Re: Unselecting residues in full_analysis.py -- May 27, 2008 - 15:55

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
> <sebastien.morin.1@xxxxxxxxx> 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
>
>