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
Re: Unselecting residues in full_analysis.py