(and text comments) where a numerical value should be
used.
Cheers
Séb :)
gary thompson wrote:
On 7/22/07, Sébastien Morin
<sebastien.morin.1@xxxxxxxxx>
wrote:
Hi,
I've add the relax-devel mailing list on this talk since most of the
subject is
now related to relax design...
I've tried to solve this issue both in the 1.2 and 1.3 lines.
For the 1.2 line :
It seems we can modify the code by changing every appearance of CSA
with a -170
ppm value to a -172 ppm value.
Dear Seb and All
shouldn't there be a central constant for the default CSA (if there is
please ignore this comment)? and shouldn't it be settable so that we
can validate both the old setup and the new one and also calculate
results with a particular CSA value overall for comparison against
older papers etc...
as an aside the presence of raw numbers in program files rather than
named constants is always bad, especially if the raw constant appears
in multiple places
regards
gary
However, this breaks
the test-suite. In fact,
the jw_mapping test breaks with this change but not the model-free test
(the
change in parameters must be too small to be detected by the
test-suite. Thus,
the test-suite values must be changed to account for the switch in CSA
value.
In the patch below, I only corrected the broken test (jw_mapping) but
not the
model-free test which is also affected (even if we don't see it). If
these
changes are right for solving this issue, the patch
'patch__default_csa__l1.2_r3351' (see below for the commit log) should
be used.
The patch 'patch__default_csa__l1.2_r3351' makes uniform the use of the
CSA
value (now -172 ppm everywhere) and fixes the test-suite (in
jw_mapping) to
account for this change.
For the 1.3 line :
I've added two constants (N15_CSA and NH_BOND_LENGTH) in the
'physical_constants.py' file. Then, I'v imported these constants in the
files
'test_suite/system_tests/jw_mapping.py',
'test_suite/system_tests/model_free.py' and
'specific_fns/jw_mapping.py'. I've
also modified some comments so the -172 ppm value for CSA is now the
default.
Finally, as the results from calculations using the CSA value will be
changed,
I've also modified the test-suite for jw_mapping, but left unchanged
other
parts of the test-suite as the changes in CSA value may not affect
these (see
above the discussion for the 1.2 line). If these changes are right, the
patch
'patch__default_csa_r__l1.3_r3351' should be used along with its commit
log
(see below).
The patch 'patch__default_csa_r__l1.3_r3351' makes uniform the use of
the CSA
value (now -172 ppm everywhere) and fixes the test-suite (in
jw_mapping) to
account for this change. It also adds two constants for the CSA and NH
bond
length default values.
Cheers
Séb :)
Selon Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>,
22.07.2007:
> Hi,
>
> I've had a look at both the 1.2 and 1.3 relax lines and have
noticed
> that the sample scripts all use the value of -172 ppm whereas
> everywhere in the relax code base the value of -170 ppm is used as
the
> default. Although the change won't make much of a difference in
the
> final results, for consistency within relax we could have
everything
> changed to -172 ppm. It's up to the authors to report the CSA
value
> they have used in their manuscripts (something which should be
> considered essential for comparison).
>
> The idea of defining the CSA and bond length in a separate file in
the
> 1.3 line is good. There is the file 'physical_constants.py' in the
> base directory just for this and you just import the constants you
> need. They may need distinctive names though (like CSA_VAL,
> BOND_LENGTH, etc.) to avoid problems with the user supplied values
in
> the code.
>
> Cheers,
>
> Edward
>
>
> On 7/19/07, Sebastien Morin <
sebastien.morin.1@xxxxxxxxx> wrote:
> >
> > Hi,
> >
> > I agree with you, Alex. You're right, this small difference
of 2 ppm for
> > the CSA is quite small compared to the real deviation observed
> > experimentally...
> >
> > However, since few people actually measure the 'real' csa, I
think that
> the
> > best available approximation should be the default and that
relax should
> > promote a consistent use, for better comparison between
published
> studies...
> >
> > Also, I think that these default values (for csa and r, for
example)
> should
> > be the same throughout all the relax program, for more
consistency...
> Maybe,
> > in the 1.3 line, these default values should be in a common
file so that
> the
> > jw_mapping and consistency_tests codes (and others if so)
could use the
> same
> > default values. (Maybe this has been discussed before...)
> >
> > Ok.
> >
> > Cheers !
> >
> >
> > Séb :)
> >
> >
> >
> >
> > Alexandar Hansen wrote:
> > I'm not a protein expert, but unless you're at ~GHz fields, a
2 ppm
> > difference in 15N CSA magnitude is going to be
negligible. The error in
> the
> > site-by-site CSA is going to be ~5-10 ppm, if not more,
anyways. The
> > important thing, I imagine, is that you know what the value
you are using
> is
> > and what assumptions are involved (ie. collinearity with NH
bond, symmetric
> > CSA tensor).
> >
> > Alex Hansen
> >
> >
> >
> > On 7/16/07, Sebastien Morin <
sebastien.morin.1@xxxxxxxxx>
wrote:
> > > Hi,
> > >
> > > It's been a long time since we discussed this (the CSA /
bond length
> > > issue in spin relaxation analysis).
> > >
> > > I would agree in using a combination of 1.02 A for bond
length and -172
> > > ppm for CSA (for 15N-1H vectors).
> > >
> > > Should the default values in the relax code be modified,
changing the
> > > CSA from -170 (at least in the jw_mapping code) to -172
ppm ?
> > >
> > > Cheers
> > >
> > >
> > > Séb :)
> > >
> > >
> > >
> > >
> > > Edward d'Auvergne wrote:
> > > > There has been much work describing the importance
of the CSA and the
> > > > bond length. It would be interesting to see how
much of a difference
> > > > measuring the CSA (and the bond length) would make
to the final
> > > > dynamic results. As Sébastien said, the 1.04
Angstrom bond length
> > > > should be used with a lower CSA value. My
preference though would be
> > > > to use -172 ppm together with 1.02 Angstrom.
> > > >
> > > > Edward
> > > >
> > > >
> > > > On 9/30/06, Michael S. Marlow <
marlowms@xxxxxxxxxxxxxxxxxx> wrote:
> > > >> I agree with the value of -170. Here are my
favorite references:
> > > >>
> > > >> Variability of the 15N Chemical Shift
Anisotropy in Escherichia coli
> > > >> Ribonuclease H in Solution
> > > >> Christopher D. Kroenke, Mark Rance, and Arthur
G. Palmer, III
> > > >> J. Am. Chem. Soc.; 1999; 121(43) pp 10119 -
10125
> > > >> "For this data set, the values of are
approximately Gaussian
> > > >> distributed with a
> > > >> mean of -172 ± 13 ppm."
> > > >>
> > > >> Protein Backbone Dynamics and 15N Chemical
Shift Anisotropy from
> > > >> Quantitative
> > > >> Measurement of Relaxation Interference Effects
> > > >> Nico Tjandra, Attila Szabo, and Ad Bax
> > > >> J. Am. Chem. Soc.; 1996; 118(29) pp 6986 - 6991
> > > >> Essentially the same value, but identified
larger outliers
> > > >>
> > > >> Another aspect of this thread which has not
received much attention
> > > >> is the bond
> > > >> length. The refence below suggest 1.04
Angstroms.
> > > >>
> > > >> Determination of Relative N-HN, N-C', C-C', and
C-H Effective Bond
> > > >> Lengths in a
> > > >> Protein by NMR in a Dilute Liquid Crystalline
Phase
> > > >> Marcel Ottiger and Ad Bax
> > > >> J. Am. Chem. Soc.; 1998; 120(47) pp 12334 -
12341
> > > >>
> > > >> Mike
> > > >> --
> > > >> Michael S. Marlow, Ph.D.
> > > >> Department of Biochemistry and Biophysics
> > > >> University of Pennsylvania
> > > >>
> > > >>
> > > >> Quoting Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>:
> > > >>
> > > >> > Salut Séb, welcome to the relax users
mailing list. Thank you for
> > > >> > responding Alex. The CSA value is
important as the example shows.
> > > >> > However I would call this a 'fringe'
example as it represents a
> > highly
> > > >> > restricted nanosecond motion. The
relaxation data for this example
> > > >> > was generated by back calculation using
the CSA value of -160 ppm.
> > > >> > Although as Alex pointed out relax is
capable of optimising the CSA
> > > >> > value, I would be wary of these models as
they are essentially
> > > >> > untested. I've played around with the
models a little and I have a
> > > >> > feeling that the R1, R2, and NOE values
are not sufficient to tease
> > > >> > out the CSA. To test these models using
just the R1, R2, and NOE at
> > > >> > multiple field strengths, the CSA would
need to be accurately
> > measured
> > > >> > using one of David Fushman's techniques
(I'll talk about this next)
> > > >> > and the values compared to those fitted
using the models built into
> > > >> > relax.
> > > >> >
> > > >> > I believe that the value of -160 ppm was
determined by solid state
> > NMR
> > > >> > of small peptides (it's been a few years
since I read the
> litterature
> > > >> > on the CSA value in proteins, so I could
be wrong). However a
> number
> > > >> > of publications have demonstrated that the
average CSA value in
> > > >> > solution is higher. I would say that the
authorative expert in the
> > > >> > field is David Fushman. The JACS
reference you cite is just one of
> > > >> > many of his publications on measuring the
CSA. He has demonstrated,
> > > >> > using I think three different techniques
now, that the CSA in
> > proteins
> > > >> > is highly variable.
> > > >> >
> > > >> > Idealy for highly accurate model-free
analysis, the CSA value should
> > > >> > be determined either prior to or during
model-free analysis using
> one
> > > >> > of his techniques. However most people
appear happy to just set the
> > > >> > CSA value to either the 'ancient' value of
-160 ppm or the solution
> > > >> > average of -170 ppm (David's work
again). Using the data you have
> > > >> > currently collected, I would personally
use the value of -170 ppm.
> > Is
> > > >> > the value of -172 ppm from the Hall and
Fushman paper you cited? I
> > > >> > haven't read that paper yet.
> > > >> >
> > > >> > Edward
> > > >> >
> > > >> >
> > > >> > P.S. I might change the sample scripts to
-170 ppm. I had intended
> > > >> > to change the value a while back but
forgot about it.
> > > >> >
> > > >> >
> > > >> >
> > > >> > On 9/30/06, Sebastien Morin <
sebastien.morin.1@xxxxxxxxx
> wrote:
> > > >> > >
> > > >> > > Hi again
> > > >> > >
> > > >> > > Thanks for your answer !
> > > >> > >
> > > >> > > I think that, for me, the CSA value
would have a significant
> > > >> impact on my
> > > >> > > analysis since my protein has a
tumbling time of about 13 ns and
> > > >> I have
> > > >> > data
> > > >> > > from 500, 600 and 800 MHz...
> > > >> > >
> > > >> > > I don't know if this is relevant,
but I performed simple tests
> > > >> with the
> > > >> > > test data and sample scripts provided
with relax (path :
> > > >> > >
> > 'relax/test_suite/data/model_free/S2_0.970_te_2048_Rex_0.149'
> > > >> > > in version 1.2.7 and the sample
script 'mf_multimodel.py')...
> > > >> > >
> > > >> > > TEST 1
> > > >> > > =====
> > > >> > > r = 1.02
> > > >> > > CSA = -160 ppm
> > > >> > > m4
> > > >> > > S2 = 0.97
> > > >> > > te = 2048
> > > >> > > Rex = 0.149
> > > >> > > X2 = 7.3e-28
> > > >> > >
> > > >> > > TEST 2
> > > >> > > =====
> > > >> > > r = 1.02
> > > >> > > CSA = -172 ppm
> > > >> > > m4
> > > >> > > S2 = 0.97
> > > >> > > te = 82
> > > >> > > Rex = 4.34
> > > >> > > X2 = 2.27
> > > >> > >
> > > >> > > As you can see, for this single
residue (with data at 500 and
> > > >> 600 MHz),
> > > >> > > there is no effect for the value of
S2, but the effect is
> > > >> important for te
> > > >> > > and Rex... And still, the best model
(the lower X2) is m4 for both
> > > >> > > situations...
> > > >> > >
> > > >> > > I think that this ambiguity in the
value for CSA leads to
> > important
> > > >> > > variations in the interpretation of
relaxation data.
> > > >> > >
> > > >> > > Thanks for getting me to understand
more this topic and also
> > > >> choose the
> > > >> > > best value to use...
> > > >> > >
> > > >> > > Séb
> > > >> > >
> > > >> > >
> > > >> > >
> > > >> > >
> > > >> > > Alexandar Hansen wrote:
> > > >> > > Hi Sebastien,
> > > >> > >
> > > >> > > I'm quite new to relax as well, but
I can give you at least a
> > > >> some answer
> > > >> > > to the questions you pose.
> > > >> > >
> > > >> > > In general, the CSA mechanism is a
little underappreciated. At
> > low
> > > >> > enough
> > > >> > > field strengths for 15N relaxation
(400-500MHz), the 15N CSA
> > > >> accounts for
> > > >> > > somewhere between 10-20% of your R1
and R2 rates. Varying the CSA
> > > >> > magnitude
> > > >> > > between 160 and 172 only changes this
by 2-3%. So, if relaxation
> > > >> rates
> > > >> > are
> > > >> > > measured with, let's say, 5% error,
there's no statistical reason
> > > >> to vary
> > > >> > > the CSA. As we go to higher fields
(800MHz), the CSA can account
> > > >> for
> > > >> > 50-60%
> > > >> > > of the R1 and R2 rates and varying
the CSA between 160 and 172
> > > >> can affect
> > > >> > > those rates by up to 10%. So, now
people are finding that this
> > > >> thing
> > > >> > called
> > > >> > > CSA is relatively improtant and
should be better understood.
> > > >> > >
> > > >> > > In many analysis techniques, such as
relax, you have the option
> of
> > > >> > letting
> > > >> > > the CSA vary. For relax, I believe
that's models m10-m19 and
> > > >> tm10-tm19.
> > > >> > > One word of warning though, I
wouldn't encourage fitting the CSA
> > > >> unless
> > > >> > you
> > > >> > > have data at multiple field strengths
as you're adding another
> > > >> variable to
> > > >> > > the analysis, so the standard 3
measurements at a single field
> > > >> strength
> > > >> > are
> > > >> > > likely not enough to do this. You
also run the risk of
> > > >> overinterpretting
> > > >> > > your data because, in my opinion,
varying the CSA freely in
> > > >> relaxation
> > > >> > > analysis is not unlike simply
throwing in a fudge factor. :-)
> > > >> > >
> > > >> > > As for what is the best value to
use, I can't really help you
> > > >> there.
> > > >> > We'll
> > > >> > > have to wait for some of the protein
people to respond (I know
> > > >> RNA better
> > > >> > > ;-) ). But if you're at low enough
fields or tiny proteins (<2-3
> > > >> ns tau(
> > > >> > m
> > > >> > > )) it shouldn't really matter what
you use.
> > > >> > >
> > > >> > > I hope all of this makes sense and I
haven't said anything
> > > >> blatantly
> > > >> > > incorrect. If I have, hopefully
someone will follow up on both
> > > >> of our
> > > >> > > posts. Thanks, and good luck!
> > > >> > >
> > > >> > > Alex Hansen
> > > >> > >
> > > >> > >
> > > >> > >
> > > >> > >
> > > >> > > Hi
> > > >> > >
> > > >> > > I am new to relax and have a quite
general question about the
> > > >> value used
> > > >> > > for the CSA while studying proteins'
15N-1H vectors with
> model-free
> > > >> > > approach.
> > > >> > >
> > > >> > > In the litterature, we mainly find
two values for the CSA (-160
> > > >> and -172
> > > >> > >
> > > >> > > ppm).
> > > >> > >
> > > >> > > There is, if I understand well, a
link between the bond length
> > > >> and the
> > > >> > > CSA, but everyone seems to agree
about using the same value of
> > > >> 1.02 A
> > > >> > > which should give rise to a mean S2
of 0.85 for secondary
> > > >> structure when
> > > >> > >
> > > >> > > combined to a CSA of -172 ppm.
> > > >> > >
> > > >> > > In the relax sample scripts (as well
as in the Model-free manual),
> > a
> > > >> > > value of -160 ppm is used for CSA.
> > > >> > >
> > > >> > > What is the best value to use and,
most importantly, why ?
> > > >> > >
> > > >> > >
> > > >> > > Also, what about the CSA variability
from one vector to another
> > > >> (JACS,
> > > >> > > 128 (24), 7855 -7870, 2006) ?
> > > >> > >
> > > >> > > Thanks !
> > > >> > >
> > > >> > >
> > > >> > > Sébastien
> > > >> > >
> > > >> > > ________________________________
> > > >> > >
> > > >> > >
_______________________________________________
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http://nmr-relax.com)
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> > > >> > > --
> > > >> > >
> > > >> >
> ______________________________________
> > > >> >
> _______________________________________________
> > > >> > > | |
> > > >> > > || Sebastien Morin ||
> > > >> > > ||| Etudiant au doctorat en
biochimie |||
> > > >> > > |||| Laboratoire de resonance
magnetique nucleaire ||||
> > > >> > > ||||| Dr Stephane Gagne |||||
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> > > | |
> > > || Sebastien Morin ||
> > > ||| Etudiant au PhD en biochimie |||
> > > |||| Laboratoire de resonance magnetique nucleaire ||||
> > > ||||| Dr Stephane Gagne |||||
> > > |||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
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> > || 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 |||
> > || ||
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>
------------------------
Sébastien Morin
Étudiant M.Sc. Biochimie
Laboratoire S. Gagné
3252 Pav. Marchand (Université Laval)
Tél : (418) 656-2131 #4530
Fax : (418) 656-7176
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|| 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 |||
|| ||
|_______________________________________________|
______________________________________
re: CSA & bond length