I deleted a line in the keyword file which was "pdbout format mmcif".
It was my first try to convert the pdb file to an mmcif file, but it
did not work!
Best
Marina
Zitat von "Krieger, James M" <krieg...@pitt.edu>:
It could be good to say how you solved it for future users.
Best wishes
James
On Aug 6, 2021, at 09:27, Marina Gárdonyi
<0000652c4b26eb10-dmarc-requ...@jiscmail.ac.uk> wrote:
Hi,
as it is often the case, the mail is out and you are able to solve
the problem on your own. Thanks anyway!
Best
Marina
Zitat von Marina Gárdonyi <0000652c4b26eb10-dmarc-requ...@jiscmail.ac.uk>:
Hi,
before I will soon finish my PhD, I have to solve one more problem.
I managed to refine occupancies and tls in Refmac. I also found
out that you can use pdb-extract to convert the pdb file to an
mmcif file so that you can validate the structure using the
validation server.
However, during validation, it came out that the bond lengths and
angles are hugely different from the expected values. I had used
the automatic weighting until then. If I do the weighting by hand
(I tried different weighting terms), I cannot convert the pdb file
into an mmcif file anymore, because the pdb file has a different
structure and pdb-extract does not recognize the pdb file as such.
Does anyone know the problem and can help me?
Best
Marina
--
Marina Gárdonyi
PhD Student, Research Group Professor Dr. Klebe
Department of Pharmaceutical Chemistry
Philipps-University Marburg
Marbacher Weg 6, 35032 Marburg, Germany
Phone: +49 6421 28 21392
E-Mail: marina....@pharmazie.uni-marburg.de
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--
Marina Gárdonyi
PhD Student, Research Group Professor Dr. Klebe
Department of Pharmaceutical Chemistry
Philipps-University Marburg
Marbacher Weg 6, 35032 Marburg, Germany
Phone: +49 6421 28 21392
E-Mail: marina....@pharmazie.uni-marburg.de
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--
Marina Gárdonyi
PhD Student, Research Group Professor Dr. Klebe
Department of Pharmaceutical Chemistry
Philipps-University Marburg
Marbacher Weg 6, 35032 Marburg, Germany
Phone: +49 6421 28 21392
E-Mail: marina....@pharmazie.uni-marburg.de
http://www.agklebe.de/
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