Re: [task #6438] To relax the BMRB.Re: [task #6438] To relax the BMRB.Hi Ed, Very good for the info and update ! Séb :) On 11-04-04 3:26 PM, Edward d'Auvergne wrote:
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<sebastien.morin.1@xxxxxxxxx> 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:<4D4841D0.1040602@xxxxxxxxxxxxx> 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:<4D484485.5090806@xxxxxxxxx> 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<edward@xxxxxxxxxxxxx> 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<elu@xxxxxxxxxxxxx> 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<elu@xxxxxxxxxxxxx> 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<edward@xxxxxxxxxxxxx> 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<edward@xxxxxxxxxxxxx> 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<elu@xxxxxxxxxxxxx> 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 relax-devel@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-devel-- Sébastien Morin, Ph.D. Postdoctoral fellow S. Grzesiek NMR Laboratory Biozentrum, Universität Basel Basel, Switzerland
-- Sébastien Morin, Ph.D. Postdoctoral fellow S. Grzesiek NMR Laboratory Biozentrum, Universität Basel Basel, Switzerland