Hi Fred
Well, it is ironic that after acquiring ability to determine
a protein structure some times in a few minutes
we are still failed my format conversions like 30 years ago :-(
Dr Felix Frolow
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and
My understanding from Gerard K is that the next version of the PDB
format will also use unjustified atom names.
Unfortunately, following mmdb, I also backed the wrong horse and assumed
space-padded atom names were here to stay. A certain amount of
re-engineering is going to be required.
My
You should be able to use the CCP4 utility coord_format though this is
not in the GUI:
coord_format xyzin ./1ivo.cif xyzout 1ivo.pdb eof
END
eof
This converts at least some of the header, including the CRYST1 card.
BUT:
1) slight glitch - you need to specify the full path for the cif file,
There is a time-honored tradition of PhD students struggling through
format conversion issues. Where is the fun and learning opportunity
if everything ran smoothly? ;)
Cheers,
Steve
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Felix Frolow
Post-doc Position at the Institute of Biochemistry at the Goethe University
Frankfurt, Germany
Robert Tampé and Martin Pos at the Institute of Biochemistry, Goethe
University Frankfurt, are looking for an experienced crystallographer at
the post-doctoral level to work on structures of
STAFF SCIENTIST IN BIOLOGICAL X-RAY CRYSTALLOGRAPHY WITH SYNCHROTRON
RADIATION
European Molecular Biology Laboratory, Hamburg, Germany
A position is available at the Structural Biology Unit of the EMBL in
Hamburg. The Unit utilises synchrotron radiation at the German
Synchrotron Research
Hi,
I wanted to do solvent flattening for my map using Wang's method. I used
CCP4-DM, and now have several questions:
1. DM seems requiring the FOM, so I generated FOM using SIGMAA by
providing FP, FC and SIFFP using the following:
sigmaa HKLIN in.mtz HKLOUT
Kurt Krause's group solved a structure from hollow crystals:
J. Mol. Biol. 2002 Apr 26;318(2):503-18.
The crystal structure of Trichomonas vaginalis ferredoxin provides insight into
metronidazole activation.
Crossnoe CR, Germanas JP, LeMagueres P, Mustata G, Krause KL.
Hi Hailiang,
Be sure to include PARTIAL WCMB in your sigmaa script. This option outputs
something more like a conventional FOM for use in DM.
Also, I would allow DM to run more cycles and suggest starting with default
parameters for solvent masking and density levels and then looking at the
On Wed, Jun 2, 2010 at 12:07 PM, Andre Ambrosio
andre.ambro...@cebime.org.br wrote:
We have recently obtained crystals from a small protein, and
interestingly, at least for me, they are hollow trigonal rods (please see
pictures attached).
Just out of curiosity, has anybody ever seen such
Andre
I had same kind of crystal like in your picture. It diffracted around 2.7A.
Even I had some crystals where one end was closed. Both hollow crystal or the
closed end (part) crystal diffracted same.
With regards
Syed
--- On Thu, 6/3/10, Andre Ambrosio andre.ambro...@cebime.org.br
Don't you worry, there's a lifetime of learning opportunities. I
used to spend almost as much time helping senior PIs with format
conversion as new students. Got to love the pdb
ho
---
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