Re: ENC 2009 poster. -- March 23, 2009 - 18:20

Hi,


For the consistency figure, the text (in Latex format) could be as follows:

$J(0)$ consistency test for PSE-4 beta-lactamase $^{15}$N spin 
relaxation data. 50.6 and 60.8 MHz data possess high consistency whereas 
81.0 MHz data possesses lower consistency. Model-free analysis confirms 
this observation for 81.0 MHz data and identifies the $R_2$ data as 
inconsistent.


For the diffusion tensor figure, the text (in Latex format) could be as 
follows:

Representation of the diffusion tensor and of the N-H vectors 
orientations for PSE-4 beta-lactamase.  Parameters for the ellipsoidal 
diffusion tensor are as follows:       
$\mathfrak{D}_{iso}$~=~13.141~($\pm$~0.024)~x~10\expsemor{6}~s\expsemor{-1}, 
     
$\mathfrak{D}_{a}$~=~3.75~($\pm$~0.19)~x~10\expsemor{6}~s\expsemor{-1}, 
     $\mathfrak{D}_{r}$~=~0.080~($\pm$~0.022)~s\expsemor{-1}, 
$\tau_m$~=~12.683~($\pm$~0.024)~ns,
$\mathfrak{D}_{x}$~=~11.59~($\pm$~0.10)~x~10\expsemor{6}~s\expsemor{-1}, 
 
$\mathfrak{D}_{y}$~=~12.19~($\pm$~0.11)~x~10\expsemor{6}~s\expsemor{-1} 
and   
$\mathfrak{D}_{z}$~=~15.64~($\pm$~0.13)~x~10\expsemor{6}~s\expsemor{-1}. 
N-H vectors orientations are shown as surface on artificial vectors of 
length 20~\AA~placed at the center of mass of the protein. Moreover, 
these vectors are duplicated in the opposite direction because of 
symmetry in the ellipsoidal diffusion tensor.


Regards,


Séb


Edward d'Auvergne wrote:
> Cheers.  Also, would you have a few lines describing your figure?  So
> I can answer questions correctly or add it as text into the poster if
> there is room (I've updated the poster with one of your figures, so
> far).
>
> Regards,
>
> Edward
>
>
>
> 2009/3/23 Sébastien Morin <sebastien.morin.1@xxxxxxxxx>:
>   
> > Edward d'Auvergne wrote:
> >     
> > > 2009/3/23 Sébastien Morin <sebastien.morin.1@xxxxxxxxx>:
> > >
> > >       
> > > > Hi Ed,
> > > >
> > > > The poster looks great ! The design is very attractive and the color
> > > > blend
> > > > is also very nice !
> > > >
> > > >         
> > > Thanks.  The butterfly and title should hopefully get people's
> > > attention.  And the pictures of diffusion tensors, etc. is a great
> > > idea that should help.
> > >
> > >
> > >
> > >       
> > > > Here are a few typos I found:
> > > >
> > > > 1. Sub-section "Interfacing with other programs"
> > > >  effectively using these ARE replacement optimisation engines
> > > >     -> effectively using these AS replacement optimisation engines
> > > >
> > > > 2. Section "The power of open source"
> > > >  all RESOURSES
> > > >     -> all RESOURCES
> > > >  will be easily ACCESSABLE
> > > >     -> will be easily ACCESSIBLE
> > > >
> > > > 3, Sub-section "Relaxation data consistency"
> > > >  the consistency of experimentally measured relaxation data
> > > >     -> the consistency of MULTIPLE-FIELD experimentally measured
> > > > relaxation
> > > > data
> > > >
> > > >         
> > > Thanks for picking these up.  It was a rough draft so I hadn't checked
> > > for this yet.  I think I've used the word 'accessible' too much there
> > > actually.
> > >
> > >
> > >
> > >       
> > > > Concerning a potential figure to add for the consistency sub-section, I
> > > > could propose one from the supplementary material of the paper you
> > > > referenced (Morin & Gagné, Biophys J, 2009 ; which should be out soon,
> > > > hopefully). Please find the eps figure as well as the grace file:
> > > >  http://maple.rsvs.ulaval.ca/users/semor/tmp/consistency__J0_semor.eps
> > > >  http://maple.rsvs.ulaval.ca/users/semor/tmp/consistency__J0_semor.agr
> > > >
> > > >         
> > > Right, I'll try to fit this in.  Cheers.
> > >
> > >
> > >
> > >       
> > > > Moreover, I would propose maybe adding a figure for the diffusion tensor
> > > > representation in the "Data visualisation" sub-section. I could propose
> > > > another figure from the supplementary material of Morin & Gagné (Biophys
> > > > J,
> > > > 2009) which shows the diffusion tensor and the distribution of the N-H
> > > > vectors along the three principal axes of diffusion for PSE-4
> > > > beta-lactamase:
> > > >  http://maple.rsvs.ulaval.ca/users/semor/tmp/PSE-4_tensor_xh.odg
> > > > http://maple.rsvs.ulaval.ca/users/semor/tmp/PSE-4_tensor_xh.eps
> > > > This figure is quite big, but a part of it could show how attractive and
> > > > useful the diffusion tensor representation is !
> > > >
> > > >         
> > > This is also very useful to show capabilities.  How did you remove the
> > > equatorial lines in the diffusion tensors?
> > >
> > >
> > >       
> > The equatorial lines were removed manually within Pymol. For each line, I
> > seleted the atoms connected using Ctrl and the center button on the mouse.
> > Then, once the two atoms were selected, I removed the line using Ctrl-d.
> > Note that you can then save the molecule to a new pdb file for further use.
> > Moreover, if, by accident, you remove a needed line, you can re-introduce it
> > using Ctrl-t.
> >
> > Cheers,
> >
> >
> > Séb  :)
> >
> >     
> > > Cheers,
> > >
> > > Edward
> > >
> > >
> > >       
> > --
> > Sébastien Morin
> > PhD Student
> > S. Gagné NMR Laboratory
> > Université Laval & PROTEO
> > Québec, Canada
> >
> >
> >     
>
>   


--
Sébastien Morin
PhD Student
S. Gagné NMR Laboratory
Université Laval & PROTEO
Québec, Canada