Hello Crystal.
Crystal Chuang wrote:
> Hello all,
>
> I've been having a problem adding terminal residues and regularizing zones.
> I have an existing chain of residues that I wish to link with another chain
> of residues. Usually, I could renumber residues so that they are consecutive
> and link into one long chain. However, in some areas, even after
> renumbering for instance, renumbering residue 230 to 101 so that it can link
> up with residue 100, an incorrect bond forms between 100 and the new 101.
> Trying to do Regularize Zone has no effect though it causes other residues
> in the background to flicker. I've checked to see that there are no other
> existing residues with the same number. Trying to delete 101 and adding a
> terminal reside to 100, also does not allow me regularize zone between those
> two residues.
>
This sounds familiar. Older versions of Coot got into a tangle when
renumber in residues and in fact added them rather than inserted them -
which mean that residues appear out of order in the actual pdb file
(inserted residues appear at the end of the chain). This leads to
errors such as you describe with residue selection.
My advice is to make sure you are using an up to date Coot and check
that the residues are in order in a pdb file (if they are not you will
have to fix them by hand in a editor - don't worry about getting
the atom numbers correct).
> Also, when I reverse direction of a chain, if I use Reverse Direction
> followed by Ca Zone-> Mainchain, a few CAs will remain without a chain. If
> I delete the preexisting residues and try to Rotate/Translate them myself
> they are automatically reversed back to their original direction once I try
> to Regularize Zone. Is there a reason for this or a way to overwrite or go
> around this?
>
That sounds like a bug. I will see if I can reproduce it.
Perhaps a work-around is to save the coordinates as a pdb file after a
Reverse direction and then read them in again. Coot will create a new
molecule for the CAs and won't reverse the direction. You need to make
sure that you don't click on the wrong molecule when you do that.
Paul.
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