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.
My problem is that I agree with the original poster that the remaining
NZ atom should continue with a confID of A, but I also agree with Paul
that the deleted C atom should be changed to a single conformation.
However, if the residue that the C atom is linked to is also split
I would feel differently. In my favorite structure there is a stretch
of five residues where the main chain has two conformation. If I deleted
a C atom from the B conformer in the middle it would not be my intention
to have only a single conformation for that atom.
How about this suggestion? If the deleted atom is bonded to an atom
with a single conformation then the other conformer becomes a single
conformation. If the deleted atom makes bonds only with atoms that
also have alternative conformations then the remaining atom retains
its partial occupancy. This would keep the poster happy, keep Paul
happy with his C atom when the neighbor has a single conformation,
and will keep me happy when there is a stretch of main chain disorder.
A problem with this scheme occurs with the lysine mentioned before.
If the user decides to delete the entire B conformation one atom at a
time the result will differ depending on the end of the side chain
they start deleting atoms from. I don't know if this is a serious
problem, or even a problem at all.
Dale Tronrud
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.
