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
