Lionel Colliandre wrote:
> Hi,
>
> I have some problems and I would like to know if there are solutions for
> these. (I use the coot version coot-0.3.3)
>
> 1- I have some residues with alternates conformation of the sidechain, and
> for each atoms with alternates conformations, the sums of the occupations is
> not equal to 1. The problem is that (with the « Real Space refine Zone »
> tool of Coot) Coot change the occupations of the alternate atoms to put the
> sum at 1. (example CB APHE 0.5 and CB BPHE 0.2; after optimization by coot
> CB APHE 0.5 and CB BPHE 0.5)
>
I am surprised by this and cannot reproduce this bug. If you could send
me a pdb file fragment (a few residues and a recipe) that shows this
problem I will try to follow this up further.
> 2- For atoms with a name of 4 Letters (HD11), coot read only 3 letters. The
> consequences are:
> --- coot can't optimize these atoms
> --- coot save the structure with the 3 letters definiton and so create
> duplicate atoms (example: atoms HD11, HD12 and HD13 at the beginning; 3
> atoms HD1 after that coot saved the structure; so refmac can't read this file).
>
>
It seem that you are using PDBv3 (which Coot does not yet support) or
non-conformant hydrogen names (which Coot also does not support).
Please use v2.3 hydrogen names for now.
Paul.
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