I agree with wtempel
Once a residue is split it means there is evidence for 2 conformations.
If one atom in one conformation has occupancy reset to 0.00, that
certainly does not imply that the other NZ A say should have occupancy 1.00
It wont the refinement in REFMAC anyway
Eleanor
Paul Emsley wrote:
wtempel wrote:
Hi all,
judging from what I see being used by my colleagues, COOT is well on
its way to world domination.
Like Linux (haha).
Anyway, suppose I have "split" a residue, say lysyl, to model
alternate conformations of its side chain. Suppose further that I
would like to remove NZ from conformer B. Upon doing so, the current
COOT implementation will remove the atom. Good. It will also remove
the confID from what was conformer A's NZ atom and re-set its
occupancy to 1. On the latter part, intuition tells me that instead,
conformer A's atoms should be unaffected, namely keep their confID and
sub-unity occupancy.
My questions:
1) What behavior is expected by other COOT users in comparable
situations?
Would the answer be different if a C or an O had been deleted? I'd
rather ask: is Coot doing the right thing in such a case? I suspect
that Garib or Pavel may know.
2) Should a few folks align themselves with my opinion, can COOT's
behavior be modified without unintended side effects?
Yes.
Specifically, I like COOT's current behavior when "Delete Residue" is
applied to alternative conformations: Delete the conformer completely
and set the remaining conformer's atoms to Occ=1 and remove the confID.
I think that that is just doing the above for many atoms.
Paul.
