onvert .phs to .mtz ,use the .mtz file refine the initial
> structure model? By the way , what's the difference between this density map
> with the density map modified after phaser-EP density modification? Thanks a
> lot!!!
> Best Regard
> Shijun
>
>> -原始邮件-
&
Dear Shijun,
hkl2map is a very nice graphical user interface that makes it easy to use the
SHELX programs; I've used it successfully around 3A. You find documentation and
download information for SHELX C/D/E and hklmap in the CCP4 community wiki, at
CH FILE IN "STRONGHKL1"". xds_par then
>get paused. I'm using virtualbox ubuntu 16.04 on win 8.1 host. I haven't
>test it on other platform though. Rebooting the machine can help to get
>around. If someone also see similar error message maybe they can help
>verify.
>
Hi Andre,
you should first optimize your data processing as much as possible ... try
different programs, and do test refinements against the data they give you.
Unfortunately Rwork/Rfree is a poor indicator unless the Wilson B is the same;
what is much more robust is the correlation
Dear all,
there is a new BUILT of the XDS package available for academic users from
http://xds.mpimf-heidelberg.mpg.de . This fixes a number of problems with the
VERSION of Nov 1, and all users of that version should update.
We believe that this has a better background treatment in particular
Hi Sabine,
my first guess would be that you are overlooking half of the reflections
meaning the cell has really twice the volume. Is the list of difference
vectors in IDXREF.LP clean in this respect?
Best,
Kay
On Wed, 16 Nov 2016 17:26:59 +0100, Sabine Schneider
Hi Hauke,
so your refinement results in P1 seem to say it's untwinned. I don't see (but I
may be overlooking something?) the evidence, from what you write, that it could
not be P21 or P2, because any P2 or P21 structure can be refined in P1 (but of
course not the other way round). In other
Dear Hauke,
the conversion of intensities to amplitudes is an area with unsatisfactory
solutions, and the approaches of (and the assumptions made by) the different
programs differ. Low-resolution data are often anisotropic, which adds
difficulties. You could try CCP4 truncate/ctruncate and
Hi Phil,
the error message occurs because your glibc is too old for this binary. The
glibc cannot easily be updated, it is tied to the distribution, in your case
RHEL6. A newer kernel does not change this, nor would an update to RHEL 6.8
This is why distributed Linux software should be built
Just a few observations:
I ran
echo MODE SFCALC XYZIN\\n SYMM P21\\n RESO 30 3 | sfall xyzin a.pdb hklout
temp.mtz a.log
and
echo MODE SFCALC XYZIN\\n SYMM P21\\n RESO 30 3 | sfall xyzin b.pdb hklout
temp.mtz b.log
and looked at a.log and b.log
They differ only as follows: a.log has
First
Hi Dale,
On Thu, 2 Jul 2015 10:45:45 -0700, Dale Tronrud de...@daletronrud.com wrote:
While I was puzzling over an entry in the PDB some years ago (since
obsoleted) I noticed that all the high resolution amplitudes were equal
to 11.0! This was before CC1/2 but for this structure it would
On Thu, 2 Jul 2015 13:25:07 -0400, Edward A. Berry ber...@upstate.edu wrote:
My take on this-
No one has been willing to specify a cutoff (and probably there is no rigorous
way to
mathematically define the cutoff) and say If CC* (or CCfree or whatever) is
below X
then it will not improve your
On Thu, 2 Jul 2015 00:15:58 +0100, Eric Karg harvard...@yahoo.com wrote:
Hi all,
I have a dataset processed in XDS to 2.3 A (based on CC1/2). I'm trying to do
paired refinement to determine the optimal resolution cutoff. Here is what I
get at different resolutions set in Phenix:
Final
I don't think the .sfrm ending means that the data can or can not be read by
non-Bruker software.
The crucial difference is between warped and unwarped data, if I understand
correctly. XDS (and I think MOSFLM) can only process unwarped data. As Harry
says, there is an unwarping utility from
if it only occurs with the Mac version of Word: a workaround would be to set up
a virtual machine on your Mac in which you run Windows and its version of Word.
Anybody tried this?
Kay
Hi Chen,
if Rmeas is high (like 50 and up) even in P1 then maybe the integration was not
right, or the indexing is offset by 1 in h or k or l ?
To check the former, look at FRAME.cbf and see if the predictions match the
spots.
To test the latter try
echo CENTRE | pointless XDS_ASCII.HKL
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
According to
http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#ROTATION_AXIS=
the definition of a positive value in the ROTATION_AXIS= line is:
When looking along the axis, the crystal would rotate clockwise when
proceeding to the next data image.
There is of
Dear LU,
yes, your spot_15.png looks good. What worries me now is the table
INDEX_ QUALITY DELTAXD YD X Y Z DH
DK DL
ORIGIN
0 0 0 1.70.1997.7 1020.9 0.0010 0.0005 1.02190.38
0.510.25
0 -1 0 3.00.4
You found it!
XDS.INP needs
ROTATION_AXIS=-1 0 0
with this setting, IDXREF indexes more than half of the reflections:
REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM 10956 INDEXED SPOTS
REFINED PARAMETERS: AXIS BEAM ORIENTATION CELL
STANDARD DEVIATION OF SPOTPOSITION (PIXELS)
Hi LU,
the reason why IDXREF is not indexing smoothly is that the spot positions in
your SPOT.XDS are not very meaningful - you pick up a lot of noise! I plotted
your SPOT.XDS using
%%:-/tmp/luo% gnuplot
gnuplot set size square
gnuplot set out tmp.png
gnuplot set term png nocrop medium size
On Mon, 20 Apr 2015 23:15:17 +, Keller, Jacob kell...@janelia.hhmi.org
wrote:
I have processed test data sets (measured at the SLS) which have only a few
non-zero pixels on each frame. Can be nicely integrated - but it was insulin.
What were the values of the non-zero pixels, I wonder?
On Fri, 17 Apr 2015 15:00:12 +, Keller, Jacob kell...@janelia.hhmi.org
wrote:
Finally, there is simply no downside in collecting more degrees with
proportionally lower dose on the Pilatus. Merging the data recovers the
_same_ signal. It has only advantages - so many that I won't write
On Fri, 17 Apr 2015 13:02:01 +, Antonio Ariza antonio.ar...@path.ox.ac.uk
wrote:
Hi,
I agree with Kay, try to fry your native crystals to get the highest overall
resolution possible,
since you mention my name in your sentence: no, this is not what I think (nor
said). Burning/frying the
Hi,
I'd say using a Pilatus detector in fine-slicing mode and lowdose/high
multiplicity will give you better chances to solve the structure. The right
strategy makes a difference ...
Best,
Kay
-2926tel:%2B1-410-955-2926
http://lupo.jhsph.edu
On Apr 17, 2015, at 9:25 AM, Kay Diederichs
kay.diederi...@uni-konstanz.demailto:kay.diederi...@uni-konstanz.de
wrote:
Hi Jürgen,
sorry - that's what I get when mailing while boarding ... No, I'd just
collect 360 degrees, and if the crystal is still ok
On Wed, 1 Apr 2015 17:52:44 -0400, Shane Caldwell shane.caldwel...@gmail.com
wrote:
Hi ccp4bb,
I'm trying to solve a problem I never quite figured out in the past. I'd
like to use the *sortwater* utility to send my picked waters to various
protein chains, and to give them the same residue
On Tue, 31 Mar 2015 15:04:31 -0400, Andreas Schenk
andreas_sch...@hms.harvard.edu wrote:
On 3/25/2015 18:10, Kay Diederichs wrote:
On Wed, 25 Mar 2015 14:16:55 -0400, David Schuller schul...@cornell.edu
wrote:
You could check the nVidia page of officially supported displays. It
includes
Sorry to come late into the discussion, and just to mention: it would be wrong
if readers of CCP4BB get the impression that Quadro cards that support quad
buffered stereo have to be high-end. To the contrary, an entry-class Quadro
K620 together with a €250 Nvidia 3D Vision 2 compatible monitor
that a lot of manufacturers are marketing their monitors
as 3D Vision2 ready or 3D capable just because they support running at
120 Hz, even if they don't have a built-in emitter.
Best,
Andreas
On 25.03.2015 05:16, Kay Diederichs wrote:
Sorry to come late into the discussion, and just
Dear all,
release notes of the new version are at
http://xds.mpimf-heidelberg.mpg.de/html_doc/Release_Notes.html . There are
improvements in XDS for weak data and in XSCALE for serial crystallography
applications. Furthermore, the multi-segment refinement was overhauled (mainly
affecting the
Hi Veronica,
as others have said, at RT the radicals travel much further than at cryo
temperature, so your lateral shifts are probably not sufficient. But it is not
clear to me that radiation damage is to blame at all. To me it sounds like you
might have to mask your beamstop better, or you
Hi Francis,
XDS (XPLAN) just prints tables. Instead of looking in these for the range that
maximizes the total completeness, you could just minimize the total
completeness. This would maximize the intersection.
HTH,
Kay
On Tue, 24 Feb 2015 11:37:05 -0500, Francis Reyes
Hmm, placeholder for me does not seem to emphasize enough the role that this
number plays in the space group names. My understanding (but I fail to remember
where I read this ...) is that the first number is the order of the rotation
(i.e. 6,4,3,2 or 1) of the unique unit cell axis (often the
Dear Jeorge,
you'll find some information about this in
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination
. A practical and easy way is described in
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless
HTH,
Kay
On Mon, 26 Jan 2015 11:24:27
Hi Patrick,
I'd do the following:
- go to www.rcsb.org and choose Advanced Search
- choose All/Experimental Type/Molecule Type, choose Experimental Method
and set to X-ray
- click the + next to Add Search Criteria
- in the pulldown menu, choose Software and enter Phenix (leave as
contains)
-
Having configured my CentOS-7 workstation for Stereo today, I have also updated
the Stereo article in the CCP4 wiki (
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo ). It turns
out that there seem to be 8 active monitors (i.e. built-in emitter) that can be
bought in Germany
Dear Rohit Kumar,
I prefer the term multiplicity instead of redundancy because the latter has
a connotation of not really needed any more.
The relation then is
multiplicity = c * number_of_frames * oscillation_range
where the constant c depends mainly on the space group.
HTH,
Kay
On Sun,
Hi,
I have difficulties to comprehend your description. I understand
- most crystals grow in P21212, with cell a=140 , b=110, c=44
- some crystals grow in P21212, with cell a=110 , b=140, c=44
Is that correct? If so, can you refine the structures? To what R-values, at
which resolution?
The
On Sun, 28 Dec 2014 15:37:22 -0600, Igor Petrik petr...@illinois.edu wrote:
...
DIRECT BEAM COORDINATES (REC. ANGSTROEM) 0.003134 0.005401 1.020962
DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM1230.87 1260.93
DETECTOR ORIGIN (PIXELS) AT 1226.25 1252.96
CRYSTAL
is in the Installation article in XDSwiki.
best wishes,
Kay
--
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
This e-mail is digitally signed. If your
to consider a range of crystal symmetries as it is possible that some
strategies which are safe in PG 422 (say) are not in PG 2.
Best wishes Graeme
On Wed Nov 12 2014 at 10:07:10 PM Kay Diederichs
kay.diederi...@uni-konstanz.de wrote:
Hi Wolfram,
it took me a while until I realized
as it is possible that some
strategies which are safe in PG 422 (say) are not in PG 2.
Best wishes Graeme
On Wed Nov 12 2014 at 10:07:10 PM Kay Diederichs
kay.diederi...@uni-konstanz.de wrote:
Hi Wolfram,
it took me a while until I realized that you mean overfitting when you
said o-word.
You
mailto:CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] To scale or
not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS
Hello all, in a discussion
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1307L=CCP4BBH=1P=186901
on this board, Kay Diederichs questioned the effect of scaling
data
On Wed, 12 Nov 2014 15:32:04 +, Kay Diederichs
kay.diederi...@uni-konstanz.de wrote:
...
It then, in a second step, re-determines all scale factors (exactly as CORRECT
does for the individual data sets), at the exact same supporting points that
CORRECT used. (This avoids over-fitting which
against the once (CORRECT) scaled or
twice (CORRECT+AIMLESS) scaled data?
Thank you,
Wolfram
On Wed, Nov 12, 2014 at 10:32 AM, Kay Diederichs
kay.diederi...@uni-konstanz.de wrote:
Hi Tim,
this is incorrect.
XSCALE determines the relative scale and B in a first step (this is what
you describe
Tim,
I would not consider this as incorrect! What sftools calculates is R_scale, a
symmetric version of an R-value. Makes sense when comparing two data sets, or
two model amplitudes. Clearly, it gives values which differ from model R
values. But at least it defines what it prints out.
I put
Hi Florian,
a couple of things come to my mind:
a) you have to be careful in your use of XDS; if you specify space group number
18 it will use P 21 21 2 as space group, whereas you seem to use the ordering
abc and call the space group P 2 21 21. (Not long ago, I tried to bring
this up on this
Hi Gabriel,
what you want to do is called MRSAD - use the partial MR model to find the
sites, combine the phase information, and complete the model. There are hits
with the keyword MRSAD if you search on phenix-online.org
HTH,
Kay
On Sun, 5 Oct 2014 13:13:14 +0200, Jose Manuel Duarte jose.dua...@psi.ch
wrote:
Well, if you simply replace that beauty by this one:
grep ^ATOM filename.cif | awk '{print $15}' | awk '{s+=$1;} END {print
s/NR;}'
the problem with this is that it will break if there is any B-factor of 100 or
On Sun, 5 Oct 2014 18:54:16 +0100, Kay Diederichs
kay.diederi...@uni-konstanz.de wrote:
grep ^ATOM filename.cif | awk '{print $15}' | awk '{s+=$1;} END {print
s/NR;}'
the problem with this is that it will break if there is any B-factor of 100 or
higher, because then the blank will be missing
of the cell axes.
This is my last message in this meanwhile highly confusing thread.
best,
Kay
Am 03.10.14 um 17:13 schrieb Ian Tickle:
Hi Kay
On 2 October 2014 15:04, Kay Diederichs kay.diederi...@uni-konstanz.de
mailto:kay.diederi...@uni-konstanz.de wrote:
Once again, citing from
On Tue, 30 Sep 2014 13:29:02 +0100, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
Be careful: the International Tables space group number may be ambiguous. For
example sg number 18 may refer to P 21 21 2 or its permuted settings P 21 2 21
or P 2 21 21, if you follow the proper IUCr convention that
On Thu, 2 Oct 2014 11:38:08 +0100, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
How does XDS decide on eg P 21 21 2 when say c b a? The initial indexing
may decide that the cell fits a primitive orthorhombic system, but I presume
that it will then have some convention, probably a b c, since the
.
thanks,
Kay
Cheers
-- Ian
On 2 October 2014 10:25, Kay Diederichs kay.diederi...@uni-konstanz.de
wrote:
On Tue, 30 Sep 2014 13:29:02 +0100, Phil Evans p...@mrc-lmb.cam.ac.uk
wrote:
Be careful: the International Tables space group number may be ambiguous.
For example sg number 18 may refer
On Thu, 2 Oct 2014 16:00:30 +0100, Ian Tickle ianj...@gmail.com wrote:
On 2 October 2014 13:51, Kay Diederichs kay.diederi...@uni-konstanz.de
wrote:
I don't see any sticking to initial indexing as worthwhile to worry
about, since in the first integration, P1 is often used anyway
Hi Jürgen,
I just checked, and generate_XDS.INP works for me as it should.
My Mac is also running 10.9.5 since Sep 20, and it updated the Command Line
Tools (OS X 10.9) to Version 6.0 on the same date.
generate_XDS.INP certainly depends on the Command Line Tools so you may want
to make sure
Charles,
your posting does not provide enough detail to base advice on.
First of all, it's a warning and probably there is no reason to worry - but one
has to look at the .LP files to be sure.
Second, it is not clear whether the warning is printed by IDXREF or by
INTEGRATE.
If it's IDXREF
Hi Yarrow,
XDS does the following:
Data is divided into resolution shells and a straight line A - 2*B*SS is fitted
to log(I), where
SS = mean of (sin(THETA)/LAMBDA)**2 in shell
I= mean reflection intensity in shell
BO = (A - logI)/(2*SS)
The value of B is reported (above the
Hi Mike,
this requires scaled but unmerged data, and there are few programs that support
unmerged MTZ files. So it is probably necessary to write your own program(s),
that process XDS_ASCII.HKL or XSCALE.HKL. Or you start by extracting from
AIMLESS code.
HTH,
Kay
On Tue, 12 Aug 2014
Rhys,
since you can obtain good native crystals, I would try Xenon phasing. I have
recently heard several success stories at the Australian Synchrotron, and it
just seems to be a straightforward and rational way.
Molecular Replacement should also be an option. I did this with beta-barrel
Hi Wolfram,
just want to point out that the mathematics of what you want to do is
conceptually really simple - see
http://en.wikipedia.org/wiki/Weighted_arithmetic_mean#Dealing_with_variance .
Programs like aimless or others (e.g. xdsconv could also be used) just
implement the two formulas
Hi Vijay,
I think your data may be good enough to solve the substructure and get phases,
but
1) you should be using the latest versions of SHELXC SHELXD SHELXE - it seems
you are using SHELXD-2006/3 .
2) you could try more cycles (100 is on the low side)
3) you might want to try searching for
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 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
On Mon, 19 May 2014 18:18:46 +0200, Almudena Ponce Salvatierra
maps.fa...@gmail.com wrote:
Dear all,
I am looking for
Dear Tony,
I renamed your LP_01.tmp to INTEGRATE.LP and ran XDSGUI - this shows nicely
that after frame 150 things fall over.
So pls try the recommendations in the Difficult datasets article of XDSwiki.
Normally you should not need to run two processing jobs; just prevent
refinement from
Hi Thomas,
strictly speaking, there is no need to re-process the data (because it wouldn't
change the data anyway). It may even be that the data beyond 2.55A contain some
signal (CC1/2 should tell you about that), which future refinement programs can
use - so you could deposit at the RCSB all
including the
development of advanced beamline instrumentation and crystallographic
methods, as well as structural biology projects in collaboration with
the Biomolecular Research Group at PSI and external partners.
In collaboration with Prof. Kay Diederichs at University of Konstanz, we
Hi,
please post the pointless table Analysing rotational symmetry in lattice
group P 6/m m m. This gives a quite clear information about the
presence/absence of rotational symmetry axes.
Look at at the following example
Analysing rotational symmetry in lattice group P 6/m m m
On Thu, 8 May 2014 16:56:01 +0200, Christophe Wirth
christophe.wi...@biochemie.uni-freiburg.de wrote:
Dear all,
To add another bit to the discussion, I would say that an increase of Rmerge
and Rmeas is just expected in such a case, isn't it?
According to your tables, in P1, the multiplicity
Hi Roberto,
for my taste the answers so far have not mentioned (or I did not understand
them) that there is a distinction between indicators of the precision of merged
data, and those for the precision of unmerged data.
It is not possible to directly compare (or equate) indicators of one
On Fri, 18 Apr 2014 12:33:30 +0200, Bernhard Rupp hofkristall...@gmail.com
wrote:
[There is] a distinction between indicators of the precision of merged data,
and those for the precision of unmerged data.
Let's take a step back - definitions matter:
(i) We have multiple observations of the
Hi Ed,
your example seems to be designed to show that the average of reciprocal values
is not the same as the reciprocal of an average value? If that is what you are
alluding to, then please not that the (relatively narrow) Wilson distribution
of intensities has the effect of making the
yes, and
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_adx does
this for all frames contributing to SPOT.XDS.
HTH,
Kay
On Tue, 15 Apr 2014 11:38:23 +0100, T. Nakane tn...@cam.ac.uk wrote:
Dear Francis,
You can visualize SPOT.XDS with adxv.
Since column 3 of SPOT.XDS is
It means that there exists a technical problem that probably has nothing
directly to do with your data and XDS: the program tried to read data that
could not be read.
I would guess that the disk is full, or your quota exceeded.
Hope this helps,
Kay
On Tue, 1 Apr 2014 17:28:48 +0200, Almudena Ponce Salvatierra
maps.fa...@gmail.com wrote:
sorry, I missed this part of the error message:
!!! ERROR !!! AUTOMATIC DETERMINATION OF SPOT SIZE PARAMETERS HAS FAILED.
YOU MAY RESTART THIS STEP AFTER SPECIFYING VALUES IN XDS.INP
FOR:
Hi,
I added some explanation for the XSCALE output to the XDSwiki at
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsconv#explanation_of_typical_output
.
hope this helps,
Kay
Dear all,
today we re-opened account creation for CCP4wiki (and XDSwiki).
It had been closed since we were hit by spammers (like e.g. PyMolwiki),
but we recently discovered a method that helps to prove that the account
is really created by a a human being - as opposed to a computer program
oops, thanks for correcting me!
Kay
On Sun, 23 Feb 2014 11:28:31 +, Harry Powell ha...@mrc-lmb.cam.ac.uk
wrote:
Hi
Kay means, of course, the ACA meeting in Albuquerque, not the IUCr in Montreal!
I agree with the general points that Mark makes. For the basic problem to find
out whether the model quality (and R-values) is limited by the data quality,
you can compare CCwork with CC* - if CCwork is significantly lower than CC*,
then this means that either your model could in principle be
Projects and problems like this are clearly a justification for asking to
deposit not only the results from data processing, but also the raw data
frames. These would allow developers to improve the models underlying their
algorithms, and to find those corner cases where the algorithms break.
On Fri, 14 Feb 2014 17:25:36 +, Derek Logan
derek.lo...@biochemistry.lu.se wrote:
Hi Tim,
I would actually recommend using pointless (or xprep) instead of
xdsconv. It is much easier to use and maybe even less error prone.
I take the point about pointless but XPREP is commercial software
On Sat, 15 Feb 2014 09:50:43 +, Kay Diederichs
kay.diederi...@uni-konstanz.de wrote:
pointless is a good program, and I also use it,
to clarify: I use pointless for space group determination. I don't use it for
producing multi-record MTZ files, since I use XDSCONV.
) and it vanishes forever. Are people suggesting we abandon
an empirically proven mechanism merely to save me the need for this tiny
hand-movement?
phx
On 14/02/2014 07:19, Kay Diederichs wrote:
Nat,
that's why I set up the CCP4 wiki at
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php
Nat,
that's why I set up the CCP4 wiki at
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Main_Page ! The
idea is that everybody benefits: experienced crystallographers/biologists can
concentrate on the new and difficult questions coming up on the bulletin board,
and novices find
Dear Shanti Pal Gangwar,
based on the information you give, this does not sound like solved structure
to me.
By the way, the ACA conference at the end of May will feature a session data
processing with the pros, where difficult projects will be analyzed, and
hopefully structures like this
Dear Bert,
as Dirk has pointed out, if P622 is the correct space group, then the twinning
statistics printed out if you process in P6 are meaningless.
Intensity statistics, like the ratio of I^2/I^2 , can be misleading if
there is (e.g. pseudo-translational) NCS in the crystal; however, the
Hi Shane,
some crystal forms of trimeric AcrB (a multi-drug resistance secondary
transporter) have 3 (or 6) monomers in the ASU and these are substantially
different, which suggests how the protein functions.
One reference is e.g. Seeger et al. (2006) Structural Asymmetry of AcrB
Trimer
On Fri, 13 Dec 2013 19:44:44 +, D Bonsor dbon...@ihv.umaryland.edu wrote:
Dear D,
I agree with Tim and Jürgen that
a) the map after Phaser, and before refinement is the most unbiased and should
be used for sequence assignment.
b) there may be a sequence register shift error that is
I'm using a 24 BenQ XL2420TX (emitter builit-in; price 500€) monitor connected
to the DisplayPort of a Quadro FX 380 card. Works very well on 64bit
ScientificLinux 6.4 with the kmod-nvidia driver from ElRepo.
Please also see
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo .
Dear Niu,
concerning XDS: there is no way, using just XDS.INP, to force the IDXREF step
to use a cell that is not compatible with the reflections that COLSPOT found.
But I can think of two ways to reach your goal (even if I believe that
crystallographically it makes no sense to ignore every
-handicapped times.
It is entirely possible that all this is exactly what you said, just
with different wording. But I guess more wording is still needed given
that people keep asking about Rmerge.
Cheers,
Ed.
On Tue, 2013-11-19 at 14:22 +, Kay Diederichs wrote:
Hi Jim,
of course the issue
On Mon, 21 Oct 2013 23:28:48 -0500, Stefan Gajewski sgajew...@gmail.com wrote:
...
5) tetartohedral twinning? what refinement software is able to deal with
that?
Refmac
HTH,
Kay
Dear Daniel,
A very good question. I have seen R_d plots jumping up and down, most often in
low-symmetry space groups. I think the mountains are due to residual
systematic differences between symmetry-related observations, differences that
the scaling could not compensate for whatever reason.
Hi Ursula,
if you look at the Wilson plot, you see a minimum near 6A resolution. This
means that in the range 7-5A, intensities are low, and Rsyms are therefore
elevated.
best,
Kay
On Mon, 14 Oct 2013 11:52:03 -0700, Ursula Schulze-Gahmen
uschulze-gah...@lbl.gov wrote:
Here is some more
Are you certain that the data are not twinned?
HTH
Kay
at 1.7 � it is 239%. Do I
have enough data to justify 1.7 � resolution? Are those Rfactor values are
justified with this resolution?Thanking you
DCB
On Sun, Oct 13, 2013 at 12:03 PM, Kay Diederichs
kay.diederi...@uni-konstanz.de wrote:
Are you certain that the data are not twinned?
HTH
The HKL2000 stats look very untypical to me. I wonder what the completeness
is.
For the XDS processing, have you tried the hints given in the Optimization
article in XDSwiki, in particular recycling of GXPARM.XDS and using the
*_E.S.D. parameters as found in INTEGRATE.LP ?
According to your
I forgot: you should be using FRIEDEL'S_LAW=TRUE
-konstanz.de/stellen or by contacting Mr. Hanns Fahlbusch
by e-mail: hanns.fahlbu...@uni-konstanz.de .
=
An application cover form (PDF) can be downloaded from
http://www.uni-konstanz.de/stellenangebote/?cont=stellauswseite=2013/136id=3
.
--
Kay Diederichshttp
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