Dear ccp4bb subscribers,
I have just learned that Proteopedia (the wikipedia-style encyclopedia
of macromolecular structures) has been voted winner in this year's
competition organized by the Scientist ( http://www.the-scientist.com/
, readers and judges choice).
So thanks to all who voted,
Dear bulletin board,
After downloading and recompiling the complete CCP4 package (we had the
precompiled 32bits version on our 64bits machines) we were able to apply
the patches of Claus and the problem case P21221 went through without
problems.
However, with the next problem case tested,
Dear All
hopefully the fix for modules.def is now in the source and binaries for ccp4
6.1.13
Charles Ballard
CCP4
On 30 Aug 2010, at 18:06, ger...@embl-hamburg.de wrote:
Dear Colleagues,
some of you might have noticed that ARP/wARP does not install cleanly with
the latest version of
I'm sure it would be a good thing if SFTOOLS recognised all possible space
groups, but I wonder why you are using SFTOOLS at all. I've almost never had
the need to use it myself. Space group changes and many other things can be
done with CAD for example
Phil
On 2 Sep 2010, at 13:31,
Dear Phil,
CAD would also be an excellent alternative. I used REINDEX which also
worked. The point I tried to make is that if people do not know that
SFTOOLS is not up to date, they may use it in good faith and get into
trouble. If they know it, they might use it to hack an mtz file when
On Thu, Sep 2, 2010 at 5:31 AM, herman.schreu...@sanofi-aventis.com wrote:
The other question is: why does phaser write 'R 3 :H' in the mtz? When
the problem with the P21221 space group first popped up last year, Randy
told me that space group numbers like 2018 are non-standard, and that
Well, CCP4 programs using the core libraries should ignore the
spacegroup symbol and use the operators instead, which bypasses the
whole problem. I would advise anyone using the CCP4 libraries in their
own programs to do the same.
That works for mtz and map, but not for pdb files of course.
FYI --
The :h suffix for R3 is described in the IUCr symmetry cif (intl tables vol G
chapter 4.7) under _space_group.reference_setting where it states For the
space groups where more than one setting is given in International
Tables, the following choices have been made. For monoclinic
space
Hi,
I am reading a ccp4 mtz file using SFTOOLS. It asked me Is this an XPLOR
RFREE flag column?. First I assume the answer is NO, since the input is a
CCP4 mtz file although the colume is for free-flags. Then, I am wondering
what is the script to automatically answer NO in a shell script.
Hi Hailiang
sftools was first and foremost designed to be used interactively, that
is why it tends to follow a question and answer user interface. Of
course you can use sftools in scripts but if it pops up a question that
was not anticipated, the script it will crash. There could be a batch
GOt it! Thanks!
Best REgards, Hailiang
Hi Hailiang
sftools was first and foremost designed to be used interactively, that
is why it tends to follow a question and answer user interface. Of
course you can use sftools in scripts but if it pops up a question that
was not anticipated, the
Hi,
I recently collected a MAD dataset on one of my xtals soaked in ~7mM KAuCN2
for 1.5 days. I had backsoaked these xtals prior to freezing and the signal
seems to be faint. I was wondering if it would help not back-soaking xtals.
I would be grateful for any comments/suggestions.
thanks,
--
See the following publication for an interesting method to resolve
pseudo-merohedral twinning in SeMet crystals:
Cansizoglu, A. E. and Chook, Y. M. (2007) Conformational heterogeneity
of Karyopherinβ2 is segmental. Structure, 15(11):1431-1441.
In an effort to obtain single selenomethionine
Dear All,
Apologies for a non-ccp4 question. I am planning to express a GPCR in
HEK293T cell line by transfecting with the requisite cDNA for performing an
assay. I would like to confirm the expression of the protein in the cell
line by western blot or histochemical studies. Any pointers in this
If I were you, I would just make a gfp-tagged construct--this is an easy way to
make sure that the protein is there, and made it to the membrane. If necessary,
you can blot for gfp, or add other tags in the process for alternative blotting
(one on each side to make sure it is not cleaved, for
Hi Qing,
I would recommend either the use of GFP as mentioned by Jacob or a his-tag
or a flag-tag. C-terminal tagging is preferred to prevent interference with
signal sequences at the N-terminus of the protein.
Flag tag is really good for detection , the commercial antibodies for
detection are
In an isolated piece of density, I want to fit a 7AA peptide fragment from a
protein.
Only the sequence of the whole protein (200AA) is known, and I don't know the
peptide sequence.
I think it's best to try from the beginning of the whole sequence to the end.
So is there any software or scripts
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