we would hereby like to announce the update release of the XDS-GUI
XDSAPP V2.0. This version presents a major update of the current XDSAPP
software (Krug et al., 2012). XDSAPP is an expert system for the
interactive and fully automatic data processing using XDS (Kabsch et
al., 2010).
The
Hi
A great way to learn about crystallographic things (including how to
run the programs and how to interpret the output) is to attend one of
the short courses that are held around the world on a regular basis,
and talk to the experts that develop the programs - CCP4 has one (I
With these trailing mails,
I tried to know the optimum pH for E1 enzyme.
What amount of E2 enzyme should I use ?
If I use excess of E2 enzyme (~ 20 time of E1) I can see only a view for
optimum pH.
If I decrease the amount of E2 (~6-8 time of E1) I can see a cleared view
of the pH profile.
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Dear Smith,
you need to attach a mouse with a scroll wheel to your computer. Once
you open a map in coot, you keep on rotation the wheel away from you
until the number in brackets reaches a value of 6-7. That way you can
make the sigma so high.
On Tue, 12 May 2015 17:24:18 -0500, Gerd Rosenbaum rosenb...@anl.gov wrote:
...
But no big deal. It's a -1 in one of the axes definitions. There are, as
you stated, many more axes definitions and they depend on the geometry
of the end station. E.g., at the SBC, the orientation of otherwise
Hi Tim,
Thanks a lot for your suggestion! I tried different versions later, and I
found that the newest version doesn't work, but an old version works... I
have no idea what is wrong, but anyway it is working now, and it is related
to version...
Thank you so much,
Chen
On Wed, May 13, 2015 at
If I place double bonded O, still there is another blob (1.4A) and density
is continuous! Should not be water!
On Wed, May 13, 2015 at 5:33 AM, Mark J van Raaij mjvanra...@cnb.csic.es
wrote:
how about SCX with a double-bonded O for the X? That may give the right
angle.
Mark J van Raaij
Being in software design myself, I want to look at it from the other
side. If I produce software I want to get from it:
1) Gratitude from the users, preferably expressed in the form of citations;
2) Nice collaborations that allow me to use my, novel software at the
edge of science;
3) The
Is there any reason to be S-S-CH3 modification of a specific CYS! Others
CYSs are fine.
On Tue, May 12, 2015 at 5:27 PM, Finke Aaron (PSI) aaron.fi...@psi.ch
wrote:
What are the bond lengths- or, rather, the centers from blob to blob?
Looks a bit short to be S-O, could be S-S-CH3?
Cheers,
Dear colleagues,
We have an opening for a Scientist-I (Structural Biology)
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To apply for this
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Are the Cys residues in question on the surface of the protein? DMSO
(which is in the crystallization mix) is a weak oxidant and could
conceivably contain impurities like dimethylsulfide and methanethiol
which could form difulfides with surface Cys residues. Or there could
have been sulfides
Shameless self-promotion aka advertisement:
http://lupo.jhsph.edu/boschlab/Xray_Workshop.html
Jürgen
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry Molecular Biology
Johns Hopkins Malaria Research Institute
615 North
Hi all,
I am sorry about this question which I should have figured out earlier. For
point group determination, does the Rmeas consider Fridel pairs
differently? (although I think it should be...) This is because I saw a
derivative dataset collected at peak (from a demo) whose Rmeas is quite
high
Hi Ethan,
Yes. My question was simply whether it calculates the statistics from
completely unmerged intensities and just compare say h,k,l with -h,-k,l (or
-h,-k,-l and h,k,-l) if there is a 2-fold? Although I believe so...
And what is a good number? Is 20 % OK? What about 30 % and even
On Wednesday, 13 May, 2015 17:51:59 Chen Zhao wrote:
Hi all,
I am sorry about this question which I should have figured out earlier. For
point group determination, does the Rmeas consider Fridel pairs
differently?
A Friedel pair consists of the [hkl] and [-h-k-l] reflections.
This pairing
Hi Ethan,
Thanks a lot for your detailed information. I am aware that in IDXREF only
the lattice symmetry was tried to be determined. I went back to check the
subtrees in IDXREF because even for P1 the Rmeas is very high, meaning that
the multiple measurements for the same reflections
On Wednesday, 13 May, 2015 18:17:04 Chen Zhao wrote:
Hi Ethan,
Sorry, I'm coming in late on this so I might have missed an
earlier explanation of exactly what programs are involved.
Yes. My question was simply whether it calculates the statistics
Applications are invited for a postdoctoral position in Dr. Fang Li's
lab at the Department of Pharmacology, University of Minnesota Twin
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Strong background in
Hello!
Friend B installed linux on the laptop of friend A. Then I installed
ccp4i/arpwarp/balbes in the laptop of friend A. Now the problem is that /
is running short on space (some weird thing with respect to the ssd ~15Gb
and ubuntu/windows7 dual setup). So B and I were trying to make some
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Dear Chen,
the fact that you differentiate between mp and non-mp version of
shelxd makes me assume you have a rather old version of shelxd
installed. Can you try again with the latest version of shelxd and
report if the (or any) error persists?
Best
Dear James,
Just a stupid question: did you contact the authors and asked them whether you
could have a copy of the software?
While I agree that one cannot expect from authors/funding agencies to support
any software forever, in my opinion they should provide the version described
in the paper
Dear Fred,
Was BME in one of the buffers used for expression or purification? Was any
other cysteine reagent used? With 1.3 Å, I would fit a BME modification and see
if it fits well. You could also setup crystallizations in the presence of DTT
to see if you can get rid of the modification.
Dear All,
For the contour level in the Properties in the Dssplay of the Display Manager
in Coot, the contour level should be exacly the sigma value we see in the
published crystallography paper, am I right? But I have paid attention to a
paper which has a sigma level of 6-7 for its densty.
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