Re: Peak list readingRe: Peak list readingHi 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 <tlinnet@xxxxxxxxxxxxx> 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.cho@xxxxxxxx>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@xxxxxxx 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@xxxxxxx 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