Hi Ed and Troels, Thank you for the comment. I will try today when I get back to my laptop.
Wish all you have merry Christmas and Happy new year! Min-Kyu Dec 21, 2013 7:14 AM "Edward d'Auvergne" <edw...@nmr-relax.com> 작성: > Hi Min-Kyu and Troels, > > From the messages, I can see 4 potential issues: > > 1) The assignment: > > 568?-? 123.445 8.765 3.45E06 > > is ambiguous, as it could be any spin pair. It is best to assign the > atoms properly, otherwise relax cannot tell if it is a N-H pair, the > Trp NE1-HE1 pair, or something more exotic. Note that you can analyse > your Trp NE1 data at the same time as the backbone N data. Troels, on > line 108 of the ./lib/spectrum/sparky.py file (as well as the other > peak list files in that package), maybe it is worth searching for the > "?-?" string in the assignment rather than matching "?-?" to skip the > line of data? Actually it might be best if we just skip every single > assignment containing "?", and just give a warning that the line is > being skipped as the assignment has a question mark in it. > > > 2) The Sparky assignment format is: > > [Group][atom1]-[Group][atom2]-[Group][atom3] > > The group is optional for the 2nd, 3rd, etc. dimensions. The format > of the "Group" is not defined in Sparky, but in its manual it uses the > convention of letters for the residue name followed by the residue > number. However despite the warnings from relax about the missing > residue name, I would assume that the data would be nevertheless read. > The spectrum.read_intensities user function will print out a list of > all the intensities read into the program at the end, so you will be > able to tell what has been read or skipped. > > > 3) For you Troels - could you have a look at line 172 of the > ./lib/spectrum/sparky.py file? It has the confusing text "Improperly > formatted NMRPipe SeriesTab file" which is probably a copy and paste > error from the ./lib/spectrum/nmrpipe.py file. > > > 4) The "IndexError: list index out of range" might be due to the > badly formatted header line, as Troels mentioned. Min-Kyu, if you fix > that, does the error go away? Alternatively, it could be that one > line in the file is differently formatted, for some unknown reason. > This can be tested by deleting lines out of the file one by one until > the error goes away (except for the header which is needed to > determine the "Data Height" column). If you do find that there is a > problem with the file, could you submit a bug report at > https://gna.org/bugs/?func=additem&group=relax and attach the > truncated peak list which still causes the error? With this, I can > construct a system test for relax and also make sure that an > informative RelaxError or RelaxWarning is given so that the user knows > exactly what the problem is and how it should be fixed. > > > As for the FASTA format, this is not supported by relax yet. This is > not a great format as you don't know the residue numbering and it will > very likely not start at one. But as Troels mentioned, you can load > the sequence from your peak lists. It might then be worth having the > amino acid names in the group part of the Sparky assignment if you > would like residue names to be present. > > Regards, > > Edward > > > P. S. I may not be able to do much until after the new year so, if > you don't hear from me until then, I wish you a merry Christmas and > happy new year! > > > > >> On 21 December 2013 02:41, Troels Emtekær Linnet <tlin...@nmr-relax.com> >> wrote: >> Hi Min-Kyu. >> >> I believe you probably need to define the right header >> for the file. >> ex: >> Assignment w1 w2 Data Height >> >> And see if you can fix the question marks. >> 568N-HN >> >> Have a look in the test-suite for some typical definition of peaks files. >> test_suite/shared_data/peak_lists >> >> If you have a peak list, the new 3.1.1 version allow you to define the spins >> from >> a typical peak list. >> spectrum.read_spins(file='peak_file.list', dir='/path/to/file') >> >> Cheers >> >> >> >> 2013/12/20 Min-Kyu Cho <min-kyu....@live.com> >>> >>> Hi , >>> >>> >>> >>> >>> >>> I got sparky peak list file written as >>> >>> >>> >>> 568?-? 123.445 8.765 3.45E06 >>> >>> . . . . . >>> >>> >>> >>> >>> >>> When I tried to read in this file through GUI, it complains >>> >>> ---------- >>> >>> Sparky formatted data file. >>> >>> >>> >>> Number of header lines found: 1 >>> >>> 2D peak list detected. >>> >>> RelaxWarning: Improperly formatted Sparky file, cannot process the residue >>> name for dimension 1 in assignment: 546N-H. Setting residue name to None. >>> >>> RelaxWarning: Improperly formatted NMRPipe SeriesTab file, cannot process >>> the residue name for dimension 2 in assignment: 546N-H. Setting residue name >>> to None. >>> >>> Traceback (most recent call last): >>> >>> File "/home/mkc9/Programs/RELAX/relax-3.1.1/gui/wizards/wiz_objects.py", >>> line 161, in _apply >>> >>> self.exec_status = self.on_execute() >>> >>> File "/home/mkc9/Programs/RELAX/relax-3.1.1/gui/uf_objects.py", line >>> 883, in on_execute >>> >>> return_status = self.execute(self.name, **kargs) >>> >>> File "/home/mkc9/Programs/RELAX/relax-3.1.1/gui/uf_objects.py", line >>> 805, in execute >>> >>> return_status = interpreter.apply(uf, *args, **kwds) >>> >>> File "/home/mkc9/Programs/RELAX/relax-3.1.1/gui/interpreter.py", line >>> 109, in apply >>> >>> apply(fn, args, kwds) >>> >>> File "/home/mkc9/Programs/RELAX/relax-3.1.1/pipe_control/spectrum.py", >>> line 530, in read >>> >>> peak_list = read_peak_list(file=file, dir=dir, int_col=int_col, >>> spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col, >>> res_name_col=res_name_col, spin_num_col=spin_num_col, >>> spin_name_col=spin_name_col, sep=sep, spin_id=spin_id) >>> >>> File "/home/mkc9/Programs/RELAX/relax-3.1.1/lib/spectrum/peak_list.py", >>> line 208, in read_peak_list >>> >>> sparky.read_list(peak_list=peak_list, file_data=file_data) >>> >>> File "/home/mkc9/Programs/RELAX/relax-3.1.1/lib/spectrum/sparky.py", >>> line 203, in read_list >>> >>> intensity = float(line[int_col]) >>> >>> IndexError: list index out of range >>> >>> ----- >>> >>> >>> >>> Since I already made sequence & spin system with correct residue number, I >>> expected the residue number in Sparky file should be enough. >>> >>> >>> >>> So,my questions are: >>> >>> >>> >>> 1. the sparky file format for relax should be made as written in the >>> manual? >>> >>> >>> >>> 2. Can relax recognize FASTA sequence and automatically generate Spin >>> system? >>> >>> >>> >>> Thanks and Happy Holiday! >>> >>> >>> >>> Min-Kyu >>> >>> >>> >>> >>> _______________________________________________ >>> relax (http://www.nmr-relax.com) >>> >>> This is the relax-users mailing list >>> relax-users@gna.org >>> >>> 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 >> >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-users mailing list >> relax-users@gna.org >> >> 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 >> _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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
