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Dear Longfei,
exploding hydrogens are most likely a naming issue: the names of the
hydrogens in the nucleic acid must match exactly the names in the
restraints-files (cif-files). Check if the hydrogens are present there
and if the names match.
However, unless you are working on neutron data or X-ray data at
_REALLY_ high resolution (0.5A, say), there is little point in loading a
PDB file into coot with hydrogens present. You refinement program should
not write them to the PDB-file.
If you are refining with shelxl, you can simply switch off the
displaying of the hydrogens (which is actually the default in coot, as
far as I know) and ignore them floating around: shelxl ignores the
coordinates of AFIX'ed atoms and simply regenerate them based on the
AFIX type.
Regards,
Tim
On 03/27/12 22:29, Longfei Wang wrote:
> Hi there,
>
> I've received a bug report about coot. I think this is a good place to
> report.
> Here is the summary of the problem. If open a molecule and try to build a
> new nucleotide, Coot crashes. This happened for the version of Coot 3936,
> both in Linux and WinCoot. A labmate suspects that there are library issues
> with regards to PDB version between Coot and REFMAC. An additional issue:
> Protein residues with hydrogens present can be real space refined in Coot.
> However, nucleic acid residues with hydrogens present cannot be real space
> refined in Coot. Attempting to do this results in exploding hydrogens.
>
>
> Best
> Longfei
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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