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.
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 ?
Should excluded residues be excluded from ALL the runs, including the
local_tm run (which serves for creating the "init" round of other runs) ?
Thanks for help !
Sébastien :)
Unselecting residues in full_analysis.py