with the residue number. If so, how are TRP indole > nitrogens handled? Which software created this format? The > spectrum.read_intensities user function is expecting a peak list from > Sparky, XEasy, NMRView, or a generic columnar formatted peak list, but > instead the relaxation rates are being fed in, causing relax to not > know what to do. I would guess that an R1 or R2 analysis has been > initialised, and the relaxation rates rather than spectral peak lists > are being fed in. > > For the formatting of the rates, this should match the loaded spins > which in this case comes from the PDB file. Therefore the line: > > R1 0.9262 0.0013 > > should be changed to: > > ARG 1 0.9262 0.0013 > > The residue name and number columns can then be specified. If you > have indole data, then an extra column can be given for the spin name > again matching the PDB naming (I would highly recommend using this > additional data). > > I have modified the relaxation curve-fitting chapter of the relax > manual and now give examples of the format for Sparky, XEasy, and > NMRView peak list files. This will only be available in the next > released version of relax. The changes can be obtained using the > subversion program if you cannot wait but, as this is in the manual, > the PDF version would need to be hand compiled (requiring the > installation of LaTeX, scons, and dvips). > > As for attaching files, it is best not to do this for mailing list > messages. The reason is because the messages are massively amplified > and sent to the many people subscribed to the mailing lists. This > puts a large strain on the open source infrastructure of Gna! > (https://gna.org/). Note that this is a public mailing list and > messages are archived permanently all over the web: > > http://news.gmane.org/gmane.science.nmr.relax.user > http://www.mail-archive.com/[email protected]/ > https://mail.gna.org/public/relax-users/2012-08/threads.html > > If large files need to be transmitted, then the relax tracker > infrastructure can be used. Either a bug report > (https://gna.org/bugs/?group=relax), a support request > (https://gna.org/support/index.php?group=relax) or a task > (https://gna.org/task/index.php?group=relax) can be created and the > files attached there. > > Regards, > > Edward > > > > > > On 27 August 2012 15:44, Nicolas Doucet <[email protected]> wrote: >> Edward, >> >> Thanks for the info. My student Donald and I are tinkering both with the >> teminal version of relax and the GUI (running on Ubuntu 12.04), but ideally >> we'd like to make the GUI work seamlessly. Please find below the first error >> message we get when trying to run a simple R1 fit using the relax GUI. Files >> are also attached. >> >> I've run ModelFree analyses with Sébastien in the distant past but this is >> our first time running relax in my lab. I'll try to provide any information >> worth mentioning from the perspective of a beginner with the interface. So >> far we've been a bit disappointed by the level of step-by-step explanations >> you'd expect to find in the manual. Python users know how to run python >> scripts, but this is really harsh for someone like Donald with no >> programming experience whatsoever. >> >> I believe this could be overcome by providing a simple example with all the >> required files (r1, r2 and noe lists in the right format, scripts, pdb, >> etc.). That way we could make sure our Sparky lists are edited exactly how >> they need to be for relax, in addition to allowing the right column number >> selection in the GUI options. I believe this might be our problem in the >> present case. >> >> Thanks for your input. >> >> Nick Doucet >> >> -- >> Nicolas Doucet >> Assistant Professor >> INRS - Institut Armand-Frappier >> University of Quebec >> Institut Pasteur International Network >> 531 Boulevard des Prairies >> Laval (Quebec) H7V 1B7 CANADA >> Phone: (450) 687-5010 #4212 >> Fax: (450) 686-5501 >> Email: [email protected] >> Web: http://www.profs.inrs.ca/ndoucet/ >> -- >> >> >> >> Below is the error message I get. I've tried multiple text formats of this >> data (two of them are listed below), but the application doesn't seem to >> recognize the residue number with the one in the PDB. I've changed the >> column numbers (mol_name_col=?, res_num_col=?, res_name_col=?, etc.) and >> tried different combinations but again, without success. >> >> >> >> >> relax 2.1.0 >> >> Molecular dynamics by NMR data analysis >> >> Copyright (C) 2001-2006 Edward d'Auvergne >> Copyright (C) 2006-2012 the relax development team >> >> 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. >> >> Assistance in using the relax prompt and scripting interface can be accessed >> by typing 'help' within >> the prompt. >> >> Processor fabric: Uni-processor. >> >> >> relax> >> structure.read_pdb(file='/home/dgagne/nmrdata/DG12-103_07AUG2012_NOE_of_ECP_free_form_800MHz/2012AUG19_NOE/1QMT.pdb', >> dir=None, read_mol=None, set_mol_name=None, read_model=None, >> set_model_num=None, parser='internal') >> >> Internal relax PDB parser. >> Opening the file >> '/home/dgagne/nmrdata/DG12-103_07AUG2012_NOE_of_ECP_free_form_800MHz/2012AUG19_NOE/1QMT.pdb' >> for reading. >> Adding molecule '1QMT_mol1' to model None (from the original molecule number >> 1 of model None) >> >> relax> structure.load_spins(spin_id='@N', ave_pos=True) >> Adding the following spins to the relax data store. >> >> # mol_name res_num res_name spin_num spin_name >> 1QMT_mol1 0 MET 1 N >> 1QMT_mol1 1 ARG 9 N >> 1QMT_mol1 2 PRO 20 N >> 1QMT_mol1 3 PRO 27 N >> 1QMT_mol1 4 GLN 34 N >> 1QMT_mol1 5 PHE 43 N >> 1QMT_mol1 6 THR 54 N >> 1QMT_mol1 7 ARG 61 N >> 1QMT_mol1 8 ALA 72 N >> 1QMT_mol1 9 GLN 77 N >> 1QMT_mol1 10 TRP 86 N >> 1QMT_mol1 11 PHE 100 N >> 1QMT_mol1 12 ALA 111 N >> 1QMT_mol1 13 ILE 116 N >> 1QMT_mol1 14 GLN 124 N >> 1QMT_mol1 15 HIS 133 N >> 1QMT_mol1 16 ILE 143 N >> 1QMT_mol1 17 SER 151 N >> 1QMT_mol1 18 LEU 157 N >> 1QMT_mol1 19 ASN 165 N >> 1QMT_mol1 20 PRO 173 N >> 1QMT_mol1 21 PRO 180 N >> 1QMT_mol1 22 ARG 187 N >> 1QMT_mol1 23 CYS 198 N >> 1QMT_mol1 24 THR 204 N >> 1QMT_mol1 25 ILE 211 N >> 1QMT_mol1 26 ALA 219 N >> 1QMT_mol1 27 MET 224 N >> 1QMT_mol1 28 ARG 232 N >> 1QMT_mol1 29 ALA 243 N >> 1QMT_mol1 30 ILE 248 N >> 1QMT_mol1 31 ASN 256 N >> 1QMT_mol1 32 ASN 264 N >> 1QMT_mol1 33 TYR 272 N >> 1QMT_mol1 34 ARG 284 N >> 1QMT_mol1 35 TRP 295 N >> 1QMT_mol1 36 ARG 309 N >> 1QMT_mol1 37 CYS 320 N >> 1QMT_mol1 38 LYS 326 N >> 1QMT_mol1 39 ASN 335 N >> 1QMT_mol1 40 GLN 343 N >> 1QMT_mol1 41 ASN 352 N >> 1QMT_mol1 42 THR 360 N >> 1QMT_mol1 43 PHE 367 N >> 1QMT_mol1 44 LEU 378 N >> 1QMT_mol1 45 ARG 386 N >> 1QMT_mol1 46 THR 397 N >> 1QMT_mol1 47 THR 404 N >> 1QMT_mol1 48 PHE 411 N >> 1QMT_mol1 49 ALA 422 N >> 1QMT_mol1 50 ASN 427 N >> 1QMT_mol1 51 VAL 435 N >> 1QMT_mol1 52 VAL 442 N >> 1QMT_mol1 53 ASN 449 N >> 1QMT_mol1 54 VAL 457 N >> 1QMT_mol1 55 CYS 464 N >> 1QMT_mol1 56 GLY 470 N >> 1QMT_mol1 57 ASN 474 N >> 1QMT_mol1 58 GLN 482 N >> 1QMT_mol1 59 SER 491 N >> 1QMT_mol1 60 ILE 497 N >> 1QMT_mol1 61 ARG 505 N >> 1QMT_mol1 62 CYS 516 N >> 1QMT_mol1 63 PRO 522 N >> 1QMT_mol1 64 HIS 529 N >> 1QMT_mol1 65 ASN 539 N >> 1QMT_mol1 66 ARG 547 N >> 1QMT_mol1 67 THR 558 N >> 1QMT_mol1 68 LEU 565 N >> 1QMT_mol1 69 ASN 573 N >> 1QMT_mol1 70 ASN 581 N >> 1QMT_mol1 71 CYS 589 N >> 1QMT_mol1 72 HIS 595 N >> 1QMT_mol1 73 ARG 605 N >> 1QMT_mol1 74 SER 616 N >> 1QMT_mol1 75 ARG 622 N >> 1QMT_mol1 76 PHE 633 N >> 1QMT_mol1 77 ARG 644 N >> 1QMT_mol1 78 VAL 655 N >> 1QMT_mol1 79 PRO 662 N >> 1QMT_mol1 80 LEU 669 N >> 1QMT_mol1 81 LEU 677 N >> 1QMT_mol1 82 HIS 685 N >> 1QMT_mol1 83 CYS 695 N >> 1QMT_mol1 84 ASP 701 N >> 1QMT_mol1 85 LEU 709 N >> 1QMT_mol1 86 ILE 717 N >> 1QMT_mol1 87 ASN 725 N >> 1QMT_mol1 88 PRO 733 N >> 1QMT_mol1 89 GLY 740 N >> 1QMT_mol1 90 ALA 744 N >> 1QMT_mol1 91 GLN 749 N >> 1QMT_mol1 92 ASN 758 N >> 1QMT_mol1 93 ILE 766 N >> 1QMT_mol1 94 SER 774 N >> 1QMT_mol1 95 ASN 780 N >> 1QMT_mol1 96 CYS 788 N >> 1QMT_mol1 97 ARG 794 N >> 1QMT_mol1 98 TYR 805 N >> 1QMT_mol1 99 ALA 817 N >> 1QMT_mol1 100 ASP 822 N >> 1QMT_mol1 101 ARG 830 N >> 1QMT_mol1 102 PRO 841 N >> 1QMT_mol1 103 GLY 848 N >> 1QMT_mol1 104 ARG 852 N >> 1QMT_mol1 105 ARG 863 N >> 1QMT_mol1 106 PHE 874 N >> 1QMT_mol1 107 TYR 885 N >> 1QMT_mol1 108 VAL 897 N >> 1QMT_mol1 109 VAL 904 N >> 1QMT_mol1 110 ALA 911 N >> 1QMT_mol1 111 CYS 916 N >> 1QMT_mol1 112 ASP 922 N >> 1QMT_mol1 113 ASN 930 N >> 1QMT_mol1 114 ARG 938 N >> 1QMT_mol1 115 ASP 949 N >> 1QMT_mol1 116 PRO 957 N >> 1QMT_mol1 117 ARG 964 N >> 1QMT_mol1 118 ASP 975 N >> 1QMT_mol1 119 SER 983 N >> 1QMT_mol1 120 PRO 989 N >> 1QMT_mol1 121 ARG 996 N >> 1QMT_mol1 122 TYR 1007 N >> 1QMT_mol1 123 PRO 1019 N >> 1QMT_mol1 124 VAL 1026 N >> 1QMT_mol1 125 VAL 1033 N >> 1QMT_mol1 126 PRO 1040 N >> 1QMT_mol1 127 VAL 1047 N >> 1QMT_mol1 128 HIS 1054 N >> 1QMT_mol1 129 LEU 1064 N >> 1QMT_mol1 130 ASP 1072 N >> 1QMT_mol1 131 THR 1080 N >> 1QMT_mol1 132 THR 1087 N >> 1QMT_mol1 133 ILE 1094 N >> >> relax> >> spectrum.read_intensities(file='/home/dgagne/nmrdata/DG12-104_13AUG2012_T1_T2_of_ECP_free_form_800MHz/T1_Analysis/relax/DG12-104_ECP_T1rh.rates', >> dir=None, spectrum_id=None, heteronuc='N', proton='HN', int_method='height', >> int_col=None, spin_id_col=None, mol_name_col=1, res_num_col=2, >> res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, >> ncproc=None) >> Opening the file >> '/home/dgagne/nmrdata/DG12-104_13AUG2012_T1_T2_of_ECP_free_form_800MHz/T1_Analysis/relax/DG12-104_ECP_T1rh.rates' >> for reading. >> Generic formatted data file. >> >> RelaxWarning: The sequence data in the line ['R1', '0.9262', '0.0013'] is >> invalid, the residue number data '0.9262' is invalid. >> RelaxWarning: The sequence data in the line ['Q4', '0.9919', '0.0066'] is >> invalid, the residue number data '0.9919' is invalid. >> RelaxWarning: The sequence data in the line ['F5', '0.9329', '0.0000'] is >> invalid, the residue number data '0.9329' is invalid. >> RelaxWarning: The sequence data in the line ['T6', '0.9712', '0.0053'] is >> invalid, the residue number data '0.9712' is invalid. >> RelaxWarning: The sequence data in the line ['R7', '0.9646', '0.0000'] is >> invalid, the residue number data '0.9646' is invalid. >> RelaxWarning: The sequence data in the line ['A8', '1.0078', '0.0026'] is >> invalid, the residue number data '1.0078' is invalid. >> RelaxWarning: The sequence data in the line ['Q9', '1.0152', '0.0021'] is >> invalid, the residue number data '1.0152' is invalid. >> RelaxWarning: The sequence data in the line ['W10', '1.0299', '0.0037'] is >> invalid, the residue number data '1.0299' is invalid. >> RelaxWarning: The sequence data in the line ['F11', '1.0128', '0.0036'] is >> invalid, the residue number data '1.0128' is invalid. >> RelaxWarning: The sequence data in the line ['A12', '1.1780', '0.0057'] is >> invalid, the residue number data '1.1780' is invalid. >> RelaxWarning: The sequence data in the line ['I13', '0.9133', '0.0041'] is >> invalid, the residue number data '0.9133' is invalid. >> RelaxWarning: The sequence data in the line ['Q14', '0.9041', '0.0050'] is >> invalid, the residue number data '0.9041' is invalid. >> RelaxWarning: The sequence data in the line ['H15', '0.9845', '0.0029'] is >> invalid, the residue number data '0.9845' is invalid. >> RelaxWarning: The sequence data in the line ['I16', '0.9941', '0.0027'] is >> invalid, the residue number data '0.9941' is invalid. >> RelaxWarning: The sequence data in the line ['S17', '0.8463', '0.0021'] is >> invalid, the residue number data '0.8463' is invalid. >> RelaxWarning: The sequence data in the line ['L18', '0.9669', '0.0018'] is >> invalid, the residue number data '0.9669' is invalid. >> RelaxWarning: The sequence data in the line ['N19', '0.9360', '0.0036'] is >> invalid, the residue number data '0.9360' is invalid. >> RelaxWarning: The sequence data in the line ['R22', '0.8289', '0.0039'] is >> invalid, the residue number data '0.8289' is invalid. >> RelaxWarning: The sequence data in the line ['C23', '0.8659', '0.0021'] is >> invalid, the residue number data '0.8659' is invalid. >> RelaxWarning: The sequence data in the line ['T24', '0.9298', '0.0034'] is >> invalid, the residue number data '0.9298' is invalid. >> RelaxWarning: The sequence data in the line ['I25', '0.9775', '0.0028'] is >> invalid, the residue number data '0.9775' is invalid. >> RelaxWarning: The sequence data in the line ['A26', '0.9659', '0.0008'] is >> invalid, the residue number data '0.9659' is invalid. >> RelaxWarning: The sequence data in the line ['M27', '0.9535', '0.0030'] is >> invalid, the residue number data '0.9535' is invalid. >> RelaxWarning: The sequence data in the line ['R28', '1.0231', '0.0030'] is >> invalid, the residue number data '1.0231' is invalid. >> RelaxWarning: The sequence data in the line ['A29', '0.9588', '0.0029'] is >> invalid, the residue number data '0.9588' is invalid. >> RelaxWarning: The sequence data in the line ['I30', '0.8175', '0.0044'] is >> invalid, the residue number data '0.8175' is invalid. >> RelaxWarning: The sequence data in the line ['N31', '1.0064', '0.0000'] is >> invalid, the residue number data '1.0064' is invalid. >> RelaxWarning: The sequence data in the line ['N32', '0.9701', '0.0042'] is >> invalid, the residue number data '0.9701' is invalid. >> RelaxWarning: The sequence data in the line ['Y33', '0.9343', '0.0023'] is >> invalid, the residue number data '0.9343' is invalid. >> RelaxWarning: The sequence data in the line ['R34', '1.0110', '0.0050'] is >> invalid, the residue number data '1.0110' is invalid. >> RelaxWarning: The sequence data in the line ['W35', '0.9141', '0.0039'] is >> invalid, the residue number data '0.9141' is invalid. >> RelaxWarning: The sequence data in the line ['R36', '0.8925', '0.0033'] is >> invalid, the residue number data '0.8925' is invalid. >> RelaxWarning: The sequence data in the line ['C37', '0.7273', '0.0107'] is >> invalid, the residue number data '0.7273' is invalid. >> RelaxWarning: The sequence data in the line ['K38', '0.8821', '0.0080'] is >> invalid, the residue number data '0.8821' is invalid. >> RelaxWarning: The sequence data in the line ['N39', '0.6992', '0.0146'] is >> invalid, the residue number data '0.6992' is invalid. >> RelaxWarning: The sequence data in the line ['Q40', '1.0784', '0.0050'] is >> invalid, the residue number data '1.0784' is invalid. >> RelaxWarning: The sequence data in the line ['N41', '0.9824', '0.0000'] is >> invalid, the residue number data '0.9824' is invalid. >> RelaxWarning: The sequence data in the line ['T42', '0.8909', '0.0000'] is >> invalid, the residue number data '0.8909' is invalid. >> RelaxWarning: The sequence data in the line ['L44', '0.7833', '0.0040'] is >> invalid, the residue number data '0.7833' is invalid. >> RelaxWarning: The sequence data in the line ['T46', '0.8507', '0.0024'] is >> invalid, the residue number data '0.8507' is invalid. >> RelaxWarning: The sequence data in the line ['T47', '0.8184', '0.0000'] is >> invalid, the residue number data '0.8184' is invalid. >> RelaxWarning: The sequence data in the line ['F48', '0.8626', '0.0032'] is >> invalid, the residue number data '0.8626' is invalid. >> RelaxWarning: The sequence data in the line ['A49', '0.8923', '0.0000'] is >> invalid, the residue number data '0.8923' is invalid. >> RelaxWarning: The sequence data in the line ['N50', '0.8667', '0.0044'] is >> invalid, the residue number data '0.8667' is invalid. >> RelaxWarning: The sequence data in the line ['V51', '0.9082', '0.0004'] is >> invalid, the residue number data '0.9082' is invalid. >> RelaxWarning: The sequence data in the line ['V52', '0.9224', '0.0004'] is >> invalid, the residue number data '0.9224' is invalid. >> RelaxWarning: The sequence data in the line ['V54', '0.9032', '0.0028'] is >> invalid, the residue number data '0.9032' is invalid. >> RelaxWarning: The sequence data in the line ['C55', '0.9394', '0.0036'] is >> invalid, the residue number data '0.9394' is invalid. >> RelaxWarning: The sequence data in the line ['G56', '0.9341', '0.0000'] is >> invalid, the residue number data '0.9341' is invalid. >> RelaxWarning: The sequence data in the line ['N57', '0.9412', '0.0018'] is >> invalid, the residue number data '0.9412' is invalid. >> RelaxWarning: The sequence data in the line ['Q58', '0.7676', '0.0000'] is >> invalid, the residue number data '0.7676' is invalid. >> RelaxWarning: The sequence data in the line ['S59', '0.9680', '0.0030'] is >> invalid, the residue number data '0.9680' is invalid. >> RelaxWarning: The sequence data in the line ['I60', '0.9814', '0.0057'] is >> invalid, the residue number data '0.9814' is invalid. >> RelaxWarning: The sequence data in the line ['R61', '0.9190', '0.0034'] is >> invalid, the residue number data '0.9190' is invalid. >> RelaxWarning: The sequence data in the line ['C62', '0.9640', '0.0060'] is >> invalid, the residue number data '0.9640' is invalid. >> RelaxWarning: The sequence data in the line ['H64', '0.8969', '0.0087'] is >> invalid, the residue number data '0.8969' is invalid. >> RelaxWarning: The sequence data in the line ['N65', '1.0110', '0.0050'] is >> invalid, the residue number data '1.0110' is invalid. >> RelaxWarning: The sequence data in the line ['R66', '0.9454', '0.0014'] is >> invalid, the residue number data '0.9454' is invalid. >> RelaxWarning: The sequence data in the line ['T67', '0.9803', '0.0010'] is >> invalid, the residue number data '0.9803' is invalid. >> RelaxWarning: The sequence data in the line ['L68', '0.9216', '0.0051'] is >> invalid, the residue number data '0.9216' is invalid. >> RelaxWarning: The sequence data in the line ['N69', '0.9010', '0.0036'] is >> invalid, the residue number data '0.9010' is invalid. >> RelaxWarning: The sequence data in the line ['N70', '0.9219', '0.0230'] is >> invalid, the residue number data '0.9219' is invalid. >> RelaxWarning: The sequence data in the line ['C71', '0.9371', '0.0033'] is >> invalid, the residue number data '0.9371' is invalid. >> RelaxWarning: The sequence data in the line ['H72', '0.8207', '0.0056'] is >> invalid, the residue number data '0.8207' is invalid. >> RelaxWarning: The sequence data in the line ['S74', '0.9350', '0.0000'] is >> invalid, the residue number data '0.9350' is invalid. >> RelaxWarning: The sequence data in the line ['R75', '0.9598', '0.0014'] is >> invalid, the residue number data '0.9598' is invalid. >> RelaxWarning: The sequence data in the line ['F76', '20.9497', '0.1411'] is >> invalid, the residue number data '20.9497' is invalid. >> RelaxWarning: The sequence data in the line ['R77', '0.8559', '0.0023'] is >> invalid, the residue number data '0.8559' is invalid. >> RelaxWarning: The sequence data in the line ['V78', '1.0847', '0.0133'] is >> invalid, the residue number data '1.0847' is invalid. >> RelaxWarning: The sequence data in the line ['L80', '0.9530', '0.0000'] is >> invalid, the residue number data '0.9530' is invalid. >> RelaxWarning: The sequence data in the line ['L81', '0.9453', '0.0000'] is >> invalid, the residue number data '0.9453' is invalid. >> RelaxWarning: The sequence data in the line ['H82', '0.9885', '0.0000'] is >> invalid, the residue number data '0.9885' is invalid. >> RelaxWarning: The sequence data in the line ['C83', '0.7381', '0.0168'] is >> invalid, the residue number data '0.7381' is invalid. >> RelaxWarning: The sequence data in the line ['D84', '1.2016', '0.0136'] is >> invalid, the residue number data '1.2016' is invalid. >> RelaxWarning: The sequence data in the line ['L85', '0.9213', '0.0030'] is >> invalid, the residue number data '0.9213' is invalid. >> RelaxWarning: The sequence data in the line ['I86', '1.0334', '0.0063'] is >> invalid, the residue number data '1.0334' is invalid. >> RelaxWarning: The sequence data in the line ['N87', '1.0182', '0.0000'] is >> invalid, the residue number data '1.0182' is invalid. >> RelaxWarning: The sequence data in the line ['G89', '0.9456', '0.0038'] is >> invalid, the residue number data '0.9456' is invalid. >> RelaxWarning: The sequence data in the line ['A90', '0.9297', '0.0000'] is >> invalid, the residue number data '0.9297' is invalid. >> RelaxWarning: The sequence data in the line ['Q91', '0.9847', '0.0013'] is >> invalid, the residue number data '0.9847' is invalid. >> RelaxWarning: The sequence data in the line ['N92', '0.9987', '0.0000'] is >> invalid, the residue number data '0.9987' is invalid. >> RelaxWarning: The sequence data in the line ['I93', '1.0320', '0.0054'] is >> invalid, the residue number data '1.0320' is invalid. >> RelaxWarning: The sequence data in the line ['S94', '1.0182', '0.0000'] is >> invalid, the residue number data '1.0182' is invalid. >> RelaxWarning: The sequence data in the line ['N95', '1.0396', '0.0000'] is >> invalid, the residue number data '1.0396' is invalid. >> RelaxWarning: The sequence data in the line ['C96', '1.0823', '0.0058'] is >> invalid, the residue number data '1.0823' is invalid. >> RelaxWarning: The sequence data in the line ['R97', '1.0260', '0.0122'] is >> invalid, the residue number data '1.0260' is invalid. >> RelaxWarning: The sequence data in the line ['Y98', '1.0372', '0.0040'] is >> invalid, the residue number data '1.0372' is invalid. >> RelaxWarning: The sequence data in the line ['A99', '0.9409', '0.0000'] is >> invalid, the residue number data '0.9409' is invalid. >> RelaxWarning: The sequence data in the line ['D100', '1.0004', '0.0040'] is >> invalid, the residue number data '1.0004' is invalid. >> RelaxWarning: The sequence data in the line ['R101', '0.8263', '0.0000'] is >> invalid, the residue number data '0.8263' is invalid. >> RelaxWarning: The sequence data in the line ['G103', '0.9267', '0.0032'] is >> invalid, the residue number data '0.9267' is invalid. >> RelaxWarning: The sequence data in the line ['R104', '0.9999', '0.0000'] is >> invalid, the residue number data '0.9999' is invalid. >> RelaxWarning: The sequence data in the line ['R105', '0.9604', '0.0015'] is >> invalid, the residue number data '0.9604' is invalid. >> RelaxWarning: The sequence data in the line ['F106', '1.0033', '0.0027'] is >> invalid, the residue number data '1.0033' is invalid. >> RelaxWarning: The sequence data in the line ['Y107', '1.0069', '0.0040'] is >> invalid, the residue number data '1.0069' is invalid. >> RelaxWarning: The sequence data in the line ['V108', '0.8934', '0.0046'] is >> invalid, the residue number data '0.8934' is invalid. >> RelaxWarning: The sequence data in the line ['V109', '0.8593', '0.0054'] is >> invalid, the residue number data '0.8593' is invalid. >> RelaxWarning: The sequence data in the line ['A110', '0.8759', '0.0038'] is >> invalid, the residue number data '0.8759' is invalid. >> RelaxWarning: The sequence data in the line ['C111', '0.9241', '0.0023'] is >> invalid, the residue number data '0.9241' is invalid. >> RelaxWarning: The sequence data in the line ['D112', '0.9246', '0.0035'] is >> invalid, the residue number data '0.9246' is invalid. >> RelaxWarning: The sequence data in the line ['N113', '0.8676', '0.0027'] is >> invalid, the residue number data '0.8676' is invalid. >> RelaxWarning: The sequence data in the line ['R114', '0.8964', '0.0000'] is >> invalid, the residue number data '0.8964' is invalid. >> RelaxWarning: The sequence data in the line ['D115', '1.0056', '0.0046'] is >> invalid, the residue number data '1.0056' is invalid. >> RelaxWarning: The sequence data in the line ['R117', '0.9775', '0.0031'] is >> invalid, the residue number data '0.9775' is invalid. >> RelaxWarning: The sequence data in the line ['N118', '0.9594', '0.0000'] is >> invalid, the residue number data '0.9594' is invalid. >> RelaxWarning: The sequence data in the line ['S119', '0.9137', '0.0019'] is >> invalid, the residue number data '0.9137' is invalid. >> RelaxWarning: The sequence data in the line ['R121', '0.9223', '0.0000'] is >> invalid, the residue number data '0.9223' is invalid. >> RelaxWarning: The sequence data in the line ['Y122', '0.8798', '0.0024'] is >> invalid, the residue number data '0.8798' is invalid. >> RelaxWarning: The sequence data in the line ['V124', '0.9197', '0.0030'] is >> invalid, the residue number data '0.9197' is invalid. >> RelaxWarning: The sequence data in the line ['V125', '0.9739', '0.0022'] is >> invalid, the residue number data '0.9739' is invalid. >> RelaxWarning: The sequence data in the line ['V127', '0.9175', '0.0000'] is >> invalid, the residue number data '0.9175' is invalid. >> RelaxWarning: The sequence data in the line ['H128', '0.8926', '0.0000'] is >> invalid, the residue number data '0.8926' is invalid. >> RelaxWarning: The sequence data in the line ['L129', '0.5300', '0.0005'] is >> invalid, the residue number data '0.5300' is invalid. >> RelaxWarning: The sequence data in the line ['D130', '1.0665', '0.0055'] is >> invalid, the residue number data '1.0665' is invalid. >> RelaxWarning: The sequence data in the line ['T131', '0.9147', '0.0053'] is >> invalid, the residue number data '0.9147' is invalid. >> RelaxWarning: The sequence data in the line ['T132', '1.0058', '0.0032'] is >> invalid, the residue number data '1.0058' is invalid. >> RelaxWarning: The sequence data in the line ['I133', '0.9390', '0.0016'] is >> invalid, the residue number data '0.9390' is invalid. >> RelaxWarning: The sequence data in the line ['W310', '0.9127', '0.0046'] is >> invalid, the residue number data '0.9127' is invalid. >> RelaxWarning: The sequence data in the line ['W335', '0.9756', '0.0000'] is >> invalid, the residue number data '0.9756' is invalid. >> RelaxError: No corresponding data could be found within the file. >> >> >> >> >> >> On 2012-08-27, at 4:24 AM, Edward d'Auvergne <[email protected]> wrote: >> >> Hi, >> >> Welcome to the relax mailing lists - well, accidentally anyway :) As >> Sebastien said, please feel free to ask here if you have any >> difficulties or problems - I should be able to help you sort out most >> issues. And all user feedback is most welcome! relax is now such a >> massive multi-developer project that I am unable to keep everything >> perfectly up to date, so any suggestions are taken seriously. >> >> For the fitting of the relaxation rates, I would strongly recommend >> relax over the Sparky fitting. The reason is because I'm pretty sure >> that Sparky does not use the gold standard for error propagation - >> Monte Carlo simulations. Hence your error estimates may not be >> accurate and this has a strong effect on the model-free analysis. >> Other programs, such as relax and Art Palmer's curvefit, perform the >> error propagation properly. >> >> As for understanding the analysis, the analysis chapters of the relax >> manual together with the user function documentation should hopefully >> provide enough details. I have just noticed that the relaxation >> curve-fitting chapter is very much out of date! If you use the GUI, I >> have redesigned it so that usage should be very obvious and not >> require any reading of the manual or user function documentation. >> Again, if anything is not 100% obvious, any suggestions for how to >> improve this are welcome. >> >> Unfortunately there is no full test data set to try the analyses on. >> This is something I plan on adding to relax in the future once I >> publish a paper from my PhD times. Note though that, although a >> single model-free calculation is extremely quick within all software >> packages, the full highly-iterative model-free analysis protocol can >> take between 1 to 2 weeks to complete. relax implements this full >> protocol into the GUI (details are available via the 'about' button in >> the model-free analysis tab) or in the >> sample_scripts/model_free/dauvergne_protocol.py script. As this takes >> such a long time, I'm not sure how useful such an example data set >> would be. You can always speed the analysis up by using Gary >> Thompson's multi-processor code within relax - see the introductory >> chapter for how to use this. >> >> Regards, >> >> Edward >> >> >> P. S. You can implement one of the original model-free analysis >> protocols from the 1990's if you can only collect single field >> strength data. relax is so flexible that it is capable of reproducing >> the results from Modelfree4 and Dasha extremely accurately, you just >> need turn the optimisation precision to very low values. However to >> be sure that the internal dynamics is real and not due to a slightly >> incorrect estimate of the diffusion tensor, data at two field >> strengths (with both temperature compensation and per-experiment >> temperature calibration) is highly recommended. >> >> _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
