On Thu, 16 May 2013 18:25:35 +0100, Frank von Delft
frank.vonde...@sgc.ox.ac.uk wrote:
Dear Gerard - thanks, very informative! Two questions:
1.
Do I understand correctly, that you say XDS will throw together for
integration counts from many images even if they're spaced widely
throughout the
... is available for academic users at
http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/
Please note that there are some incompatibilities; most notably, the new
format of XPARM.XDS is different so that the new INTEGRATE does not work
with an old XPARM.XDS.
best,
Kay
smime.p7s
Sorry, Wolfgang Kabsch has decided against it.
Kay
Jacob Keller j-kell...@fsm.northwestern.edu schrieb:
Any thoughts of making a Windows executable? Might help a lot of
users
JPK
On Wed, May 29, 2013 at 4:20 PM, Kay Diederichs
kay.diederi...@uni-konstanz.de wrote:
... is available
and I
would like to learn about these. In particular, Mac experts please tell me how
to solve the problems explained at the bottom of the Wiki article ...
thanks,
Kay
--
Kay Diederichs
http://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.de Tel +49
Dear Ed,
AFAIK James Holton found the same issue, and a similar problem also existed in
XDSCONV. In my view, it is an example of the problem that most programs so far
have dealt with weak data in a suboptimal way, and have undergone little
testing with such data.
The latest version of XDSCONV
Hi Frank,
older versions of XDSCONV, for datasets with weak high-resolution data, printed
a long list starting with:
SUSPICIOUS REFLECTIONS NOT INCLUDED IN OUTPUT DATA SET
(at most 100 are listed below)
SUSPICIOUS REFLECTIONS NOT INCLUDED IN OUTPUT DATA SET
(at
Hi Jeff,
what I did in XDSCONV is to mitigate the numerical difficulties associated with
low h (called Score in XDSCONV output) values, and I removed the h -4
cutoff. The more negative h becomes, the closer to zero is the resulting
amplitude, so not applying a h cutoff makes sense (to me,
Hi James,
Concerning XDSCONV, I cannot reproduce your plot. A Linux (64bit) program
test_xdsconv which allows to input I, sigI, I, and mode, where
I: measured intensity
sigI: sigma(I)
I: average I in resolution shell
mode: -1/0/1 for truncated normal/acentric/centric prior
is at
On Wed, 19 Jun 2013 14:19:19 +0100, Kay Diederichs
kay.diederi...@uni-konstanz.de wrote:
I wonder if problem b) is why Evans and Murshudov observe little contribution
of reflections in shells with CC1/2 below 0.27 in one of their test cases,
which had very anisotropic data.
sorry, forgot
+0100, Kay Diederichs wrote:
Hi Jeff,
what I did in XDSCONV is to mitigate the numerical difficulties associated
with low h (called Score in XDSCONV output) values, and I removed the h
-4 cutoff. The more negative h becomes, the closer to zero is the resulting
amplitude, so not applying a h
Douglas,
the intensity is negative if the integrated spot has a lower intensity than the
estimate of the background under the spot. So yes, we are not _measuring_
negative intensities, rather we are estimating intensities, and that estimate
may turn out to be negative. In a later step we try
have
reported a negative integrated intensity to begin with.
I also understand that (Iobs-Icalc)^2 is not the actual refinement target, but
the same point applies, and the actual target is based on a fundamental
Gaussian assumption for the Is.
On Jun 20, 2013, at 2:13 PM, Kay Diederichs
please share the Gnuplot magic for doing so?
thanks,
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
Hi Peter,
my estimate of the distance between the peaks would be based on bond distances
and about twice that of Dale, but I agree with his general conclusion. Either a
reflection (roughly in the h 0 0 direction) is stronger than it should be
(ice?), or a very strong reflection was considered
that should have been
sort -gk5 XDS_ASCII.HKL | more
(I should have tested before posting!)
best,
Kay
On Tue, 25 Jun 2013 09:16:52 +0100, Kay Diederichs
kay.diederi...@uni-konstanz.de wrote:
...
b) inspect the outliers in XDS_ASCII.HKL with something like
sort -nk5 XDS_ASCII.HKL | more
Hi Sebastiano,
sorry, I don't see immediately what's wrong. The console seems to show the XDS
output of an INTEGRATE job that only looked at a single (judging from the small
number of reflections ...) frame (number 10, I'd guess; you could check this if
you scroll up a bit). Could you please
to me so that they can be fixed!
best,
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
Hi Stefan,
you write
The diffraction pattern looks great, the 3.4A reflections are visible by eye
and the edge of the detector is about 2.8A.
and for the 3.4A data Mean((I)/sd(I)) in the highest shell is 2.3 .
I'm tempted to ask: what prevents you from using higher resolution data to,
say,
Hi Sam,
one possibility: there was a little bug in a recent build of XSCALE that
resulted in one of the header lines of the output file to not specify the name
XSCALE - it wrote:
!GENERATED BY: July 4, 2012
and it should have been
!GENERATED BY: XSCALE (VERSION March 30, 2013)
The lack of
Hi Sam,
Your version of XSCALE is OK since it prints out the string XSCALE (the date
is OK - my fault!).
Rp.i.m. is indeed not listed in XSCALE.LP.
Best,
Kay
--
Diese Nachricht wurde von meinem Android-Mobiltelefon mit K-9 Mail gesendet.
Hi,
I completely agree with what Andrew writes. It's very easy: negative CORR means
that the reflection profile after background subtraction has a negative
correlation coefficient with the standard profile. How can this happen? Well,
this situation occurs when the reflection is very weak and
I have a very different experience with NFS: we are using Gigabit Ethernet, and
a 64bit RHEL6 clone with ECC memory as a file server; it has RAID1 ext4 home
directories and RAID6 ext4 for synchrotron data. We have had zero performance
or reliability problems with this in a computer lab with ~
@JISCMAIL.AC.UK (on behalf of Kay
Diederichs kay.diederi...@uni-konstanz.de)
Subject: Re: [ccp4bb] Advise on setting up/ maintaining a Ubuntu cluster
To: CCP4BB@JISCMAIL.AC.UK
I have a very different experience with NFS: we are using Gigabit Ethernet,
and a 64bit RHEL6 clone with ECC memory as a file
-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
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
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
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
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.
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 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
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 .
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
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
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
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
) 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
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.
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.
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!
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
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
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:
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
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
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
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
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
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
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 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 Dale,
my experience is that high-B regions may become visible in maps only late in
refinement. So my answer to the original poster would be - both global
reciprocal-space (phase quality) and local real-space (high mobility) features
contribute to a region not appearing ordered in the map.
) know; in such a case pls consider sharing the data
(confidentially) with us that allow to reproduce the problem.
If you wish to be notified of future new versions, please send me an
email and I'll add you to my list.
thanks,
Kay
--
Kay Diederichshttp://strucbio.biologie.uni
Hi,
there are two points in Herman's post that I'd like to comment upon:
1) in case of XDS, there are two modes of reporting the completeness: one is
triggered with FRIEDEL'S_LAW=TRUE, and the other with FRIEDEL'S_LAW=FALSE.
Obviously the reported completeness will differ between these two
Dear Michael,
the purpose of our paper (http://www.sciencemag.org/content/336/6084/1030) was
to develop and document methods that enable to check for yourself what the best
high resolution cutoff is - no rules of thumb are necessary!
However, repeated use of the paired refinement technique (3
Hi Jürgen,
I'd be willing to share my datasets obtained since 1999, which I have online.
Older ones are on tape and it would be a significant effort to retrieve them,
if at all possible.
best,
Kay
Hi Vincent,
my advice is: if in doubt, scale at the highest of those resolution choices.
This way you don't have to go back to scaling later. There is no harm in using
the highest resolution. Don't let yourself be fooled by Rmerge.
best,
Kay
On Thu, 19 Jul 2012 17:52:14 +0200, vincent Chaptal
Hi Narayan,
there's nothing wrong with using data with I/sigmaI 2.5, Rsym 224.3 % for
multiplicity 7.8 and completeness 98.2 %.
However, when you discarded frames you might have made the data worse - one
should only reject data if they deviate systematically (e.g. from radiation
damage).
On Tue, 17 Jul 2012 06:26:39 +, LEGRAND Pierre
pierre.legr...@synchrotron-soleil.fr wrote:
Hi Jason,
To answer your initial question about overlaps versus finer slicing, you can
get a good description of the problem in Fig10
of Z. Dauter article Data-collection strategies (open
Hi Jason,
I looked at the part of FRAME.cbf you posted, and I'd say it looks ok (i.e.
nothing to worry about).
Some overlap of a reflection doesn't matter much; if its full profile is not
available then INTEGRATE replaces the missing intensity by an estimate based on
the known fraction of
myself, at least not with
reasonable effort ...
thanks a lot,
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
Dear Marcus,
I have a few comments:
- we do not suggest any fixed value (like 0.125) for a CC1/2 cutoff. One reason
why a fixed value should not be carved in stone is that future data processing
and refinement programs might extract more information from the weak data than
current ones do.
Dear all,
thanks for the many answers sent privately or posted to CCP4BB! I cannot answer
them all individually, and I also cannot answer the questions that some people
asked, since I have not yet heard back from my colleague whose experiment that
is. But I'm sure there are some options for
Hi Fred,
on today's PC hardware, a 64bit Linux should be used.
We have been using
coot-0.7-pre-1-revision-3965-binary-Linux-x86_64-centos-5-python-gtk2 on our
64bit SL 6.3 systems without problems.
I just now installed
coot-0.7-pre-1-revision-4360-binary-Linux-x86_64-centos-6-python-gtk2 on
Dear Theresa,
concerning your first sentence which is a bit short to my taste: if you index,
you expect to find the cell parameters. These enable you to process the
dataset. At the end of processing, a decision has to be made about the
spacegroup. Only then structure solution can be tried,
Dear Iris,
just to add to Fred's posting: since XDS Version June 2, 2008 re-indexing is no
longer necessary if REFERENCE_DATA_SET is used - XDS then does the re-indexing
automatically in the CORRECT step. This makes it very easy to avoid the problem
of alternative indexing in space groups like
Dear Xinghua,
it seems that you have hit a bug: assert violation indicates that an internal
error has occurred, i.e. some situation was hit that the program is not
prepared to handle.
There must be something very special about your dataset - maybe a very small
number of reflections, maybe only
Dear Jay,
I met Wladek Minor last week and I understood that there would be a version of
SCALEPACK this week which outputs CC1/2. So ask the HKL crew, I'd suggest.
Furthermore, the latest nightly builds of Phenix (since dev-1208) have
mmtbx.cc_star which calculates CC1/2 and other quantities
On Fri, 30 Nov 2012 17:27:41 -0500, Sarathy Karunan Partha
sarathyus...@gmail.com wrote:
Dear all,
Here is the XSCALE.LP output after scaling for the izit dye stained
crystak. Sorry for attaching the .INP file.
Sarathy
On Fri, Nov 30, 2012 at 4:19 PM, Sarathy Karunan Partha
Dear Sebastiano,
sorry, it is not possible. Indeed, only XCSALE allows you to define the
resolution ranges yourself.
HTH,
Kay
On Tue, 15 Jan 2013 16:22:14 +0100, Sebastiano Pasqualato
sebastiano.pasqual...@gmail.com wrote:
Hi all,
I was wondering if XDS allows to change the number of
Sebastiano,
CORRECT does scale the data. XSCALE is only needed for two or more datasets, or
if other requirements exist - you named one.
The two varieties of FRIEDEL'S_LAW differ in their rejections!
HTH,
Kay
Sebastiano Pasqualato sebastiano.pasqual...@gmail.com schrieb:
Thanks to Kay
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/R-factors would be
a start ...
HTH,
Kay
On Fri, 18 Jan 2013 09:37:12 +0530, Teri Arman teriar...@gmail.com wrote:
Hi, it would be nice if you highlight different type of R-factors used in
the literature. I like to understand various
Hi Andrey, Eugene and others -
it is time to say that this new system is extremely useful, and so easy to use
at the same time! Gone are the times when one had to worry about manually
updating parts of CCP4.
I just wonder why there should ever be a need for a CCP4 6.4.0 release; a
rolling
On Mon, 11 Mar 2013 11:46:03 -0400, Ed Pozharski epozh...@umaryland.edu wrote:
...
Notice that I
only prepared one sample, so if on that particular instance I picked up
4.8ul and not 5.0ul, this will translate into systematically
underestimating protein concentration, even though it could have
Dear Herman,
some pros and cons are documented at
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Wishlist#Would_be_nice_to_have
, and the workaround is at
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Ice_rings . These
XDSwiki articles are old, and nobody has
On Thu, 21 Mar 2013 08:28:27 +, herman.schreu...@sanofi.com wrote:
Dear Tim,
It could be that COLSPOT does not rely on experimental setup parameters.
However, XDS must have reasonably close starting values for distance, direct
beam position etc., otherwise the autoindexing would fail, so
is painful, and a lot of
additional work! But man twinning is always enlightening reading.
Kay
--
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
are suitable for deciding about the resol cutoff.
HTH,
Kay
--
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
smime.p7s
Description: S/MIME
.
Biochemistry and Molecular Biology Dept.
201 Althouse Lab., University Park
Pennsylvania State University, PA16802
Tel. (814)863-8703
Fax. (814)865-7927
--
--
Kay Diederichs
the rotation matrix
a11 a12 a13
a21 a22 a23
a31 a32 a33
then
(a11 + a22 + a33 - 1) / 2
is the cosine of the angle you're looking for.
HTH,
Kay
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie
. The gui pops up normally. But
when I try to run a process the gui shows the process as starting and
it hangs there never switching to running. And there is no log file
available in the gui as well. Any ideas?
Thanks,
John Bruning
--
Kay Diederichs http
occupancy or high B factor or mutating to Ala help decrease Rfree
substantially? If not, is there any better strategies to lower down R
factors? I will be very appreciative if you have any suggestions or
comments to offer. Thank you in advance.
Best,
Joe
--
Kay Diederichs
group of the processed data, and it is
definitely P21212.
Does anyone have any suggestions of what I may be doing wrong?
Thanks in advance for your help.
Kind regards,
Satinder
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED] Tel +49 7531
this idea, and reduces the potential benefit.
Kay
For hierarchies, parallel efforts, GPL, I agree. ;-)
Tassos
PS Kay, your digital signature has some trouble for me - cant read it -
you may want to know.
On Jul 27, 2007, at 11:14, Kay Diederichs wrote:
Kevin Cowtan schrieb:
Yes
Anastassis Perrakis schrieb:
I also have to say that (for once!) I dont agree with Kay. I have tried
in the past to refine against datasets processed with different
programs, and I know people that do that a lot; the differences are
minor at best (1-2 % Rfree, mostly differences are in the
Kevin Cowtan schrieb:
Yes, that is our intention. CCP4 would probably be at the third level of
a hierarchy including:
Macromolecular crystallographic techniques
Structure solution, analysis and visualisation software
The CCP4 suite
Kevin,
why does/will/should the CCP4 Wiki have a
of the
ripples.
best,
Kay
--
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
smime.p7s
Description: S/MIME Cryptographic Signature
.) to develop new methods to make their point. Hopefully this is
only a starting point.
best,
Kay
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457
and
usermode software. Intel CPUs are quite different from AMD ones in that respect.
HTH,
Kay
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
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