Re: r24772 - /branches/r1rho_plotting/specific_analyses/relax_disp/data.py -- July 28, 2014

Another way to think of this is to consider an imaginary system consisting of:

- A DNA molecule of 10 bases, where 15N and 13C data has been
collected for all bases, and 13C data collected for the ribose.
- A promoter protein, which is a dimer, attached to the DNA.  Here you
have collected backbone 15N data and sidechain methyl 13C data.
- A drug binding between the two proteins.  Here you have collected
natural abundance 13C dispersion data.

In relax you can currently analyse this all together.  You can cluster
spins in the drug with spins in the protein (and also the DNA if you
wish).  The infrastructure already exists for this in the dispersion
analysis.  If you keep such 'exotic' systems in mind while designing,
as well as keeping in mind that all parts will be independent of R1rho
vs. CPMG, then the resultant code will be just as flexible as the rest
of the dispersion analysis.

Cheers,

Edward

On 28 July 2014 12:17, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:

Hi Troels,

I have a problem with this title as it is far too protein-centric.  I
know you are using the residue name here because the spin ID does not
contain that information.  But you need to consider that this analysis
will be applied to different systems, for example things that might
look like this ensemble:
http://www.nmr-relax.com/manual/phthalic_acid_ens_600x600.png.  In
these cases the residue name will be None.  In other cases the residue
number will be None but a residue name will exist and will be in the
spin ID string.

Therefore I would suggest creating a special function in
pipe_control.mol_res_spin that will create a nicely formatted string
of the molecule name, residue name and number, and spin name and
number.  This would need to be flexible in that any of these 5
elements can be None and hence should not be included.  You pass in
the mol_name, res_name, res_num, spin.name, and spin.num values and it
returns a formatted string.  One needs to always keep in mind that all
analyses in relax can be applied to proteins, RNA/DNA,
polysaccharides, and small organic molecules.  Flexibility is one of
relax's strong points.

Cheers,

Edward





On 26 July 2014 13:34,  <tlinnet@xxxxxxxxxxxxx> wrote:

Author: tlinnet
Date: Sat Jul 26 13:34:09 2014
New Revision: 24772

URL: http://svn.gna.org/viewcvs/relax?rev=24772&view=rev
Log:
Added the spin specific residue name and spin_id to the title of the 
dispersion plots.

This is handy, since it is often of interest to have this information at 
hand, when looking through many graphs.

sr #3124(https://gna.org/support/?3124): Grace graphs production for R1rho 
analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through 
spin-lock offset [Omega], rather than spin-lock field strength [w1].

Modified:
    branches/r1rho_plotting/specific_analyses/relax_disp/data.py

Modified: branches/r1rho_plotting/specific_analyses/relax_disp/data.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/r1rho_plotting/specific_analyses/relax_disp/data.py?rev=24772&r1=24771&r2=24772&view=diff
==============================================================================
--- branches/r1rho_plotting/specific_analyses/relax_disp/data.py        
(original)
+++ branches/r1rho_plotting/specific_analyses/relax_disp/data.py        
Sat Jul 26 13:34:09 2014
@@ -1607,7 +1607,7 @@

     # Loop over each spin. Initialise spin counter.
     si = 0
-    for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
+    for spin, mol_name, res_num, res_name, spin_id in 
spin_loop(full_info=True, return_id=True, skip_desel=True):
         # Skip protons for MMQ data.
         if spin.model in MODEL_LIST_MMQ and spin.isotope == '1H':
             continue
@@ -1681,7 +1681,7 @@
                             data[i][j][k][l] = 0.0

         # Write the header.
-        title = "Relaxation dispersion plot"
+        title = "Relaxation dispersion plot for:    %s %s"%(res_name, 
spin_id)
         graph_num = len(data)
         sets = []
         legend = []
@@ -1725,7 +1725,7 @@

     # Loop over each spin. Initialise spin counter.
     si = 0
-    for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
+    for spin, mol_name, res_num, res_name, spin_id in 
spin_loop(full_info=True, return_id=True, skip_desel=True):
         # Skip protons for MMQ data.
         if spin.model in MODEL_LIST_MMQ and spin.isotope == '1H':
             continue
@@ -1808,7 +1808,7 @@
                             data[i][j][k][l] = 0.0

         # Write the header.
-        title = "Relaxation dispersion plot"
+        title = "Relaxation dispersion plot for:    %s %s"%(res_name, 
spin_id)
         subtitle = "Interpolated through Spin-lock field strength 
\\xw\\B\\s1\\N"
         graph_num = len(data)
         sets = []


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Re: r24772 - /branches/r1rho_plotting/specific_analyses/relax_disp/data.py

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