I2 and C2 are different settings of the same group. The official IUCr
convention is to use the one which gives the beta angle closer to 90 degrees.
As far as I know all programs should now be able to use the I2 setting, but if
it worries you, you can reindex to C2
Phil
On 21 May 2014, at 17:54
Hi Will,
I previously used an extinction coefficient of 600M-1cm-1 for phosphotyrosine
at 280nm estimated from figure 2 of this publication:
http://www.ncbi.nlm.nih.gov/pubmed/2418612
Hope that helps,
Bernhard
Bernhard C. Lechtenberg, PhD
Postdoctoral Fellow
Riedl Lab
Sanford-Burnham Medical
If you do not specify that you prefer C2, pointless change to I2. This is
sometimes odd, for instance when running molrep or shelx (hkl2map) afterwards
Armando
I am out of the lab
> El 21/05/2014, a las 18:54, Roberto Battistutta
> escribió:
>
> Dear All,
> a question about C2 and I2 space g
Hello folks,
I would like to measure the concentrations of proteins containing
phosphotyrosines using absorbance at 280nm.
I'm wondering about calculating extinction coefficients by the Edelhoch
method - as used in ProtParam for example:
http://web.expasy.org/protparam/protparam-doc.html
Given
You can always re-index a monoclinic unit cell with beta greater than 120deg.
Usually the beta closer to 90deg is preferred, but either will work.
Bernie Santarsiero
On May 21, 2014, at 11:54 AM, Roberto Battistutta wrote:
> Dear All,
> a question about C2 and I2 space groups.
> Processing
Dear All,
a question about C2 and I2 space groups.
Processing a dataset, XDS output says C2, with dimensions 122.8, 56,9 81,5 and
beta 125.1°.
Aimless reindexes to I2 with 81.6, 56.9, 101.1 and 96.2°.
Phenix (refine) returns a warning "NOTE: non-standard setting used: I 1 2 1".
In the PDB there ar
On 21/05/14 14:57, Remie Fawaz-Touma wrote:
Thank you so much for your replies.
CCP4 refinement file is showing warnings that the Glc units are at
distance (1.4-2.1A) greater than the acceptable one by the program
(1.33A) from each other even though I got the model from a published
pdb file.
the R-factor is a complicated thing that depends on things like
> weighting factors and solvent model - several things that are not part
> of your model and that need to be adjusted by the refinement program
> during refinement.
>
I think a more accurate is "are not part of your ATOMIC model".
Bul
Thanks for the neat command line! In fact the MolProbity web server can
handle the original file as well as the 'timmed' file, so this
seems to be a peculiarity in the implementation in coot (win7.2.1) in which
neither works. I did download the latest reduce/probe, btw.
I'll dig more.
Thx, BR
-
Thank you so much for your replies.
CCP4 refinement file is showing warnings that the Glc units are at distance
(1.4-2.1A) greater than the acceptable one by the program (1.33A) from each
other even though I got the model from a published pdb file. so the pdb file
generated only shows me dott
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Hi Bernhard,
I am not sure this represents your problem: when I only select the
ATOM cards and of those only columns 1-56
grep "^ATOM" 9INS.pdb | cut -c 1-56 > 9INS_coords.pdb
the molprobity server has no problems analysing this file including
the a
Thank you very much for useful suggestions! :-)
Best,
Almu
2014-05-20 9:44 GMT+02:00 Kay Diederichs :
> Dear Almudena,
>
> if you follow the recommendations given in the "Difficult datasets"
> article on XDSwiki, your problem would have a good chance to be solved.
>
> best wishes,
>
> Kay
>
>
Dear All,
I experienced an odd observation with some philosophical consequences (here
we go again)
When I run a model obtained from a perhaps popular but until further
examination unnamed server,
and validate through coot/validate, the model kills probe/reduce which
normally works great.
Hi Venkat,
I think there are maybe a few things you could do.
- Have you tried to lower the concentration of your protein? Maybe these
clusters appear like so because there is little time for better ordered
growth. If you decrease the protein concentration, supersaturation will
occur slower and y
Dear Venkat,
Crystals are
categorized as extremely thin needles that are clustered and protrude around a
single nucleation site, and appear “fuzzy” in nature. I would particularly
recommend three different ways to optimize them, which I prioritized in
descending order:
1.
Dear V.
are you sure these are crystalline? - I have had similar growth from
'spherulites' that I thought was promising. But then when I went in with a
needle to break them for seeding, it turned out they were fibrous not
crystalline. This made me think they were a product of denatured protein
An obvious point - remember refinement exists to give you the best possible
model so you need to look at the maps.
And I guess that has to be a subjective assessment - if you SEE anything
more clearly at the higher resolution - I would use that data, but if the
maps do not improve discard it..
Th
Hi Thomas,
I too would use the data out to 2.55A, as you did. The main point is that the
2.45A model produces a worse Rfree (30.16%) at 2.55A than the 2.55A model does
(30.03%). And this tendency is confirmed for the 2.35A model, so there's no
point in going beyond 2.55A.
best,
Kay
Dear all,
kind reminder for PhD fellowship opportunities at the International PhD program
of the IGBMC, notably for Integrated Structural Biology.
Deadline for applications is 3rd of june 2014: http://phdprogramme.igbmc.fr/
Interested candidates are invited to visit the home pages of the team
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Dear Remie,
the R-factor is a complicated thing that depends on things like
weighting factors and solvent model - several things that are not part
of your model and that need to be adjusted by the refinement program
during refinement.
That's why I th
This is fixed now if you re-install updates and
Armando - this is crude but if you edit the log file and replace
v. resln :N:1,6,7 11 12with v. resln :N:1,6,7,11,12
it will work.
On 21 May 2014 10:20, Armando Albert wrote:
> Dear all,
>
> does anyone experience a problem viewing ref
Dear all,
does anyone experience a problem viewing refmac results with Log Graph?
The window appears and disappears in less than one second and this is the
output on the terminal window:
Error in startup script: syntax error in expression "10 11 12 + 12": extra
tokens at end of expression
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