On Thu, Jul 15, 2010 at 01:02:30AM -0400, Hailiang Zhang wrote:
> Hi all:
>
> Does CCP4 or Phenix provide any utilities which can summarize the data
> statistics (particularly looking for the average Fo_sigma/Fo for each
> resolution shell)? Truncate seems to be able to do that but didn't get the
Hi all:
Does CCP4 or Phenix provide any utilities which can summarize the data
statistics (particularly looking for the average Fo_sigma/Fo for each
resolution shell)? Truncate seems to be able to do that but didn't get the
desired answer. Any short script will be greatly appreciated!
Best Regard
Welcome to crystallography and the PhD. Expect a lot of failure before your
degree. I know its frustrating but all of the challenges you encounter will
teach you and increase your skills. I had crystals my first year, moderate
resolution around 3 A and it took until end of my 4th year to phase a
Hi Pascal,
I suspect the protein is aggregating in the presence of
FosCholine. In addition to the suggestions made by others, you can
also try changing the salt concentration or including additives like
glycerol in your FosCholine buffer. This can make an enormous
difference in the stability
Positions Available: Electron Crystallography of Membrane Proteins
A number of different positions are available with the
Transcontinental Electron Microscopy Initiative for Membrane Protein
Structure (TEMIMPS;http://temimps.nysbc.org). TEMIMPS is a new center
funded by the NIH Protein Stru
Positions Available: Electron Crystallography of Membrane Proteins
A number of different positions are available with the
Transcontinental Electron Microscopy Initiative for Membrane Protein
Structure (TEMIMPS;http://temimps.nysbc.org). TEMIMPS is a new center
funded by the NIH Protein Stru
Thanks a lot for all the quick replays to my post. It seems to be a
controversial topic. Bellow are to replays which more or less summarize
the answers to my post.
Cheers,
Ariel
On Wed, 2010-07-14 at 07:44 -0500, Eleanor Dodson wrote:
> Everything said is true, but one of the most important fac
Better link with nice tutorial from Andrey is:
www.ysbl.york.ac.uk/mxstat/
In the JLigand section there are some tutorials from Andrey to
demonstrate how covalent links can be generated and used.
Garib
On 14 Jul 2010, at 14:35, Paul Emsley wrote:
On 14/07/10 12:56, Vandana Kukshal wrote:
On 14/07/10 12:56, Vandana Kukshal wrote:
how to make covalent bond between ligand and protein residue by using
CCp4 package
JLigand
http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html
p.s. Don't "Reply" if you are not following the same thread - doing so
causes confusion to threaded ma
how to make covalent
bond between ligand and protein residue by using CCp4 package
Everything said is true, but one of the most important factors in
calculating structure factors and hence Rvalues is the scaling and
solvent model. All of these are pretty inadequate - probably all protein
"crystals" have large volumes of multiply ordered atoms - water
networks, alternate confo
Hi Harry,
Your remark was the solution to our "wish" problem. We have change the line:
setenv MOSFLM_WISH ${CCP4I_TCLTK}/wish
to
setenv MOSFLM_WISH /usr/bin/wish8.4
and now imosflm runs as expected.
Thank you very much for your help!
Martin
Dr. Martin
Hi
As Tim says, the Wish you seem to have set to $MOSFLM_WISH can't be
run on OSX 10.6.4 - further to what he suggests, it's always
worthwhile trying in case of problems (at the command line) -
which $MOSFLM_WISH
(in your case I guess it's set to "/usr/local/ccp4-6.1.13/bin/wish")
Dear Tim,
Thank you very much for your help. In fact, the answer to:
file /usr/local/ccp4-6.1.13/bin/wish
is not a link. It answers just the following:
/usr/local/ccp4-6.1.13/bin/wish: data
So I am posting it also to the board...
Martin
Dr. Martin Mart
Which is why I said "make available" rather than "post it" or "email
me" :)
And he has done just that will go have a look
m
On Tue, 2010-07-13 at 18:42 -0700, James Holton wrote:
>
> The original poster just told me that the map file is 2.6 GB. Please
> don't encourage him to attach
Dear Martin,
the error message 'cannot execute binary file' probably means that this is a
binary for a different platform (maybe PC, or a 64bit binary while your OS is
32bit).
check out the result of
file /usr/local/ccp4-6.1.13/bin/wish
and if that 'wish' is a link, follow it until you get to t
Hi, this is to report that imosflm on MAC OSX 10.6.4 fails with the
following errors:
testing MOSFLM_WISH (/usr/local/ccp4-6.1.13/bin/wish)
/usr/local/ccp4-6.1.13/share/ccp4i/imosflm/src/imosflm: line 135:
/usr/local/ccp4-6.1.13/bin/wish: cannot execute binary file
/usr/local/ccp4-6.1.13/shar
... yes, and this is the reason why sfcheck should be replaced by a
more modern program at the Protein Data Bank!
Best regards,
Dirk.
Am 13.07.10 22:15, schrieb Ethan Merritt:
Should be in an FAQ somewhere:
Q: Why does sfcheck not reproduce my original R factors?
A: Because instead of using
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