Hi Eldon,
Another entry to look at would be bmr16925.str. This has model '5' in
the Order_parameter saveframe ('S2f, S2, ts'), but
_Order_param.Sf2_val is blank. Either the deposited data is missing,
or those numbers were not deposited.
Cheers,
Edward
On 4 April 2011 16:13, Eldon Ulrich <[email protected]> wrote:
> Hi,
>
> Thank you for the reminder. The next step in this remediation process will
> be to go through and incorporate the missing data that was deposited into
> the entries. This will take more time, but we will be working on it this
> month.
>
> The original relaxation tags were developed in collaboration with Art Palmer
> and the 'model_fit' was set up to capture the best fit model (or model
> designated by the depositor) from a modelfree analysis. As Edward pointed
> out, after much discussion the following enumerations for the tag are now in
> the dictionary.
>
>
> save__Order_param.Model_fit
> loop_
> _item_enumeration_value
> _item_enumeration_description
>
> No internal model-free motions:
>
> '' .
> 'Rex' .
>
> Original Lipari-Szabo (Lipari and Szabo, 1982), plus additional params
> such as Rex:
>
> 'S2' .
> 'S2, te' .
> 'S2, Rex' .
> 'S2, te, Rex' .
>
> Extended model-free (Clore et al., 1990), plus additional params such as
> Rex:
>
> 'S2f, S2, ts' .
> 'S2f, S2s, ts' .
> 'S2f, tf, S2, ts' .
> 'S2f, tf, S2s, ts' .
> 'S2f, S2, ts, Rex' .
> 'S2f, S2s, ts, Rex' .
> 'S2f, tf, S2, ts, Rex' .
> 'S2f, tf, S2s, ts, Rex' .
>
> stop_
> save_
>
> Cheers,
> Eldon
>
> On 4/4/11 8:03 AM, Sébastien Morin 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)
>>>
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>>>
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>>> reminder, or change your subscription options,
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>>
>
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