discussion.
Abstracts can be submitted at: https://acaonline.secure-platform.com/a/
If you have any questions, you can direct them to:
raquel.bromb...@utsouthwestern.edu or zbys...@work.swmed.edu.
Best,
Zbyszek Otwinowski and
Raque
Google Scholar profile and other information about you that you consider to be
the most important. Although the deadline for the application is February 15th,
I will be interviewing candidates by Skype or in person (for Texas-based
applicants) as soon as they are identified.
Zbyszek Otwinowski
UT
again.
Zbyszek Otwinowski
> Dear Veronica,
>
> with 1st, 2nd, 3rd map you mean the density for the same dataset after
> three consecutive cycles of building-refining or three different maps from
> three different crystals?
> If it's the first case, it could be fine, i
riggs>
>>
>> On 26 June 2015 at 11:39, Ashok Nayak wrote:
>>
>>>Dear Weifei,
>>>
>>> It can also be done manually in Pymol by changing the mouse mode from
>>> 3
>>> button viewing to 3 button editing and later moving the envelope onto
>>> the
>>> X-ray structure or vice-versa, however the best fit can be achieved in
>>> SUPCOMB.
>>>
>>> regards
>>> Ashok Nayak
>>> CSIR-CDRI, Lucknow
>>> India
>>>
>>>
>>
>>
>
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
; Hi All,
>
> Scalepack output says 98.8% complete data but after converted to .mtz file
> it reduced to 64%.
> I have tried in CCP4 and phenix both.
> How is it possible?
>
> Ayan
>
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX
t; can anyone shed some light on this ..or point me in the right direction?
>
>
> Thanks in advance
>
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
g
> XDS. This of course doesn't affect XDS one iota, and I can change the MTZ
> header to the correct space group at my leisure (but definitely no
> re-indexing!). So I don't understand why the choice of P2122 vs P2221 etc
> is relevant as far as XDS is concerned: it just needs to know that the
> space group is P222. I can even tolerate C2 from XDS since where
> necessary
> it will get auto-re-indexed to I2 on first entry into the database (but
> never subsequently!).
>
> Cheers
>
> -- Ian
>
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
other packing contacts; however,
for conformations close to rotational axis, symmetry operator cannot
preserve conformer ID, and this issue cannot be avoided.
Zbyszek Otwinowski
>>I would probably make the two waters alternates of each other.
>
>
>
> Quite possible, but the gro
correctly, this comes
with least-squares-routines. I only pointed out that cell errors are
listed in the XDS output (provided you refine them, of course). I am
sure those errors are well defined.
Best wishes,
Tim
On 07/22/2014 06:53 PM, Zbyszek Otwinowski wrote:
Error estimates for the unit cell
.
The main question is: what the unit cell uncertainty means? For most
samples I could defend to use values: 0.001A, 0.01A, 0.1A and 1A as
reasonable, depending on particular point of view.
Without defining what the unit cell uncertainty means, publishing its
values is pointless.
Zbyszek Otwinowski
So there are good reasons to report
both types of completeness in the publication and in the deposit, even if
there is no such custom yet.
Zbyszek Otwinowski
> There is some disagreement on terms used to deposit data. We need a
> definition and an algorithm
> for each definition.
>
>
scattering.
An alternative explanation is that you crystallised a proteolitic fragment
of your protein.
Zbyszek Otwinowski
> Dear all
> i have a small query to ask and seek your suggestions:
>
> I have collected a data for a protein with 324 residues and processed at
> its best
lower resolution will change anything other than
overall R-merge and other R-statistics. To calculate these statistics it
is enough to re-merge the data with lower resolution.
Zbyszek Otwinowski
> Hi all,
>
> This is a basic question and I'm sure the answer is widely known, but
> I
crystal exposed
to constant high dose. If anything, the helical scan method is more
suitable to study radiation damaged state of the crystal.
Zbyszek Otwinowski
> Dear Dean,
>
> You have already received excellent insight into radiation effects on
> metals. From personal experience
does not matter! It is an urban legend that
shorter wavelength will help. I remember it being debunked two decades
ago, and somehow it is still alive.
Zbyszek Otwinowski
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Dean,
>
> this is probably a very common observati
Why not improve "effective resolution" to include consideration of solvent
content? Due to constant packing density of proteins, it would become a
synonim (by appropriate transformation) to number of observations per
modelled atom.
Zbyszek Otwinowski
> Dear Dale, dear Kay,
>
;>>>>> big, sturdy, salty, yellow crystals. He claims I have the best kit
for single-crystal diffraction on campus.
>>>>>> I would very much appreciate advice on how to deal with this,
anything
>>>>>> in the range from "won't work" to "use software X to analyze data
in
>>>>>> space group P-43N" would be welcome.
>>>>>> Thanks.
>>>>>> Andreas
>>>> --
>>>> Dr Tim Gruene
>>>> Institut fuer anorganische Chemie
>>>> Tammannstr. 4
>>>> D-37077 Goettingen
>>>> GPG Key ID = A46BEE1A
> --
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry,
> University of Goettingen,
> Tammannstr. 4,
> D37077 Goettingen, Germany
> Tel. +49-551-39-33021 or -33068
> Fax. +49-551-39-22582
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
e.mtz hklout newfile.mtz
labi file 1 allin
end
I think (and hope) that the data and phases will be converted correctly to the
CCP4 asymmetric unit.
Eleanor
On 25 Mar 2014, at 09:16, Zbyszek Otwinowski wrote:
I am reading an external file, which contains phases and ABCDs in the space group
P
ct for
reflections with initial h not equal to zero, but gives wrong result for 0 k l
reflections.
Zbyszek Otwinowski
Zbyszek Otwinowski
UT Southwestern Medical Center
5323 Harry Hines Blvd., Dallas, TX 75390-8816
(214) 645 6385 (phone) (214) 645 6353 (fax)
zbys...@work.swmed.edu
ir structure factors will vary and can
change quite a lot. Cryo-cooled crystals definitely can have high degree of
internal non-isomorphism resulting from this effect.
Zbyszek
--
Zbyszek Otwinowski
UT Southwestern Medical Center
5323 Harry Hines Blvd., Dallas, TX 75390-8816
(214) 645 6385 (ph
D: 9757100 [PubMed - indexed for MEDLINE]
--
Zbyszek Otwinowski
UT Southwestern Medical Center
5323 Harry Hines Blvd., Dallas, TX 75390-8816
(214) 645 6385 (phone) (214) 645 6353 (fax)
zbys...@work.swmed.edu
ions need to be handled on
case by case basis.
Zbyszek
Presence of multiple, similar unit cells in the sample is completely different
and unrelated condition to statistical disorder.
Agreed!
Jacob
--
Zbyszek Otwinowski
UT Southwestern Medical Center
5323 Harry Hines Blvd., Dallas, T
crystals. However, this requires separate data
set collection rather than mixing such crystals during one rotation sweep.
Presence of multiple, similar unit cells in the sample is completely
different and unrelated condition to statistical disorder.
Zbyszek Otwinowski
> Not sure I underst
disorder.
Zbyszek Otwinowski
> Hi,
>
> If there's an NCS translation, recent versions of Phaser can account for
> it and give moment tests that can detect twinning even in the presence of
> tNCS. But I agree with Eleanor that the L test is generally a good choice
> in these c
Dear All,
The purpose of statistics in the output of Scalepack is to help the
experimenter to assess the data. The question is, what is the purpose of
R-merge statistics and its usefulness when its value exceeds 100%?
When Scalepack was originally written 20 years ago, I made a decision to
output
ation that the particular crystal presented is twinned or
highly mosaic, so chances are good that this project will be solved.
Zbyszek Otwinowski
> Hi CCP4 folks
> I have a data set which is looks twinned ( see the image-1 - I zoomed
on to the image so that one can spot the twinning. Furth
n
solving twinning issues during crystal growth
>
> Thanks in advance !
>
> Mahesh[image: Inline image 2][image: Inline image 3]
>
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
Zbyszek Ot
share their experiences on solving twinning
> issues during crystal growth
>
> Thanks in advance !
>
> Mahesh[image: Inline image 2][image: Inline image 3]
>
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
n a
lower symmetry.
Zbyszek Otwinowski
> Dear all,
> We have solved the problem. Data processing in P1 looks better (six
> molecules in ASU), and Zanuda shows a P 1 21 1 symmetry (three molecules
> in
> ASU), Rfactor/Rfree drops to 0.20978/0.25719 in the first round
> of re
The difference between one and the correlation coefficient is a square
function of differences between the datapoints. So rather large 6%
relative error with 8-fold data multiplicity (redundancy) can lead to
CC1/2 values about 99.9%.
It is just the nature of correlation coefficients.
Zbyszek
unauthorized review, use, disclosure, dissemination, forwarding,printing
> or copying of this email or any action taken in reliance on this e-mail is
> strictly prohibited and may be unlawful.
>
> Visit us at http://www.aurigene.com
>
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
Space groups F23 and P4132 are not subgroups of each other (without
invoking pseudotranslational symmetry) so they cannot be related by
twinning. The end of theoretical analysis.
Zbyszek Otwinowski
> You need to say what the cell dimensions are for these 2 options..
> Eleanor
>
&g
. Consequently, the answer is that typically one should not see
ripples.
Ripples should not be confused with the effect of electron density maps
being smoothed by vibrations and other forms of disorder.
Zbyszek Otwinowski
>
> Dear All, Hi. I was asked in a manuscript revision to discuss
>
cooling rates and
variability in the crystal lattice. Merging statistics should be
acceptable, however they may not be perfect. Better cryo-cooling is likely
to help.
Zbyszek Otwinowski
> Dear Colleagues,
>
> I'm collecting a dataset on our recently repaired Rigaku home source.
Crysta
2000.
The reindexing will change the beta angle automatically.
> Dear all,
>
> I have a P2 derivative dataset with beta=89.6. I try to change the beta
to 90.4 to be consistent with the native dataset. Should I do sth with
the HKL, like applying a matrix? Thanks a million!
>
> Best,
> Zhiy
monic restraints on U (square root of B) rather than on Bs
themselves.
It is not we who cram too many meanings on the B-factor, it is the quite
fundamental limitation of crystallographic refinement.
Zbyszek Otwinowski
> The fundamental problem remains: we're cramming too many meanings into
.
Zbyszek
Frank von Delft wrote:
This is a lovely summary, and we should make our students read it. - But
I'm afraid I do not see how it supports the closing statement in the
last paragraph... phx.
On 31/03/2011 17:06, Zbyszek Otwinowski wrote:
The B-factor in crystallography represent
ee
implemented, require a model-building like approach. The test of the
success of such approach would be a substantial decrease of R-free
values. If anybody can show it, it would be great.
Zbyszek
Dale Tronrud
On 3/31/2011 9:06 AM, Zbyszek Otwinowski wrote:
The B-factor in crystallography
to the previous thread, representing poorly-ordered (so
called 'disordered') side chains by the most likely conformer with
appropriately high B-factors is fully justifiable, and currently is
probably the best solution to a difficult problem.
Zbyszek Otwinowski
>>> - they all
ation.
Hope that helps,
Zbyszek Otwinowski
>
> Hi all,
>
> I have collected one iodine soaked data in our home source, and processing
> the data using HKL2000. Exposure time per frame is 5min/1 degree.
> While processing I have noticed that the Chisq values, cell parameters and
>
Concerning the last point, a wiki seems to be a good place to collect
> the results (a table can be used to follow progress in a program, but
> also to see the differences between programs). But that brings me to my
> last point - a wiki article does not count as a paper.
>
> best,
>
to eliminate peaks at higher
resolution during autoindexing and then extend the resolution during the
refinement. Sometimes it helps for very mosaic crystals.
Zbyszek Otwinowski
> Dear colleagues,
>
> I am working on one dataset that is hard to process. The data are about
3A of resoluti
the following 2 scripts:
(1)
./omit hklin ${f}.mtz mapout ${f}.map <
concerned about which one is more appropriate for the sigmaa-weighted
2mFo-DFc composite omit map.
(mFo is what I generated from the SIGMAA output)
Thanks for any suggestions!
Best Regards, Hailiang
Zbyszek Otwinowski
UT So
the SIGMAA output)
>
> Thanks for any suggestions!
>
> Best Regards, Hailiang
>
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
files (which are very similar) and calculate
the R-merge between them. I tried looking into CCP4 and Phenix, but could
not find a direct path. Does anybody know how I can do this R-merge calculation?
Best regards,
Jason Porta
--
Zbyszek Otwinowski
UT Southwestern Medical Center
5323 Harry
Scalepack as such.
Zbyszek Otwinowski
> Can you send a bit of your scalepack unmerged data - that would allow us
> to check format and pointless behavior..
>
> It sounds a bit like a scalepack problem though..
> Eleanor
>
> Alexandra Deaconescu wrote:
>> Dear all:
&
inement is used), denzo overestimates it somewhat.
--
Zbyszek Otwinowski
UT Southwestern Medical Center
5323 Harry Hines Blvd., Dallas, TX 75390-8816
(214) 645 6385 (phone) (214) 645 6353 (fax)
zbys...@work.swmed.edu
nt by user, they can
be refined iteratively by experimenter by adjusting parameters in subsequent
runs of scalepack, but most of the time it is not required. New version will
adjust all these parameters automatically.
Zbyszek Otwinowski
Richard Gillilan wrote:
Thanks Joe and others.
Bit
ern all be very different.
I do not where this idea originated, but for anomalous data there is only one
way of indexing them (unless you are Chang et all.)
Zbyszek Otwinowski
UT Southwestern Medical Center
5323 Harry Hines Blvd., Dallas, TX 75390-8816
(214) 645 6385 (phone) (214) 645 63
ognized as such. Independently, I value the possibility
of data simulation in methods development and for teaching purposes.
Zbyszek Otwinowski
UT Southwestern Medical Center
5323 Harry Hines Blvd., Dallas, TX 75390-8816
(214) 645 6385 (phone) (214) 645 6353 (fax)
[EMAIL PROTECTED]
t to be.
* I take into account that person taking the bet with me can always
ask for more time.
Zbyszek Otwinowski
UT Southwestern Medical Center
5323 Harry Hines Blvd., Dallas, TX 75390-8816
(214) 645 6385 (phone) (214) 645 6353 (fax)
[EMAIL PROTECTED]
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