Dear Chris,
Did you specify your residues in the pdb as alternative conformation,
e.g. name your conformers in the pdb ASER and BSEP? For buster and
ligands this works for me and I would expect this to work for other
programs as well.
Best,
Herman
Fro
Hello,
I have a structure with a phosphorylated residue, but it looks like the residue
may not be completely phosphorylated. I've currently modelled the residue
purely as the phosphorylated variant, and have now been trying to put in a
second conformer for the unmodified residue, but I'm findin
Is it possible the solution structure of SAXS, NMR and EM neglect the
existence of a very small percentage conformation of the molecule due to
the overwhelming signals from the majority conformations? But this state of
the molecule is trapped and enriched by the crystallization condition.
Nian
O
The short answer is: no. Wavelength does not matter. Not for native
data anyway.
I wrote a paper about this recently. It is open access:
http://dx.doi.org/10.1107/S0907444910007262
In particular, check out Figure 2. The two solid lines are pretty darn
flat, and that means the wavelength
There could be many causes for this. Perhaps you do not have the best def.site
file for your detector / beamline / hardware. What do your local HKL2000
experts tell you?
You could e-mail me an image and I can help you.
Jim
From: CCP4 bulletin board [C
Hi all,
I recently collected a data set off a single crystal and have had problems with
indexing it. Every time I go pick peaks for indexing it constantly picks peaks
that are just slightly off the actual peak. After indexing, it would always be
that 2 of the 3 cell dimensions would be fairly n
This is a case where it is really helpful to keep some record of the
unmerged integrated data.
And again rejecting the odd outlier does no harm to most analyses..
I like to use scala to check for outliers looking at all i+ I-
measurements; if there is a wild discrepancy for weak anomalous signa
Thanks, Artem!
PDE2A also uses three domains to form a homodimmer. However, without the
catalytic domain, the GAF B domain swings out. This is an excellent
example for the restrictions set by the multidomain context.
Anyone knows other examples?
Thanks a lot!
> PDE2 full length versus domain only
Herman,
Thanks for clarifying the difference between map coefficients and map files
for me. What I really need are only map files, and I could generate those
masked maps by following Paul's suggestion.
Yu
2012/2/20 Paul Emsley
>
> Like Herman, it was not apparent to me what exactly you want w
Hi all,
In April we will once again organise the EMBO practical course on
"Computational structural biology - from data to structure to function". The
application deadline is only a week away - 24 February.
For more information about the course and how to apply, surf to:
http://www.e
Dear All,
I would like to draw your attention to a x-ray crystallographer position in
Jiangsu, P. R. China.
Best,
Job ID
Biortus_0131201201PS
Posting Title
Scientist or Senior Scientist, Structural Biology, Protein Structure Group
Country
P. R. China
Work Location
Jiangyin City, Jiangsu, P.R
Postdoctoral positions are available for highly motivated scientists in the
laboratory of Dr. Xin Liu at the University of Texas Southwestern Medical
Center at Dallas
(http://www.utsouthwestern.edu/fis/faculty/127166/xin-liu.html).
The research of the laboratory is focused on the regulation of
Dear All,
I would like to draw your attention to the following job vacancy in
Jiangsu, P.R. China.
Job ID
Biortus_0131201201PS
Posting Title
Scientist or Senior Scientist, Structural Biology, Protein Structure Group
Country
P. R. China
Work Location
Jiangyin City, Jiangsu, P.R. China
Company/Le
Hi,
it might well be possible that molrep used only lower resolution data
(the default cutoff isd 2.5 A, if I remember correctly), when refmac
uses all available data in the MTZ file...
Check that both steps were performed at the same resolution !
Another possibility is that molrep performed
Dear Sir/Madam,
I am very new to this CCP4 program. Usually I know that after rigid body
refinement the R factor reduces from the R factor what ever we get from Molrep.
One of my data is showing some different characteristics. After running Molrep
the R factor is showing 38% and score is 64%, b
Like Herman, it was not apparent to me what exactly you want wanted.
If you want a map that covers only [1] or excludes [2] a particular atom
selection then you can do that in Coot.
Extensions -> Maps... -> Mask Map by Atom Selection,
e.g. to show only the "A" chain, use an atom selection of
Dear Yu,
You seem to be mixing up map coefficients and map files. Map coefficients are
modified reflections, e.g. 2*Fobs-Fcalc multiplied by a weighting factor with
h,k,l indices and are stored in a .mtz file. From these map coefficients, you
can calculate a map file with an FFT program. A map
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