Cheers! I have now modified relax to catch these files and send a RelaxError message to the user which says:
RelaxError: The old Protein Dynamics Center (PDC) files are not supported. This message may not be exactly correct, but I'm guessing it should have the right effect on the user. Regards, Edward On 7 September 2012 10:35, Dr. Klaus-Peter Neidig <[email protected]> wrote: > Dear, Edward, dear all, > > thanks for providing this information to me. It is indeed of general > interest > because there is a bug in the output when exporting the relaxation results. > The bug is that the output table also contains the fitted amplitudes and > their errors. > These 2 extra columns should not have been there if the user does not want > them, but in any case the columns you need (e.g. R1 and errorR1) were not > filled > anymore. > > I will correct this today and trigger an upload to our server. The new DC > version > will be named 2.0.7. > > Thanks again and best regards, > Peter > > > > On 07.09.2012 10:12, Edward d'Auvergne wrote: > > Hi Mengjun (and Peter), > > Peter, I have added you to the email cc list just so you can follow > the discussions - you may have an interest in these public messages. > > The problem here is that the Bruker DC test file you have used is an > old format. Newer R1 and R2 files will have two columns called "R1 > [rad/s]" and "R1 sd [rad/s]" (or the R2 equivalent). Actually relax > relies on these two columns to extract the data! This old format is > from the days when Bruker Dynamics Center was known as the Protein > Dynamics Center (PDC), but relax only supports the new Bruker DC > format. I think that the only way I can handle this is to try to > detect the old PDC files and throw a RelaxError saying that these > files cannot, and will not be supported. These R2 data columns were > added, I think, to allow programs such as relax to be able to read the > data in the format required for Abragam's relaxation equations which > are in terms of rates, not times. In the file you attached to the bug > report (https://gna.org/bugs/?20152), these two columns do not have > titles and have the values of 'null'. The new Bruker DC format > required for relax looks like that of the relax files: > > test_suite/shared_data/bruker_files/testT1.txt > test_suite/shared_data/bruker_files/testT2.txt > test_suite/shared_data/bruker_files/testNOE.txt > > The only solution is to use newer Bruker DC files - unfortunately the > old ubiquitin data, as it is, cannot be handled by relax. > > Regards, > > Edward > > > > > On 7 September 2012 08:41, Edward d'Auvergne <[email protected]> > <[email protected]> wrote: > > Hi Mengjun, > > I'm looking into this problem now, but one thing I noticed is that you > didn't set up the tryptophan indole NE1 spins. Note that for your own > analysis that you would need to set up these spins too. > > Regards, > > Edward > > > > On 6 September 2012 23:00, anonymous <[email protected]> > <[email protected]> wrote: > > URL: > <http://gna.org/bugs/?20152> <http://gna.org/bugs/?20152> > > Summary: Import T1 demo.txt from DC to Relax > Project: relax > Submitted by: None > Submitted on: Thu 06 Sep 2012 09:00:04 PM UTC > Category: GUI > Severity: 3 - Normal > Priority: 5 - Normal > Status: None > Privacy: Public > Assigned to: None > Originator Name: > Originator Email: [email protected] > Open/Closed: Open > Discussion Lock: Any > Release: 2.1.0 > Operating System: Microsoft Windows > > _______________________________________________________ > > Details: > > Details: > > operating system: windows7 > > > version of Relax: 2.1.0 > > > operation steps: > > > 1. start Relax_gui_mode.py > > 2. click new analysis > > 3. click model-free analysis > > 4. click next > > 5. click start > > 6. click spin viewer window > > 7. load 1UBQ_H.pdb > > 8. click next > > 9. choose The spin ID sting: @N > > 10. click next > > 11. click finish > > 12. click Add (bruker) > > 13.type 'r1_700' in the term of The relaxation data ID string > > 14. load the file 'T1 demo.txt' > > 15. click Next > > 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='C:UsersMengjun XueDesktopNew folder > (3)1UBQ_H.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 'C:UsersMengjun XueDesktopNew folder (3)1UBQ_H.pdb' for > reading. > Adding molecule '1UBQ_H_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 > 1UBQ_H_mol1 1 MET 1 N > 1UBQ_H_mol1 2 GLN 9 N > 1UBQ_H_mol1 3 ILE 18 N > 1UBQ_H_mol1 4 PHE 26 N > 1UBQ_H_mol1 5 VAL 37 N > 1UBQ_H_mol1 6 LYS 44 N > 1UBQ_H_mol1 7 THR 53 N > 1UBQ_H_mol1 8 LEU 60 N > 1UBQ_H_mol1 9 THR 68 N > 1UBQ_H_mol1 10 GLY 75 N > 1UBQ_H_mol1 11 LYS 79 N > 1UBQ_H_mol1 12 THR 88 N > 1UBQ_H_mol1 13 ILE 95 N > 1UBQ_H_mol1 14 THR 103 N > 1UBQ_H_mol1 15 LEU 110 N > 1UBQ_H_mol1 16 GLU 118 N > 1UBQ_H_mol1 17 VAL 127 N > 1UBQ_H_mol1 18 GLU 134 N > 1UBQ_H_mol1 19 PRO 143 N > 1UBQ_H_mol1 20 SER 150 N > 1UBQ_H_mol1 21 ASP 156 N > 1UBQ_H_mol1 22 THR 164 N > 1UBQ_H_mol1 23 ILE 171 N > 1UBQ_H_mol1 24 GLU 179 N > 1UBQ_H_mol1 25 ASN 188 N > 1UBQ_H_mol1 26 VAL 196 N > 1UBQ_H_mol1 27 LYS 203 N > 1UBQ_H_mol1 28 ALA 212 N > 1UBQ_H_mol1 29 LYS 217 N > 1UBQ_H_mol1 30 ILE 226 N > 1UBQ_H_mol1 31 GLN 234 N > 1UBQ_H_mol1 32 ASP 243 N > 1UBQ_H_mol1 33 LYS 251 N > 1UBQ_H_mol1 34 GLU 260 N > 1UBQ_H_mol1 35 GLY 269 N > 1UBQ_H_mol1 36 ILE 273 N > 1UBQ_H_mol1 37 PRO 281 N > 1UBQ_H_mol1 38 PRO 288 N > 1UBQ_H_mol1 39 ASP 295 N > 1UBQ_H_mol1 40 GLN 303 N > 1UBQ_H_mol1 41 GLN 312 N > 1UBQ_H_mol1 42 ARG 321 N > 1UBQ_H_mol1 43 LEU 332 N > 1UBQ_H_mol1 44 ILE 340 N > 1UBQ_H_mol1 45 PHE 348 N > 1UBQ_H_mol1 46 ALA 359 N > 1UBQ_H_mol1 47 GLY 364 N > 1UBQ_H_mol1 48 LYS 368 N > 1UBQ_H_mol1 49 GLN 377 N > 1UBQ_H_mol1 50 LEU 386 N > 1UBQ_H_mol1 51 GLU 394 N > 1UBQ_H_mol1 52 ASP 403 N > 1UBQ_H_mol1 53 GLY 411 N > 1UBQ_H_mol1 54 ARG 415 N > 1UBQ_H_mol1 55 THR 426 N > 1UBQ_H_mol1 56 LEU 433 N > 1UBQ_H_mol1 57 SER 441 N > 1UBQ_H_mol1 58 ASP 447 N > 1UBQ_H_mol1 59 TYR 455 N > 1UBQ_H_mol1 60 ASN 467 N > 1UBQ_H_mol1 61 ILE 475 N > 1UBQ_H_mol1 62 GLN 483 N > 1UBQ_H_mol1 63 LYS 492 N > 1UBQ_H_mol1 64 GLU 501 N > 1UBQ_H_mol1 65 SER 510 N > 1UBQ_H_mol1 66 THR 516 N > 1UBQ_H_mol1 67 LEU 523 N > 1UBQ_H_mol1 68 HIS 531 N > 1UBQ_H_mol1 69 LEU 541 N > 1UBQ_H_mol1 70 VAL 549 N > 1UBQ_H_mol1 71 LEU 556 N > 1UBQ_H_mol1 72 ARG 564 N > 1UBQ_H_mol1 73 LEU 575 N > 1UBQ_H_mol1 74 ARG 583 N > 1UBQ_H_mol1 75 GLY 594 N > 1UBQ_H_mol1 76 GLY 598 N > > relax> bruker.read(ri_id='r1_700', file='C:UsersMengjun XueDesktopNew folder > (3)T1 demo.txt', dir=None) > Opening the file 'C:UsersMengjun XueDesktopNew folder (3)T1 demo.txt' for > reading. > RelaxWarning: The spin '#1UBQ_H_mol1:1@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:2@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:3@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:4@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:5@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:6@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:7@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:8@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:9@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:10@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:11@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:12@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:13@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:14@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:15@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:16@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:17@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:18@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:19@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:20@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:21@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:22@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:23@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:24@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:25@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:26@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:27@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:28@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:29@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:30@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:31@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:32@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:33@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:34@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:35@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:36@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:37@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:38@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:39@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:40@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:41@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:42@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:43@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:44@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:45@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:46@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:47@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:48@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:49@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:50@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:51@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:52@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:53@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:54@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:55@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:56@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:57@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:58@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:59@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:60@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:61@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:62@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:63@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:64@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:65@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:66@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:67@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:68@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:69@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:70@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:71@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:72@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:73@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:74@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:75@N' is already named. Set the force > flag to rename. > RelaxWarning: The spin '#1UBQ_H_mol1:76@N' is already named. Set the force > flag to rename. > Traceback (most recent call last): > File "C:UsersMengjun XueDesktopdesk120816relax > nmrabcrelax-2.1.0.Win32relax-2.1.0guiinterpreter.py", line 299, in run > apply(fn, args, kwds) > File "C:UsersMengjun XueDesktopdesk120816relax > nmrabcrelax-2.1.0.Win32relax-2.1.0generic_fnsbruker.py", line 165, in read > rx = float(row[-2]) > ValueError: could not convert string to float: null > Traceback (most recent call last): > File "C:UsersMengjun XueDesktopdesk120816relax > nmrabcrelax-2.1.0.Win32relax-2.1.0guiwizard.py", line 682, in _go_next > self._display_page(self._current_page) > File "C:UsersMengjun XueDesktopdesk120816relax > nmrabcrelax-2.1.0.Win32relax-2.1.0guiwizard.py", line 610, in _display_page > self._pages[i].on_display_post() > File "C:UsersMengjun XueDesktopdesk120816relax > nmrabcrelax-2.1.0.Win32relax-2.1.0guicomponentsrelax_data.py", line 418, in > wizard_update_int_type > page.uf_args['ri_id'].SetValue(value=id) > File "C:UsersMengjun XueDesktopdesk120816relax > nmrabcrelax-2.1.0.Win32relax-2.1.0guiinput_elementsvalue.py", line 314, in > SetValue > raise RelaxError("The Value element is read only, cannot set the value > '%s'." % value) > relax_errors.RelaxError: RelaxError: The Value element is read only, cannot > set the value 'r1_700'. > > > > > > > _______________________________________________________ > > File Attachments: > > > ------------------------------------------------------- > Date: Thu 06 Sep 2012 09:00:04 PM UTC Name: 1UBQ_H.pdb Size: 122kB By: > None > <http://gna.org/bugs/download.php?file_id=16482> > <http://gna.org/bugs/download.php?file_id=16482> > ------------------------------------------------------- > Date: Thu 06 Sep 2012 09:00:04 PM UTC Name: T1 demo.txt Size: 61kB By: > None > <http://gna.org/bugs/download.php?file_id=16483> > <http://gna.org/bugs/download.php?file_id=16483> > > _______________________________________________________ > > Reply to this item at: > > <http://gna.org/bugs/?20152> <http://gna.org/bugs/?20152> > > _______________________________________________ > Message sent via/by Gna! > http://gna.org/ > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-devel mailing [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page athttps://mail.gna.org/listinfo/relax-devel > > . > > > > -- > ** > > *Dr. Klaus-Peter Neidig > *Software Development / Head of Analysis Group > > Bruker BioSpin GmbH > Silberstreifen > 76287 Rheinstetten, Germany > Phone: +49 721 5161-6447 > Fax: +49 721 5161-6480 > > [email protected] <[email protected]> > www.bruker.com > ------------------------------ > Bruker BioSpin GmbH: Sitz der Gesellschaft/Registered Office: > Rheinstetten, HRB 102368 Amtsgericht Mannheim > Geschäftsführer/Managing Directors: Jörg Laukien, Dr. Bernd Gewiese, Dr. > Gerhard Roth, Dr. Wulf-Ingo Jung > > Diese E-Mail und alle Anlagen können Betriebs- oder Geschäftsgeheimnisse, > oder sonstige vertrauliche Informationen enthalten. Sollten Sie diese > E-Mail irrtümlich erhalten haben, ist Ihnen eine Kenntnisnahme des Inhalts, > eine Vervielfältigung oder Weitergabe der E-Mail und aller Anlagen > ausdrücklich untersagt. Bitte benachrichtigen Sie den Absender und > löschen/vernichten Sie die empfangene E-Mail und alle Anlagen. Vielen Dank. > > This message and any attachments may contain trade secrets or privileged, > undisclosed or otherwise confidential information. If you have received > this e-mail in error, you are hereby notified that any review, copying or > distribution of it and its attachments is strictly prohibited. Please > inform the sender immediately and delete/destroy the original message and > any copies. Thank you. >
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