Hi Paul and fellow cooters,
My enthusiasm was high yesterday, I downloaded
coot-0.4-pre-1-revision-355 but found the following...
Paul Emsley wrote:
>>* I think the anisotropic U's are not read or converted correctly from
>>my shelx .res files... All atoms have B=10.0 ([ResidueInfo] and
>>[GoToAtom])
>
>
> This bug is now fixed as of revision 332. It will be available in 0.4
> SHELX molecules (from .res) now have B factors that correspond to the
> SHELX pdb file.
>
>
>>and even though ellipsoids are drawn when [Show Anisotropic
>>Atoms] are on they are different from the ellipsoids from the
>>corresponding .pdb file (written by Shelxl with WPDB 2 flag)... Am I
>>doing something wrong here?
>
>
> Fixed.
>
This seems only to be a partial fix as it appears ok for an othorhombic
crystal system, but there are still significant differences when looking
at a triclinic system.
I guess it comes down to the definitions relative to crystal axes vs.
orthogonal axes or... ? (See cut&paste below)
Another point, though related: U12 and U23 are switched (i.e. following
the pdb convention) when I save coordinates as an .ins file (or choose
SHELXL refine in the Extensions menu).
Cheers,
Annette
This a cut&paste from Thomas Schneiders SHELX FAQ:
" Q72: Some of the Uij's in the .res file and in the .pdb file match,
although they are in different order, others are completely different.
Is this a bug or a feature ?
It is a feature. The order in the .res file is: 11 22 33 23 13 12 (see
SHELXL-manual). The order in the .pdb file is: 11 22 33 12 13 23 (pdb
convention). The differences in the numbers arise from the Uij's in the
.res file being relative to the crystal axes and the values in the .pdb
file being relative to orthogonal axes and multiplied by 10000."
>
>>I can use the .pdb files and shelxpro-update to generate .ins files but
>>another perhaps related problem is that:
>>* The [B factor variance graphs] from [Validate] are all red and out of
>>scale with values of a few thousands when reading coordinates from .res
>>file (both after isotropic and anisotropic refinement).
>
>
> As a consequence of above fixes, this works now.
>
> Thanks,
>
> Paul.
>
--
______________________________________
Annette Langkilde, ph.d. student
Biophysical Chemistry Group
Department of Chemistry
University of Copenhagen
Universitetsparken 5
DK-2100 Copenhagen
Denmark
e-mail: [log in to unmask]
phone: +45 35 320283
fax: +45 35 320322
______________________________________
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