Dear Andreas,
did you try the option '-t' to make SHELXE try harder, or other building
related options (take a look at the SHELX web page for talks and
presentations).
Can you make use of the phases without model building? (sfall)
Since you seem to get a PDB-file, could you use the coordinates to calculate
the phases off it? You can also provide the PDB-file as input file and restart
phasing.
Best,
Tim
On Monday, July 10, 2017 5:51:57 PM CEST Andreas Förster wrote:
> Dear all,
>
> since SHELX is now part of CCP4, this question is not entirely off-topic.
>
> I'm trying to solve structures by S-SAD. Substructure looks weak but ok if
> the right resolution cutoff is picked in SHELXD.
>
> SHELXE is happy to do its thing for a while but then gives up with a
> "Peptide occupancy has refined to negative value" error in one hand. The
> other hand is quite obviously (CC for partial structure, number of residues
> built) wrong, but the PDB obtained with the antimatter peptides looks like
> protein, is 80% complete and quite obviously the right solution.
>
> Because of the error, SHELXE doesn't write phases. How do I get these? (I
> could do MR, but there must be a more elegant way...) Better yet, what
> might cause the "negative occupancy" error and how do I avoid it?
>
> Thanks and all best.
>
>
> Andreas
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