Hi,
Thank you very much for your email. One question about the
consistency_tests.py file, when using consistency_tests.py to extract
J (0) from one field strength data R1/R2/NOE, following parameter is
needed to set:
# Set the angle between the 15N-1H vector and the principal axis of
the 15N chemical shift tensor
value.set(val=15.7, param='orientation')
# Set the approximate correlation time.
value.set(val=13 * 1e-9, param='tc')
When using consistency_tests.py, how to set the angle between the
15N-1H vector and the principal axis of the 15N chemical shift tensor
? perhaps, val=15.7 ? And the correlation time is also needed to set,
I am confused about setting the global correlation time before a
complete model free analysis since the global correlation time can be
extracted after the complete model free analysis.
However, in jw_mapping.py, which can also be used to exctract J (0),
no such parameter is needed to set ?
Thank you.
With best regards,
Mengjun
Quoting Sébastien Morin <sebastianomorino@xxxxxxxxx>:
Hi,
Indeed, as Edward pointed, the consistency testing procedure
involves two steps, the first one being to load data from each
magnetic field separately and calculating the J(0) (or F_R2 or
F_eta) values for each spin. The second step, performed outside
relax, is the comparison of the calculated values at two magnetic
fields (e.g. using correlation plots).
It is important that data (all of R1, R2, and NOE) from a single
magnetic field are loaded in order to calculate the J(0) (or F_R2 or
F_eta) values.
In the best of world, someone could implement the calculation of the
J(0) (or F_R2 or F_eta) values at different fields and subsequent
plotting and consistency assessment all within relax and in a single
step. That would be a real enhancement compared to the current
situation... :)
I hope this helps.
Best,
Sébastien
On 13-03-28 8:07 PM, Edward d'Auvergne wrote:
Hi again,
I was wondering if you have read the consistency testing part of the
relax manual written by Sebastien Morin (the person who implemented
this analysis). Specifically this section:
http://www.nmr-relax.com/manual/Consistency_testing_script_mode_relaxation_data_lo.html
Note the text, "For this analysis, only data for a single field
strength can be loaded". This may possibly be the source of some of
your problems.
Regards,
Edward
On 28 March 2013 20:02, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
Hi Mengjun,
Could you also attach the PDB file? I need it to be able to run the
script and replicate the problem.
Cheers,
Edward
On 28 March 2013 16:39, anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
Additional Item Attachment, bug #20674 (project relax):
File name: T1 dhp 700.txt Size:74 KB
File name: T2 dhp 500.txt Size:67 KB
File name: T2 dhp 700.txt Size:68 KB
File name: logconsistency Size:371 KB
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Re: [bug #20674] UnboundLocalError in consistency_tests.py