Hi, I just added one myself as I think it will be useful elsewhere (http://article.gmane.org/gmane.science.nmr.relax.scm/22538). This is the verbose version I described at http://thread.gmane.org/gmane.science.nmr.relax.scm/22522/focus=6534. I know this formatting is already somewhere else in relax, but I can't find it. Having a collection of different formatting functions would be good for consistency.
Cheers, Edward On 29 July 2014 09:55, Troels Emtekær Linnet <[email protected]> wrote: > 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
