Hi Edward. I have already implemented this, and have it in my git branch.
I will soon submit it. I am currently not adding strings "Molecule", "residue", "spin", as I think this is superfluous. Best Troels 2014-07-29 9:39 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi Troels, > > For this, I was thinking of adding a simple function to the > pipe_control.mol_res_spin module in the trunk called format_info(). > This would have the arguments: > > def format_info(mol_name=None, res_num=None, res_name=None, > spin_num=None, spin_name=None): > > Let's say that: > > mol_name = 'Ubi' > res_name = 'Ala' > res_num = '10' > spin_num = None > spin_name = 'N' > > Then the returned string could be: > > string = "Molecule Ubi, residue Ala 10, spin N" > > Each part is only added if it is not None. This string could then be > used in the title of your grace plots here: > > "Relaxation dispersion plot for: %s" % string > > To end up with: > > "Relaxation dispersion plot for: Molecule Ubi, residue Ala 10, spin N" > > This will then work for all systems and you won't be restricting these > plot titles to only protein and only backbone data. Do you have ideas > for this? > > Cheers, > > Edward > > > > On 28 July 2014 12:44, Edward d'Auvergne <[email protected]> wrote: >> 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 <[email protected]> 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, <[email protected]> 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 = [] >>>> >>>> >>>> _______________________________________________ >>>> relax (http://www.nmr-relax.com) >>>> >>>> This is the relax-commits mailing list >>>> [email protected] >>>> >>>> To unsubscribe from this list, get a password >>>> reminder, or change your subscription options, >>>> visit the list information page at >>>> https://mail.gna.org/listinfo/relax-commits > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-devel mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
