Hi,
When I adapted the jw_mapping code to yield the consistency_test code, I
didn't understand why, in the test suite, the following lines :
if abs(self.relax.data.res[self.run][index].j0 -
j0[index]) > j0[index]/1e6:
print 'Error in residue',
self.relax.data.res[self.run][index].num, 'j0 calculated value'
return
if abs(self.relax.data.res[self.run][index].f_eta -
f_eta[index]) > f_eta[index]/1e6:
print 'Error in residue',
self.relax.data.res[self.run][index].num, 'f_eta calculated value'
return
if abs(self.relax.data.res[self.run][index].f_r2 -
f_r2[index]) > f_r2[index]/1e6:
print 'Error in residue',
self.relax.data.res[self.run][index].num, 'f_r2 calculated value'
return
had a '/1e6' in the end and why those lines were not simply :
if abs(self.relax.data.res[self.run][index].j0 -
j0[index]) > j0[index]:
print 'Error in residue',
self.relax.data.res[self.run][index].num, 'j0 calculated value'
return
if abs(self.relax.data.res[self.run][index].f_eta -
f_eta[index]) > f_eta[index]:
print 'Error in residue',
self.relax.data.res[self.run][index].num, 'f_eta calculated value'
return
if abs(self.relax.data.res[self.run][index].f_r2 -
f_r2[index]) > f_r2[index]:
print 'Error in residue',
self.relax.data.res[self.run][index].num, 'f_r2 calculated value'
return
I tried to modify those lines and the test-suite code still works, anyway.
Could you explain this issue to me, please ? Or is it a mistake and
should the '/1e6' part be taken off..?
Thanks !
Séb :)
Edward d'Auvergne wrote:
> Oh well, it doesn't matter if it's not documented in the code then.
>
> Regards,
>
> Edward
>
>
> On 7/13/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
>>
>> Hi,
>>
>> For the eta value calculated in the consistency_tests code, I don't
>> know if
>> it is the eta_z or eta_xy value. In the original paper by Fushman &
>> Cowburn
>> (1998, JACS, 120: 7109-7110) as well as in the consistency tests paper
>> (Fushman et al., 1998, JACS, 120: 10947-10952), eta is only described
>> as the
>> cross-correlation rate between 15N CSA and 15N-1H dipolar interaction.
>>
>> Cheers
>>
>>
>> Séb :)
>>
>>
>>
>>
>>
>> Sébastien Morin wrote:
>> Hi Ed,
>>
>> Here is the first part of the split patch as you asked for.
>>
>> This one if for docstrings and comments in files :
>> /branches/consistency_tests_1.2/prompt/consistency_tests.py
>> /branches/consistency_tests_1.2/maths_fns/consistency_tests.py
>> /branches/consistency_tests_1.2/test_suite/consistency_tests.py
>> /branches/consistency_tests_1.2/sample_scripts/consistency_tests.py
>> /branches/consistency_tests_1.2/specific_fns/consistency_tests.py
>>
>> Should the commit log be something like what follows ?
>>
>> "This patch
>> (patch_consistency_tests__l1.2_r3340__docstrings_and_comments)
>> corrects docstrings and comments errors which were remnants of the
>> jw_mapping
>> code from which the consistency_tests code was inspired. Also, this
>> patch
>> adds
>> docstrings and comments to the code for making it easier for users to
>> understand what the code actually does."
>>
>> Cheers
>>
>>
>> Séb :)
>>
>>
>>
>>
>> Selon Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>, 13.07.2007:
>>
>>
>>
>> Hi,
>>
>> This patch will need a few small changes before being committed. The
>> first is the docstring of the set_frq function of
>> 'prompt/consistency_tests.py'. In the user function docstrings, the
>> list of keyword arguments need to be separated by newlines. This is a
>> relax convention as can be seen in the equivalent function of
>> 'prompt/jw_mapping.py'. One problem with this is that the docstring
>> parser used to generate the relax manual might fail in this keyword
>> argument section. An additional formatting convention is the use of
>> two blank lines in front of the section titles in the docstring. This
>> allows easier reading of the much longer docstrings.
>>
>> This isn't important but for the eta value, do you know if this is
>> eta_z or eta_xy? A more important point is that the patch should be
>> split up so that there are different patches for different types of
>> fixes. For example there are docstring and comment changes which
>> could be grouped together into a single patch. Then there are
>> modifications to the test suite for the consistency tests which should
>> be separate. In 'specific_fns/consistency_tests.py' there
>> is a change
>> to the default value of the CSA and a number of other fundamental
>> changes. These should all be separate.
>>
>> It would be a good exercise in preparation for having full commit
>> access to the relax repository to split this patch into a number of
>> small patches. No patch or commit to the relax repository should
>> contain two unrelated changes, even if these are tiny one line
>> changes. For each commit to the repository, a detailed description of
>> the changes should be placed into the commit log (which is
>> automatically emailed to the relax-commits mailing list but remains in
>> the repository and is important for repository maintenance). You can
>> see these messages by typing something like 'svn log -v --limit=100 |
>> less' within your checked out copy. So if you could prepare a similar
>> commit message for the patches, it would be much appreciated.
>>
>> Cheers,
>>
>> Edward
>>
>>
>> P.S. A small fix is needed in 'prompt/consistency_tests.py' at line
>> 4. And as for the self.__relax_help_ string, this isn't actually a
>> docstring but is used by the relax prompt help system. These
>> __init__() functions don't have docstrings, and I don't remember if
>> this was deliberate because of the special help system or not.
>>
>>
>> On 7/13/07, Sébastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
>>
>>
>> Hi,
>>
>> Here is a patch for the consistency tests branch of the 1.2 line
>> (r3340).
>>
>> Some comments and docstrings were added as well as errors corrected from
>>
>> the
>>
>>
>> adaptation of this code from the jw_mapping code...
>>
>> The following file are modified :
>> prompt/consistency_tests.py
>> maths_fns/consistency_tests.py
>> test_suite/consistency_tests.py
>> sample_scripts/consistency_tests.py
>> specific_fns/consistency_tests.py
>>
>> Formating should be OK in these files except maybe for one thing for
>> which
>>
>> I'm
>>
>>
>> not sure. It's between lines 29 and 33 of
>> prompt/consistency_tests.py where
>>
>> I
>>
>>
>> don't know if the docstring should be below the line 'def
>> __init__(self,
>> relax):' or below the line 'self.__relax_help__ = \' as it is now...
>> Note
>>
>> that
>>
>>
>> this is seen in many other code files...
>>
>> Cheers
>>
>>
>> Sébastien :)
>>
>>
>>
>> Selon Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>, 09.07.2007:
>>
>>
>>
>> Hi,
>>
>> Both patches have been applied to the repository. The patch
>> 'patch_sample_scripts_consistency_tests' was committed at
>> r3331.
>> Change from 5000 to 500 simulations is reasonable. The large number
>> of simulations was because the calculation was so quick, but 500
>> should be more than sufficient. The addition of Grace plotting
>> functions to the Reduced Spectral Density Mapping sample script is
>> very useful and I will probably port this commit very soon to the 1.3
>> line. The patch 'patch_sample_scripts_jw_mapping' was
>> applied (at
>> r3332) directly to the 1.2 line rather than the
>> 'consistency_tests_1.2' branch.
>>
>> Cheers,
>>
>> Edward
>>
>>
>> On 7/9/07, Sébastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
>>
>>
>> Hi again !
>>
>> I added lines for plotting using grace in the sample script. Since this
>>
>> sample
>>
>>
>> script was inspired by the jw_mapping sample script, I also submit a
>>
>> patch
>>
>>
>>
>> for
>>
>>
>> this file (adding lines for plotting, changing the number of Monte
>>
>> Carlo
>>
>>
>>
>>
>> simulations from 5000 to 500 and changing the sequence file from
>>
>> noe.500.out to
>>
>>
>> noe.600.out for more consistency)...
>>
>> Ciao !
>>
>>
>> Sébastien :)
>>
>>
>>
>>
>> Selon Sébastien Morin <sebastien.morin.1@xxxxxxxxx>, 09.07.2007:
>>
>>
>>
>> Hi Ed
>>
>> Tell me if this works better. I'm now using the mail server directly
>>
>> from
>>
>>
>>
>> the
>>
>>
>>
>> internet GUI... (not with Thuderbird).
>>
>> If this does not work neither, maybe we could try with the task...
>>
>> Ciao !
>>
>>
>> Sébastien
>>
>>
>> Selon Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>, 09.07.2007:
>>
>>
>>
>> I've tried cutting an pasting the patch but I get the following:
>>
>> edau@klymene:/media/usbdisk/relax/branches/consistency_tests_1.2>
>> patch -p0 < patch
>> patching file prompt/consistency_tests.py
>> Hunk #2 FAILED at 26.
>> Hunk #3 FAILED at 40.
>> Hunk #4 FAILED at 49.
>> Hunk #5 FAILED at 74.
>> 4 out of 5 hunks FAILED -- saving rejects to file
>> prompt/consistency_tests.py.rej
>> edau@klymene:/media/usbdisk/relax/branches/consistency_tests_1.2>
>>
>> I don't know why, but thunderbird is destroying the attachment.
>>
>> The
>>
>>
>>
>>
>>
>>
>> failed 'hunks' are the wrapped lines. Maybe there is a way to
>>
>> prevent
>>
>>
>>
>>
>>
>>
>> thunderbird from doing this. Otherwise using another email client
>>
>> (or
>>
>>
>>
>>
>>
>>
>> webmail) may work. I could also create a task for this consistency
>> test work and these could be attached to the task. It's best that,
>> for the record, the files are located within the permanent relax
>> infrastructure.
>>
>> Cheers,
>>
>> Edward
>>
>>
>>
>>
>> On 7/9/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
>>
>>
>> Hi again !
>>
>> Here is again the first patch for the file
>>
>> 'prompt/consistency_tests.py'.
>>
>>
>>
>>
>>
>> I modified the header for the copyrights.
>>
>> Also, the former patches were not copied-pasted, but attached
>>
>> using
>>
>>
>>
>>
>>
>>
>>
>> Thunderbird after their creation using a command like 'svn diff >
>>
>> patch'
>>
>>
>>
>>
>>
>> under Linux. When I send those kinds of files as attachment, I
>>
>> usually
>>
>>
>>
>>
>>
>> see them as text in the e-mail, but also as an attachment that
>>
>> can be
>>
>>
>>
>>
>>
>>
>>
>> save. Tell me if it is okay and if it is still a problem, I'll
>>
>> put
>>
>>
>>
>> them
>>
>>
>>
>>
>>
>> on my lab's website...
>>
>> Cheers
>>
>>
>> Séb :)
>>
>>
>>
>> Edward d'Auvergne wrote:
>>
>>
>> Hi,
>>
>> Just add some text such as 'Copyright (C) 2007 Sebastien Morin
>> <sebastien.morin.1 at ulaval.ca>' underneath the already
>>
>> existent
>>
>>
>>
>>
>>
>>
>>
>>
>> copyright text. The can be changed later, for example I can
>>
>> give
>>
>>
>>
>> you
>>
>>
>>
>>
>>
>>
>> a ???@nmr-relax.com email address which is an alias for any
>>
>> other
>>
>>
>>
>>
>>
>>
>>
>>
>> email address (once voted in as a relax developer). Could you
>>
>> add
>>
>>
>>
>>
>>
>>
>>
>>
>> this and then resend the patches? Ta. If they are attached
>>
>> rather
>>
>>
>>
>>
>>
>>
>>
>>
>> than cut and paste that would be much easier for applying the
>>
>> patches
>>
>>
>>
>>
>>
>>
>> (as email wraps lines). Also, maybe responding to your
>>
>> original
>>
>>
>>
>> posts
>>
>>
>>
>>
>>
>>
>> will allow the patches to be more easily tracked in the mailing
>>
>> list
>>
>>
>>
>>
>>
>>
>> https://mail.gna.org/public/relax-devel/.
>>
>> Cheers,
>>
>> Edward
>>
>>
>> On 7/9/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
>>
>>
>> Hi !
>>
>> I'm about to create the patches to merge the consistency tests
>>
>> code
>>
>>
>>
>> into
>>
>>
>>
>>
>>
>> the 1.2 branch.
>>
>> However, I have one question. How do I treat the copyrights ?
>>
>> Do I
>>
>>
>>
>>
>>
>> leave
>>
>>
>>
>>
>>
>> the original author from which I copied the code and then
>>
>> modified
>>
>>
>>
>> it
>>
>>
>>
>> or
>>
>>
>>
>>
>>
>> do I had my name to the code headers..?
>>
>> Thanks !
>>
>>
>> Sébastien :)
>>
>>
>>
>>
>> Edward d'Auvergne wrote:
>>
>>
>> Oh, I've committed your patch at
>>
>>
>>
http://maple.rsvs.ulaval.ca/mediawiki/index.php/Patch_consistency_tests_2007-06-26
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> as revision r3324, applying it to the 1.2 branch. I've
>>
>> carefully
>>
>>
>>
>>
>>
>>
>>
>>
>> checked the code and none of the changes are detrimental or
>>
>> could
>>
>>
>>
>>
>>
>>
>>
>>
>> affect the stability of the stable 1.2 relax codebase. Note
>>
>> however
>>
>>
>>
>>
>>
>>
>>
>>
>> that the code in the branch will not run as the
>>
>> consistency_test.py
>>
>>
>>
>>
>>
>>
>>
>>
>> files are still identical copies of the jw_mapping.py files.
>>
>> Cheers,
>>
>> Edward
>>
>>
>> On 7/9/07, Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>
>>
>> wrote:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Hi,
>>
>> I've now created two branches within the relax repository
>>
>> for
>>
>>
>>
>> you
>>
>>
>>
>> to
>>
>>
>>
>>
>>
>>
>>
>> play with. The first is a copy of the 1.2 line and is
>>
>> located
>>
>>
>>
>> at
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> svn.gna.org/svn/relax/branches/consistency_tests_1.2/. The
>>
>> second
>>
>>
>>
>> is
>>
>>
>>
>>
>>
>>
>>
>> a copy of the 1.3 line and is located at
>> svn.gna.org/svn/relax/branches/consistency_tests_1.3/.
>>
>> I've
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> initially
>>
>>
>>
>> used 'svn cp' to create the 5 consistency_tests.py files as
>>
>> described
>>
>>
>>
>>
>>
>>
>>
>> in
>>
>> https://mail.gna.org/public/relax-devel/2007-07/msg00001.html
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> (Message-id:
>>
>>
>> <7f080ed10707090251ve1c4a8fl7f8618843e5c9459@xxxxxxxxxxxxxx>).
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Would you be able to create patches for these files (in
>>
>> the
>>
>>
>>
>> 1.2
>>
>>
>>
>> line
>>
>>
>>
>>
>>
>>
>>
>> first, no need to worry about the 1.3 line yet), and then
>>
>> post
>>
>>
>>
>> the
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> individual patches as text file attachments to the mailing
>>
>> list?
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Thanks. I will then be able to commit these patches
>>
>> individually,
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> checking them in fine detail.
>>
>> Things to note in creating the patches from the code at
>>
>>
>> http://maple.rsvs.ulaval.ca/mediawiki/index.php/Relax_development
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> include the copyright preservation, a number of integers in
>> 'maths_fns/consistency_tests.py' which should be floating
>>
>> point
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> numbers (just add '.0' to the end of the number), the
>>
>> addition
>>
>>
>>
>> of
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Grace plots as an output in the
>>
>> 'sample_scripts/consistency_tests.py'
>>
>>
>>
>>
>>
>>
>>
>> script to be able to create a picture similar to that on
>>
>> your
>>
>>
>>
>> relax
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> development site, maybe only allowing 'Tc' and 'tc' in the
>> return_data_name() function and not 'TC', and 'degrees'
>>
>> instead
>>
>>
>>
>> of
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> 'degree' in the return_units() function.
>>
>> One bug includes:
>>
>> setattr(self.relax.data.res[self.run][index],
>>
>> 'csa',
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> float(value[0]))
>> setattr(self.relax.data.res[self.run][index],
>>
>> 'r',
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> float(value[1]))
>> + setattr(self.relax.data.res[self.run][index],
>> 'orientation', float(value[1]))
>> + setattr(self.relax.data.res[self.run][index],
>>
>> 'tc',
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> float(value[1]))
>>
>> value[1] has been used twice. I have a feeling there is
>>
>> another
>>
>>
>>
>> bug
>>
>>
>>
>>
>>
>>
>>
>> somewhere where an index has been repeated a few times when
>>
>> it
>>
>>
>>
>>
>>
>> should
>>
>>
>>
>>
>>
>>
>>
>> be different indices, but I can't find it at the moment.
>>
>> The
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> individual patches should help. Finally, I have a feeling
>>
>> that
>>
>>
>>
>>
>>
>> there
>>
>>
>>
>>
>>
>>
>>
>> is unused code which can be deleted as it is a relic from
>>
>> the
>>
>>
>>
>> copy
>>
>>
>>
>> of
>>
>>
>>
>>
>>
>>
>>
>> the J(w) mapping code and is not needed. For the 1.3 line
>>
>> code
>>
>>
>>
>> I
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> would recommend that identical functions are shifted into
>>
>> files
>>
>>
>>
>>
>>
>> such
>>
>>
>>
>>
>>
>>
>>
>> as 'specific_fns/base_class.py', but for the 1.2 line code
>>
>> I
>>
>>
>>
>> would
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> prefer the duplication as this means that the current
>>
>> stable
>>
>>
>>
>> code
>>
>>
>>
>>
>>
>>
>>
>> base
>>
>>
>>
>> remains stable.
>>
>> Cheers,
>>
>> Edward
>>
>>
>>
>> On 6/26/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx>
>>
>> wrote:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Hi,
>>
>> I started working on implementing the consistency tests
>>
>> last
>>
>>
>>
>> week
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> before
>>
>>
>> the last post was made and, hence, I worked on repository
>>
>> line
>>
>>
>>
>> 1.2
>>
>>
>>
>>
>>
>>
>>
>>
>> (revision 3303).
>>
>> I implemented the consistency tests as a new type of run
>>
>> ('ct')
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> similar
>>
>>
>> to the one for Jw mapping.
>>
>> The calculations are made for J(0), F_eta and F_R2
>>
>> separately
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> for each
>>
>>
>>
>>
>> magnetic field (one at a time). The output results file
>>
>> is
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> similar to
>>
>>
>>
>>
>> the one for Jw mapping. The user then needs to plot them
>>
>> and
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> look for
>>
>>
>>
>>
>> consistency with its own criteria (calculation
>>
>> correlation
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> coefficients, mean ratios and standard deviations, etc).
>>
>> Please look at the followinr URL for a listing of the
>>
>> modifications to
>>
>>
>>
>>
>> old files and also necessary new files.
>>
>>
>>
>> http://maple.rsvs.ulaval.ca/mediawiki/index.php/Relax_development
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> The file 'sample_scripts/consistency_tests.py' should be
>>
>> useful
>>
>>
>>
>> to
>>
>>
>>
>>
>>
>>
>>
>>
>> understand how the new procedure works.
>>
>> Even if this was done on repository line 1.2, I think it
>>
>> is
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> quite fine
>>
>>
>>
>>
>> since nothing was deleted but only things added (maybe
>>
>> too
>>
>>
>>
>> much,
>>
>>
>>
>>
>>
>>
>>
>> as I
>>
>>
>>
>>
>> reproduced the Jw mapping approach, maybe too much as I
>>
>> added
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> lines in
>>
>>
>>
>>
>> the codes for grace, molmol, etc, maybe too much also
>>
>> since
>>
>>
>>
>> some
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> code is
>>
>>
>> duplicated from the Jw mapping code). The test-suite
>>
>> still
>>
>>
>>
>> works
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> perfectly and, so, I think it could be fine to add the
>>
>> tests
>>
>>
>>
>> to
>>
>>
>>
>> the
>>
>>
>>
>>
>>
>>
>>
>> 1.2
>>
>>
>> line as well... However, if necessary, I could implement
>>
>> the
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> consistency
>>
>>
>> testing procedure on line 1.3, following your comments as
>>
>> I
>>
>>
>>
>> am
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> quite new
>>
>>
>> to Python and maybe made things somehow not perfectly...
>>
>> Please tell me what you think about this.
>>
>> Cheers,
>>
>>
>> Sébastien :)
>>
>>
>>
>> Edward d'Auvergne wrote:
>>
>>
>> Hi,
>>
>> I have previously talked about data set consistency.
>>
>> For
>>
>>
>>
>>
>>
>> example
>>
>>
>>
>>
>>
>>
>>
>> see
>>
>>
>>
>> the post at
>>
>> https://mail.gna.org/public/relax-users/2007-06/msg00001.html
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> in which a few reasons for inconsistencies have been
>>
>> explained. I
>>
>>
>>
>>
>>
>> have, from experience, noticed that small changes in
>>
>> protein
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> concentration can change the collected relaxation rates
>>
>> significantly
>>
>>
>>
>> - most likely because of packing interactions. All
>>
>> samples
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> should
>>
>>
>>
>>
>>
>> essentially be identical in all respects for the
>>
>> relaxation
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> rates to
>>
>>
>>
>>
>>
>> be compared. And the temperate should always be fine
>>
>> tuned
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> between
>>
>>
>>
>>
>>
>> experiments and spectrometers using methanol (and
>>
>> always
>>
>>
>>
>>
>>
>> checked
>>
>>
>>
>>
>>
>>
>>
>> later
>>
>>
>>
>> on if there is a large time between collecting the same
>>
>> experiment).
>>
>>
>>
>>
>>
>> Therefore these tests would be quite useful. Data
>>
>> consistency
>>
>>
>>
>> is
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> essential for the model-free results to be correct (as
>>
>> well
>>
>>
>>
>> as
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> reduced
>>
>>
>>
>> spectral density mapping, SRLS, etc.) as this affects
>>
>> both
>>
>>
>>
>> the
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> optimisation and model selection and can result in
>>
>> artificial
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> motions
>>
>>
>>
>> appearing. However I don't know how these test would
>>
>> currently fit
>>
>>
>>
>>
>>
>> within relax. Maybe a new type of analysis should be
>>
>> created
>>
>>
>>
>> for
>>
>>
>>
>>
>>
>>
>>
>> this
>>
>>
>>
>> (see the pipe.create() user function in the 1.3 line or
>>
>> the
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> run.create() user function in the 1.2 line). These
>>
>> ideas
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> should all
>>
>>
>>
>>
>>
>> go into the 1.3 line (via a branch) as the 1.2 line is
>>
>> stable
>>
>>
>>
>>
>>
>>
>>
>> and no
>>
>>
>>
>>
>>
>> new major features will be added to this code. What
>>
>> are
>>
>>
>>
>> the
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ideas you
>>
>>
>>
>> have been playing with?
>>
>> Cheers,
>>
>> Edward
>>
>>
>> On 6/15/07, Sebastien Morin
>>
>> <sebastien.morin.1@xxxxxxxxx>
>>
>>
>>
>>
>>
>> wrote:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Hi everyone
>>
>> During the last months, I was astonished to realize
>>
>> that
>>
>>
>>
>> some
>>
>>
>>
>>
>>
>>
>>
>> spin
>>
>>
>>
>>
>>
>>
>> relaxation data I had acquired at different fields
>>
>> were
>>
>>
>>
>> not
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> consistent
>>
>>
>>
>>
>> between each other. The way I realized that was by
>>
>> seeing
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> discrepancy
>>
>>
>>
>>
>> between J(0) values calculated with those different
>>
>> datasets.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> I looked a little bit in the litterature and found
>>
>> some
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> interesting
>>
>>
>>
>>
>>
>>
>> consistency tests in a paper by Fushman (Fushman et
>>
>> al.,
>>
>>
>>
>> JACS,
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> 1998,
>>
>>
>>
>>
>> 120:10947-10952).
>>
>> This paper present 2 consistency tests to compare
>>
>> datasets
>>
>>
>>
>>
>>
>> from
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> different magnetic fields / samples / time / etc.
>>
>> I think it would be interesting to implement those
>>
>> simple
>>
>>
>>
>>
>>
>> tests
>>
>>
>>
>>
>>
>>
>>
>> in relax
>>
>>
>>
>>
>> so the user can, before trying to fit their data, know
>>
>> the
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> quality of
>>
>>
>>
>>
>> those... Regrettably, very few people look at the
>>
>> consistency
>>
>>
>>
>> of
>>
>>
>>
>>
>>
>>
>>
>> their
>>
>>
>>
>>
>> datasets before analysis...
>>
>> The underlying principle is the same as when looking
>>
>> at
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> consistency for
>>
>>
>>
>>
>> J(0). Thus, I think that those two tests and a J(0)
>>
>> test
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> should be
>>
>>
>>
>>
>>
>>
>> implemented altogether...
>>
>> I'll try to work a bit on this. Mimicking the code for
>>
>> ...
>>
>> [Message clipped]
>
--
______________________________________
_______________________________________________
| |
|| Sebastien Morin ||
||| Etudiant au PhD en biochimie |||
|||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne |||||
|||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
||| 1-418-656-2131 #4530 |||
|| ||
|_______________________________________________|
______________________________________