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/
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>
>>
>
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