Hi Ed, This is exactly what I was thinking.
Thanks for translating my idea into something which can be implemented into relax..! Séb Edward d'Auvergne wrote: > Hi, > > This proposal could be quite useful, and simple to implement in the > full_analysis.py script. I could add a variable called something like > EXCLUDE which points to another file. This would then be used with > the spin system deselection user function (unselect.read() in the 1.2 > line and deselect.read() in the 1.3 line). These would then not only > be excluded in the multi_model() method of the script, but also in the > 'init' round of optimisation to cover all places in the script. Then > you could take any relax model-free results file as the input, and the > spins in EXCLUDE will never be used in the analysis. Is this along > the lines of what you were thinking? The UNRES file would still be > there, but this would serve a different purpose than then EXCLUDE > file. > > Regards, > > Edward > > > > On Tue, May 27, 2008 at 3:55 PM, Sébastien Morin > <[EMAIL PROTECTED]> wrote: > >> Hi, >> >> First, thanks for answering this question. >> >> Here are some precisions... >> >> If one wants to analyze a protein and doesn't know much about the global >> dynamics, the first step will probably be to make a full analysis on all >> of the protein. >> >> Then, if that person thinks an hybrid would be better, tests could be >> made excluding, let's say, the flexible C-terminus. To save time, one >> could take advantage of the already minimized "local_tm" run... Hence, >> this user could just exclude the C-terminus residues with the 'UNRES' >> variable in the different scripts for the other different diffusion >> tensor (but not the "local_tm" which is already available, even though >> for more residues). >> >> So, my question was about knowing if initializing a diffusion tensor >> with more residues would be bad. You answered yes, i.e. that one should >> initialize diffusion tensors using only the wanted residues. >> >> So, would it be a good idea to add a variable in the full_analysis >> script so a different 'UNRES' variable can be used for "local_tm" and >> other diffusion tensors..? If a different 'UNRES' variable would be >> used, the "init" run could only use the selected residues and exclude >> others, even if they are present in the "local_tm" run... This would >> allow one to skip the "local_tm" run when trying some hybrids... This >> would save lots of time... >> >> What do you think of this proposal ? Is this useful ? Is this feasible ? >> >> Thanks ! >> >> >> Séb >> >> >> >> >> Edward d'Auvergne wrote: >> >>> On Sun, May 11, 2008 at 10:33 PM, Sébastien Morin >>> <[EMAIL PROTECTED]> wrote: >>> >>> >>>> Hi, >>>> >>>> When using the full_analysis.py script, unselecting residues is possible >>>> by inputing a list of residues under the variable name UNRES. >>>> >>>> Two approaches are possible. >>>> >>>> 1. >>>> Excluding residues a priori. >>>> >>>> 2. >>>> Excluding residues after an initial test where at least the local_tm run >>>> as been completed. Let's say, for example, that one wants to produce an >>>> hybrid after an initial test with all residues fitted together. >>>> >>>> >>> Both are fine because the local tm models are completely independent >>> of each other. >>> >>> >>> >>> >>>> In situation 2, one may want to re-use the local_tm run and exclude >>>> residues from there on (to save time). This works fine for subsequent >>>> rounds for diffusion tensors sphere, prolate, oblate and ellipsoid. >>>> >>>> However, the "init" round (before round 1) still includes the residues >>>> to be excluded, since those were present in the local_tm run. >>>> >>>> Is this a problem ? Will this presence of subsequently excluded residues >>>> bias the diffusion tensor and avoid the user from finding the global >>>> minimum ? >>>> >>>> >>> This is a problem as the initial diffusion tensor optimisation should >>> only include spins located within this isolated diffusion unit. >>> >>> >>> >>> >>>> Should excluded residues be excluded from ALL the runs, including the >>>> local_tm run (which serves for creating the "init" round of other runs) ? >>>> >>>> >>> Well, that depends on why you are excluding them. If the relaxation >>> data is rubbish, then these should be excluded everywhere. This is >>> the case with the spin list in UNRES, and this will be propagated in >>> full_analysis.py into the 'init' round of optimisation because of the >>> loading of the local tm results file. For a hybrid model, this needs >>> to be constructed differently. If you place the spins to exclude into >>> the UNRES file, then these will be excluded in all parts of the >>> full_analysis.py script. >>> >>> I hope this helps. >>> >>> Regards, >>> >>> Edward >>> >>> >>> >> > > >
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