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 > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users 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-users
