doebbler wrote:
> Hi,
>
> I am using COOT for my work and I keep running into the same
> problem time and again. At first I thought that it only happened with
> mutate, but now it seems to be happening (sometimes) when I do
> regularize zone as well. I start off with a .pdb file with the atoms
> in order:
> N, CA, C, O, sidechain. Once either mutate or regularize zone is done
> on a subset of side chains the order is changed, for them, to: N, CA,
> sidechain atoms, C, O, the rest of the residues are fine. I know for
> most folks this is not an issue, but I am trying to put my coordinates
> into GSAS and the restraint files expect COOT not to mess with the
> atomic ordering. Why are the atoms reordered like this? If this is a
> feature, what was the impetus behind it?
Dear Jennifer,
You are right to complain that Coot reorders your atoms - the atom
ordering is part of the PDB standard.
This is an oversight of mine and I will add the fix for this to the
specification list for 0.5. I know that mutating can change the atom
order, but are you completely sure that simply regularizing will change
the atom order? (I very rarely use regularize zone in every-day
building. I do use it to check that I haven't damaged anything when I'm
messing with restraints code, but that is not something
crystallographers would be usually doing).
It seems to me that PDBSET would be the program to correct atom
ordering, but I can't see that it does so.
Regards,
Paul.
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