Hi Seb, You need to have a look at the v3.1 file at:
http://www.bmrb.wisc.edu/ftp/pub/bmrb/entry_lists/nmr-star3.1 The Rex and J(w) values are missing in this version too. In the Order_parameter saveframe (equivalent to the v2.1 S2_parameters saveframe), you'll see that the models are consistent. We did however agree, after a detailed and complete discussion, to a new model naming scheme for all different model-free model possibilities: https://mail.gna.org/public/relax-devel/2009-03/msg00022.html https://mail.gna.org/public/relax-devel/2009-03/msg00024.html https://mail.gna.org/public/relax-devel/2009-03/msg00027.html https://mail.gna.org/public/relax-devel/2009-03/msg00028.html https://mail.gna.org/public/relax-devel/2009-03/msg00038.html https://mail.gna.org/public/relax-devel/2009-03/msg00039.html In the end, from memory I thought we decided that the model_fit tag would consist of the following: "" "S2" "S2,te" "S2,Rex" "S2,te,Rex" "S2f,S2,ts" "S2f,tf,S2,ts" "S2f,S2,ts,Rex" "S2f,tf,S2,ts,Rex" "Rex" and that no other values would be accepted, it would be a closed enumeration, I think the terminology is called. There are many v3.1 entries that would need to be updated for this. Regards, Edward On 4 April 2011 15:03, Sébastien Morin <[email protected]> wrote: > Hi Eldon, > > Entry 6838 indeed does not contain any Rex, but should as these were > deposited: > > https://mail.gna.org/public/relax-devel/2011-02/msg00005.html > # Message-id: <[email protected]> > > Moreover, there are still other missing data, i.e. reduced spectral density > values (J0, JwN, JwH at 500, 600 and 800 MHz), in this entry that were > deposited but never incorporated: > > https://mail.gna.org/public/relax-devel/2011-02/msg00006.html > # Message-id: <[email protected]> > > I just had a look at the entry > (http://www.bmrb.wisc.edu/data_library/generate_summary?6838) and realized > the "Model_fit" tags in the "S2 Parameters" saveframe were filled. This is > good, but leads me to another consideration which probably has already been > discussed (sorry if this is the case)... In some entries as 6838, > "Model_fit" is a model name (e.g. "m3"), whereas in other entries, it is a > list of parameters used for the model (e.g. "S2, Rex", which is equivalent > to "m3"). Should these be standardized ? If yes, how ? > > Thanks for the follow-up on the different entries, especially on 6838 ! > Best regards, > > > Séb :) > > > > > On 11-04-01 6:38 PM, Eldon Ulrich wrote: >> >> Hi, >> >> The order of the tags is fixed, so what will need to be done is move the >> data columns to match the appropriate tag. It appears that the entry >> does not contain any Rex data, if the Model_fit information and >> following data are offset by two columns. The entry has been modified >> and should appear tomorrow. >> >> Thanks, >> Eldon >> >> On 4/1/11 8:12 AM, Edward d'Auvergne wrote: >>> >>> Hi, >>> >>> The 6838 entry also has the tag names mixed up in the Order_parameter >>> saveframe. The following change is necessary, otherwise the Rex >>> errors are the model-free model names! >>> >>> diff -urd --ignore-all-space --ignore-space-change >>> --ignore-blank-lines ./bmr6838.str >>> ../../../../../../bmr3.1_files/bmr6838.str >>> --- ./bmr6838.str 2011-04-01 05:01:00.000000000 +0200 >>> +++ ../../../../../../bmr3.1_files/bmr6838.str 2011-04-01 >>> 15:11:00.000000000 +0200 >>> @@ -7712,14 +7712,14 @@ >>> _Order_param.Tau_f_val_fit_err >>> _Order_param.Tau_s_val >>> _Order_param.Tau_s_val_fit_err >>> - _Order_param.Rex_val >>> - _Order_param.Rex_val_fit_err >>> _Order_param.Model_free_sum_squared_errs >>> _Order_param.Model_fit >>> _Order_param.Sf2_val >>> _Order_param.Sf2_val_fit_err >>> _Order_param.Ss2_val >>> _Order_param.Ss2_val_fit_err >>> + _Order_param.Rex_val >>> + _Order_param.Rex_val_fit_err >>> _Order_param.SH2_val >>> _Order_param.SH2_val_fit_err >>> _Order_param.SN2_val >>> >>> Regards, >>> >>> Edward >>> >>> >>> On 1 April 2011 15:06, Edward d'Auvergne<[email protected]> wrote: >>>> >>>> Hi, >>>> >>>> It is now fixed. But I noticed that the Rex data from bmr6838.str in >>>> the Order_parameter saveframe is missing? >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> >>>> On 31 March 2011 19:02, Eldon Ulrich<[email protected]> wrote: >>>>> >>>>> Hi, >>>>> >>>>> Thanks for the catch. The entry has been fixed and should be available >>>>> tomorrow. >>>>> >>>>> Eldon >>>>> >>>>> On 3/31/11 3:21 AM, Edward d'Auvergne wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>> I noticed also that entry 15183 was recently updated with a fix to the >>>>>> sequence numbering. However there are still some problems with the >>>>>> residue names in one of the Order_parameter saveframes. The following >>>>>> is the diff: >>>>>> >>>>>> >>>>>> diff -urd --ignore-all-space --ignore-space-change >>>>>> --ignore-blank-lines ./bmr15183.str >>>>>> ../../../../../../bmr3.1_files/bmr15183.str >>>>>> --- ./bmr15183.str 2011-03-30 05:02:47.000000000 +0200 >>>>>> +++ ../../../../../../bmr3.1_files/bmr15183.str 2011-03-30 >>>>>> 11:47:09.000000000 +0200 >>>>>> @@ -1562,14 +1562,14 @@ >>>>>> 107 . 1 2 117 117 THR N N . 0.981 >>>>>> 0.01 1.00E-09 2.90E-10 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> 108 . 1 2 118 118 ASP N N . 0.957 >>>>>> 0.001 1.00E-09 0.00E+00 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> 109 . 1 2 119 119 GLU N N . 0.91 >>>>>> 0.001 1.00E-09 0.00E+00 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> - 110 . 1 2 120 120 GLN N N . 0.967 >>>>>> 0.001 1.00E-09 0.00E+00 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> + 110 . 1 2 120 120 GLU N N . 0.967 >>>>>> 0.001 1.00E-09 0.00E+00 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> 111 . 1 2 121 121 VAL N N . 0.972 >>>>>> 0.003 1.00E-09 0.00E+00 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> 112 . 1 2 122 122 ASP N N . 0.962 >>>>>> 0 1.00E-09 0.00E+00 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> 113 . 1 2 123 123 GLU N N . 0.953 >>>>>> 0 1.00E-09 0.00E+00 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> 114 . 1 2 125 125 ILE N N . 0.972 >>>>>> 0.002 1.00E-09 0.00E+00 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> 115 . 1 2 126 126 ARG N N . 0.957 >>>>>> 0.002 1.00E-09 0.00E+00 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> 116 . 1 2 127 127 GLU N N . 0.981 >>>>>> 0.009 1.00E-09 5.20E-10 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> - 117 . 1 2 128 128 SER N N . 0.953 >>>>>> 0.009 1.00E-09 1.80E-10 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> + 117 . 1 2 128 128 ALA N N . 0.953 >>>>>> 0.009 1.00E-09 1.80E-10 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> 118 . 1 2 129 129 ASP N N . 0.707 >>>>>> 0.008 1.57E-11 1.00E-12 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> 119 . 1 2 130 130 ILE N N . 0.962 >>>>>> 0.009 2.16E-11 1.06E-11 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> 120 . 1 2 131 131 ASP N N . 0.91 >>>>>> 0.01 5.00E-14 0.00E+00 . . . . . . . . . . >>>>>> . . . . . . . . . . . 15183 1 >>>>>> >>>>>> Regards, >>>>>> >>>>>> Edward >>>>>> >>>>>> >>>>>> >>>>>> On 30 March 2011 17:28, Eldon Ulrich<[email protected]> wrote: >>>>>>> >>>>>>> Yea, I just noticed that 6474 and 6577 were not quite right as I was >>>>>>> double >>>>>>> checking the released files, not sure what happened. >>>>>>> >>>>>>> Thanks, >>>>>>> Eldon >>>>>>> >>>>>>> On 3/30/11 7:17 AM, Edward d'Auvergne wrote: >>>>>>>> >>>>>>>> Oh, the new v3.1 bmr6577.str entry is missing the S2 error as well. >>>>>>>> This data is in the v2.1 files but not the new v3.1 files. >>>>>>>> >>>>>>>> Regards, >>>>>>>> >>>>>>>> Edward >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 30 March 2011 14:14, Edward d'Auvergne<[email protected]> >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> I'm just looking at the new v3.1 entries and noticed that >>>>>>>>> bmr6474.str >>>>>>>>> is missing the S2 and Rex errors. >>>>>>>>> >>>>>>>>> Regards, >>>>>>>>> >>>>>>>>> Edward >>>>>>>>> >>>>>>>>> >>>>>>>>> On 30 March 2011 11:06, Edward d'Auvergne<[email protected]> >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> The values should all be ps for 17041, 17046, and 17047. The >>>>>>>>>> numbers >>>>>>>>>> for tau_e, tau_f, and tau_s range from about 10 ps to 2000-4000 >>>>>>>>>> ps. >>>>>>>>>> So it can be seen from the data that the three tags in all these >>>>>>>>>> entries should be: >>>>>>>>>> >>>>>>>>>> _Order_parameter_list.Tau_e_val_units ps >>>>>>>>>> _Order_parameter_list.Tau_f_val_units ps >>>>>>>>>> _Order_parameter_list.Tau_s_val_units ps >>>>>>>>>> >>>>>>>>>> For the attachments, these are not attached to the email, but >>>>>>>>>> rather >>>>>>>>>> attached to the link https://gna.org/task/?6438. >>>>>>>>>> >>>>>>>>>> Regards, >>>>>>>>>> >>>>>>>>>> Edward >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 29 March 2011 17:15, Eldon Ulrich<[email protected]> >>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> I am finishing the edits on the first batch of v2.1 and v3.1 >>>>>>>>>>> files >>>>>>>>>>> today. In >>>>>>>>>>> looking at the related entries 17041, 17046, and 17047, one has a >>>>>>>>>>> tau >>>>>>>>>>> e >>>>>>>>>>> value of ns (17041) and the others are ps (17046 and 17047). I >>>>>>>>>>> changed >>>>>>>>>>> 17041 >>>>>>>>>>> to ps, although I did not see this change in your list. Although, >>>>>>>>>>> I >>>>>>>>>>> may >>>>>>>>>>> have >>>>>>>>>>> missed the suggested change. Could you please review these three >>>>>>>>>>> entries >>>>>>>>>>> once they are released, hopefully tomorrow or Thursday. >>>>>>>>>>> >>>>>>>>>>> Also, This email did not seem to have the attachments. I have a >>>>>>>>>>> feeling >>>>>>>>>>> I >>>>>>>>>>> may have lost a followup email, but could you resend the >>>>>>>>>>> attachments. >>>>>>>>>>> >>>>>>>>>>> I will start to look at the blacklisted entries after finishing >>>>>>>>>>> the >>>>>>>>>>> less >>>>>>>>>>> offensive problems. >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> Eldon >>>>>>>>>>> >>>>>>>>>>> On 3/24/11 5:43 AM, Edward d Auvergne wrote: >>>>>>>>>>>> >>>>>>>>>>>> Follow-up Comment #10, task #6438 (project relax): >>>>>>>>>>>> >>>>>>>>>>>> This set of diffs for the v2.1 and v3.1 files now includes the >>>>>>>>>>>> relaxation >>>>>>>>>>>> data BMRB entries (with no model-free data). The following >>>>>>>>>>>> entries >>>>>>>>>>>> have >>>>>>>>>>>> been >>>>>>>>>>>> blacklisted, as relax cannot use them: >>>>>>>>>>>> >>>>>>>>>>>> # The blacklist. >>>>>>>>>>>> blacklist = [] # Init. >>>>>>>>>>>> blacklist = blacklist + ['bmr16933.str'] # Rubbish relxn2.2 >>>>>>>>>>>> data! >>>>>>>>>>>> blacklist = blacklist + ['bmr4697.str'] # Unknown >>>>>>>>>>>> spectrometer >>>>>>>>>>>> frequency. >>>>>>>>>>>> blacklist = blacklist + ['bmr5520.str', 'bmr5521.str'] # >>>>>>>>>>>> Entity >>>>>>>>>>>> problem >>>>>>>>>>>> with 2 molecules. >>>>>>>>>>>> blacklist = blacklist + ['bmr5715.str', 'bmr6758.str', >>>>>>>>>>>> 'bmr16639.str'] >>>>>>>>>>>> # >>>>>>>>>>>> Sequence corruption. >>>>>>>>>>>> blacklist = blacklist + ['bmr6332.str', 'bmr7205.str'] # >>>>>>>>>>>> Totally >>>>>>>>>>>> mangled >>>>>>>>>>>> sequence! >>>>>>>>>>>> >>>>>>>>>>>> Most of these require work on the BMRB side. The model-free >>>>>>>>>>>> entries >>>>>>>>>>>> read >>>>>>>>>>>> into relax include: >>>>>>>>>>>> >>>>>>>>>>>> 4096, 4245, 4267, 4364, 4365, 4366, 4390, 4689, 4970, 5153, >>>>>>>>>>>> 5154, >>>>>>>>>>>> 5330, >>>>>>>>>>>> 5331, >>>>>>>>>>>> 5548, 5549, 5550, 5808, 5841, 5991, 6243, 6466, 6470, 6474, >>>>>>>>>>>> 6577, >>>>>>>>>>>> 6838, >>>>>>>>>>>> 7126, >>>>>>>>>>>> 7139, 7219, 15097, 15144, 15183, 15184, 15185, 15186, 15187, >>>>>>>>>>>> 15188, >>>>>>>>>>>> 15191, >>>>>>>>>>>> 15230, 15445, 15451, 15536, 15562, 15910, 16392, 16925, 16931, >>>>>>>>>>>> 17010, >>>>>>>>>>>> 17012, >>>>>>>>>>>> 17013, 17041, 17046, 17047, 17069 >>>>>>>>>>>> >>>>>>>>>>>> The purely relaxation data entries read into relax are: >>>>>>>>>>>> >>>>>>>>>>>> 4376, 4671, 4762, 4763, 4764, 4801, 4870, 5076, 5079, 5080, >>>>>>>>>>>> 5131, >>>>>>>>>>>> 5272, >>>>>>>>>>>> 5505, >>>>>>>>>>>> 5518, 5519, 5569, 5687, 5707, 5720, 5746, 5762, 5801, 5818, >>>>>>>>>>>> 5839, >>>>>>>>>>>> 5858, >>>>>>>>>>>> 5995, >>>>>>>>>>>> 5996, 6060, 6092, 6182, 6494, 6495, 6579, 6880, 6881, 6899, >>>>>>>>>>>> 7021, >>>>>>>>>>>> 7035, >>>>>>>>>>>> 7036, >>>>>>>>>>>> 7056, 7088, 7112, 7190, 7208, 7288, 7414, 7415, 7432, 15014, >>>>>>>>>>>> 15064, >>>>>>>>>>>> 15065, >>>>>>>>>>>> 15066, 15067, 15252, 15254, 15255, 15364, 15408, 15437, 15441, >>>>>>>>>>>> 15481, >>>>>>>>>>>> 15486, >>>>>>>>>>>> 15521, 15541, 15578, 15650, 15655, 15703, 15708, 15728, 15766, >>>>>>>>>>>> 15793, >>>>>>>>>>>> 15795, >>>>>>>>>>>> 15830, 15831, 15832, 15852, 15923, 15975, 15989, 16033, 16034, >>>>>>>>>>>> 16069, >>>>>>>>>>>> 16234, >>>>>>>>>>>> 16342, 16360, 16426, 16480, 16482, 16483, 16485, 16523, 16657, >>>>>>>>>>>> 16659, >>>>>>>>>>>> 16845, >>>>>>>>>>>> 16904, 16907, 17018, 17080, 17263, 17266, 17308 >>>>>>>>>>>> >>>>>>>>>>>> The first attached file is the v2.1 diff, the second is the v3.1 >>>>>>>>>>>> diff: >>>>>>>>>>>> >>>>>>>>>>>> (file #12700, file #12701) >>>>>>>>>>>> _______________________________________________________ >>>>>>>>>>>> >>>>>>>>>>>> Additional Item Attachment: >>>>>>>>>>>> >>>>>>>>>>>> File name: diff Size:192 KB >>>>>>>>>>>> File name: diff Size:356 KB >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________________ >>>>>>>>>>>> >>>>>>>>>>>> Reply to this item at: >>>>>>>>>>>> >>>>>>>>>>>> <http://gna.org/task/?6438> >>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Message sent via/by Gna! >>>>>>>>>>>> http://gna.org/ >>>>>>>>>>>> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-devel 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-devel > > -- > Sébastien Morin, Ph.D. > Postdoctoral fellow > S. Grzesiek NMR Laboratory > Biozentrum, Universität Basel > Basel, Switzerland > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel 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-devel
