My personal experience is ( I frequently re-refine structures I cite
if all the data for that exist
in PDB) that PDB possesses a significant number of artifacts
unsupported by reality but by the wild imagination only. These
artifacts are originated from the modest, good and excellent
Dear All,
Just to clarify that I completely agree with the interest and
relevance of the two papers discussed in the News Views and with 99%
of the News Views article itself - it is just that readers from non-
structural biology fields may get the wrong impression from the 2
was words
Mark J. van Raaij schrieb:
...
And these wrong impressions are all too common, at least around here. As
another example, more than once I have been asked by someone if they
give me the sequence or name of a protein (even membrane proteins), how
many days would it take us to provide them the
Hi all
I am refining an dataset of 2.9 A resolution. I am using TLS+restained
refinemnet+ isotropic B factor and simple scaling. After reinement 10 cycle
of refinemnt after geometry optimisation i found that b factor of the
coordinates drastically goes down to 2.0 of att the atoms of the PDB. If
Dear Guenter,
There is a very convenient option in SHELXL for cases like this
where it is reasonable to assume that some distances are equal
but one does not know how long they are: the SADI equal
distance restraint. For an Fe4S4 cluster this might look like:
SADI_FS4 0.02 Fe1 S2 Fe1 S3 Fe1 S4
Hello,
1. As long as all proteins have seventy amino-acids or less and express in
E. coli in mM concentrations - we're in business.
2. As for the question below - my favorite answer is 'It will take a week
and ten million dollars in unmarked bills. We begin as soon as the money
arrives.'.
Artem
ar...@xtals.org wrote:
Hello,
1. As long as all proteins have seventy amino-acids or less and express in
E. coli in mM concentrations - we're in business.
2. As for the question below - my favorite answer is 'It will take a week
and ten million dollars in unmarked bills. We begin as soon as
I installed CPP4 version 6.1.1 on a Linux laptop which is running ubuntu.
Following which I also installed ARP/WARP 7.0.1 version.However, when I attempt
to launch ARP/WARP using the CCP4I GUI interface, I get the following message
Can not get environment variable for warpdoc.
Could someone
Dear all,
http://www.nature.com/nature/journal/v458/n7234/fig_tab/nature07819_F3.html
Just came across this figure Fig. 3b) and would like to know what is the
general and easiest way to make things like this, as a non-brainer. Thank
you, -Jacob
Please make sure you source arpwarp_setup.csh (or .bash) after you
source CCP4, this should cure the problem. Instructions on how to source
arpwarp_setup are printed when you install ARP/wARP with the install.sh
script.
Best regards,
Victor
Sridhar Prasad wrote:
I installed CPP4 version
Questions, issues, rational decision making, and time saving tips while
building, refining, and validating X-ray structures that have alternate
confirmers.
I am currently trying to build/refine a 1.2 A resolution structure using
Coot and Refmac5. There is clear interpretable Fo-Fc difference
Hi,
I would like to override the new ligand encountered error message in
refmac5 by using the make check none command but don't know how to do
this in the ccp4i GUI. Does the command go into the .cif or .pdb? If so,
what is the format/script? Any help is appreciated.
Alex J. Vecchio
On Friday 13 March 2009, Jacob Wong wrote:
Dear all,
http://www.nature.com/nature/journal/v458/n7234/fig_tab/nature07819_F3.html
Just came across this figure Fig. 3b) and would like to know what is the
general and easiest way to make things like this, as a non-brainer. Thank
you, -Jacob
I
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