Hi Tommi,
two remarks:
1) setting the PATH on macOS: put the line
export PATH=/Users/xxx/XDS-Apple_M1/:$PATH
into ~/.zshrc
2) you don't have to convert .hdf5 files to .cbf ; just use the
LIB=/some/directory/dectris-neggia-Apple-arm64.so
line in XDS.INP, and give the master file in the NAME_TEMPLA
Dear all,
just to let you know that the latest XDS BUILT=20250327
for academic users is available from https://xds.mr.mpg.de
@users of the 20230630 version: this will expire on April 1, so pls consider
upgrading.
Best wishes,
Kay
Dear Yves, and all respondents on the list and privately,
thank you for your answers!
I've understood the message that we need to keep compiling XDS (and XDSGUI) on
CentOS7 for a while.
Maybe I'll ask again in one year from now.
Best wishes,
Kay
P.S. Those of you running an operating system wi
a set of
relatively new tools and compilers, up to GCC 12, for RHEL7. It might
be the best solution unless you need GCC 13+.
Marcin
On Wed, Mar 26, 2025 at 6:18 PM Kay Diederichs
wrote:
Dear all,
when compiling XDS or any other software distributed as binaries, the question
comes up whether it
Dear all,
when compiling XDS or any other software distributed as binaries, the question
comes up whether it will be compatible with the users' operating system.
For Linux, the main stumbling point is the GLIBC version: a binary compiled on
a relatively new distribution (like Redhat Enterprise L
Hi Harry,
can't resist to suggest 1PPR, peridinin-chlorophyll-protein from Amphidinium
carterae, in which each polypeptide constitutes a scaffold with pseudo-twofold
symmetry surrounding a hydrophobic cavity filled by two lipid, eight peridinin,
and two chlorophyll a molecules.
Best wishes,
Ka
I tried
https://you.com/search?q=calculate%20the%20impact%0Afactor%20of%20*Nucleic%20Acids%20Research*%2C%20excluding%20citations%20of%20articles%0Apublished%20in%20the%20special%20issues%20dedicated%20to%20databases%20and%20web%20servers&fromSearchBar=true&tbm=youchat
and this says:
"
Impact Fact
Hi Tom,
What happens if you enter these commands in a terminal window, just on their
own?
If the same error is shown, you could look at the scripts.
Another idea: did you install CCP4 while a USB or other device was plugged in ?
And it is trying to use that device?
Best wishes,
Kay
On Sat
perhaps the user could select whether to do the
>background estimation using either the old or new way (with or without
>local fitting), via the XDS.INP file?
>
>Thanks again,
>John
>
>On Sat, Oct 5, 2024 at 11:27 AM Kay Diederichs <
>kay.diederi...@uni-konstanz.de> wrote:
John Bacik wrote:
> Dear Kay, do have any more information or would you mind explaining a bit
> more what changes in the XDS code led to these significantly different
> statistics in the different XDS versions?
>Thanks,John
>
>
>
>On Wednesday, October 2, 2024
Dear Yimin,
similar shortcomings were observed with other datasets with XDS VERSION Jun 30,
2024 that was posted on July 23 at
https://xds.mr.mpg.de/html_doc/downloading.html . I am sorry for that! The
testing of that version had not uncovered this problem.
Corrected binaries were posted today
Dear XDS users,
just a heads-up: non-commercial users of XDS should update their binaries;
download link and release notes are at https://xds.mr.mpg.de/ .
A few little things have changed so you may have to adapt your scripts.
Best wishes,
Kay
##
Hi Charlie,
I don't see a relation between P212121 and F222 that would arise from some kind
of duplication or halving of axes. These spacegroups have different super- and
subgroups (see
https://wiki.uni-konstanz.de/xds/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_the
Dear Jordi,
for XDS/XSCALE users, there is XDSCC12 (see
https://wiki.uni-konstanz.de/xds/index.php/Xdscc12 ).
It is integrated in XDSGUI (statistics tab) where it shows, for a single
XDS_ASCII.HKL, how much batches of the run contribute towards CC1/2 of the
dataset, i.e. what there delta-CC1/2
Hi Matt,
I guess that the datasets have the same spacegroup and very similar cell
parameters?
And that you have two similar models that you obtained by refining against the
datasets?
What you can do is to find out which dataset gives the better model, and is
therefore better
(i.e. generally
Dear Gerard,
I disagree in two points with what you write:
On Mon, 10 Jun 2024 19:15:43 +0100, Gerard Bricogne
wrote:
...
> Much worse, in fact: that quantity (I_avg/sigI_avg) makes no sense
>whatsoever in statistical terms. It must be a relic of a quantity that may
>have seemed like a good
Hi Aline,
I see nothing wrong with / being 0.83
Mean((I)/sd(I)) is , which is not the same as / so you cannot
expect the numerical values to be the same (even in case the resolution shell
definition is identical), although the two values usually do not differ much.
Take for example two reflect
Hi Catherine,
I think you meant to write "giving high R-factors".
To add to what Esko and Eleanor wrote: There is nothing wrong with your data or
spacegroup or refinement; it is just that the tNCS produces two sets of
reflections: half or your reflections are statistically "normal" (as if no t
On Fri, 17 May 2024 08:27:02 -0700, James Holton wrote:
...
>
>With a bit of a caveat on how many photons/pixel you need for stable
>background subtraction. XDS starts having issues around 1 photon/pixel
>or less, and DIALS claims to be able to get to 0.01 photons/pixel, but I
>have not personall
Dear Martin,
one suspicion comes to my mind: could it be a "computer problem" in the sense
that you are using different computing environments for the two calculations
(arpWarp vs standalone refmac5)? That could lead to different decimal
separators ("." versus a ","; see
https://en.wikipedia.o
Hi Harry,
same here. Actually we skipped RHEL8 and its alternatives, so moved directly
from CentOS7 to Rocky9. We are happy with that decision.
Best wishes,
Kay
On Fri, 26 Apr 2024 15:57:46 +, Andy Purkiss
wrote:
>Hi Harry,
>
>We've been migrating to Rocky Linux as it is built on RHEL in
good detective work indeed!
Kay
On Tue, 16 Apr 2024 14:40:15 +0100, Yehudi BLOCH
wrote:
>Dear Adewumi
>
>I'm afraid the 85% complete dataset is a contaminant as well.
>PDB 2r6s and related entries for E.coli Gab protein have near identical unit
>cell parameters. The autoprocessed (?) .mtz file
of Biochemistry, Genetics, and Microbiology
Structural Biology Group,
Room 3-7, Agricultural Sciences Building,
University of Pretoria
c/o University & Lynnwood Roads
Hatfield
Pretoria
0083
Cell: +27638643131
South Africa
--
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
Hi Venkat,
so what I suggested is not the real problem.
To get to the bottom of this, I suggest you show the logfiles from REFMAC5 and
phenix.refine, and the output of the following command:
mtzdmp experimental_data.mtz >& mtzdmp.log
run on the command line.
Please upload the files to some clou
Hi Venkatareddy Dadireddy,
do the unit cell parameters of your MTZ file and PDB file agree exactly ?
Take for example a cell of (100,110,120,90,90,90) in the header of the MTZ
file,
and (97,110,120,90,90,90) in the CRYST1 line of the PDB file.
In this example, the (50,0,0) reflection would be
Hi Len,
a possible theory: your crystals may be macroscopically twinned, i.e.
consisting of single crystals attached to each other in the way that the twin
operation describes.
At your home source, you employ a rather big beam that hits more than one
single crystal. So the data appear twinned.
Fred,
nobody would be offended if you'd just post your SHELXL .ins file here; there
are enough experienced crystallographers to spot the mistake.
Best would be if you could pare it down to small size, but such that it is
still reproducible (my own experience is that this almost always makes me
Hi Rafael,
I guess that you ask for a number to be used as a "cutoff", but there is no
such number. Completeness is measured on a continuous scale, typically from 0
to 100%. Higher is better, of course. Resolution shells with low completeness
just carry proportionally less information about the
Hi Vaheh,
for this purpose, I use
pointless hklin refmacXY.mtz < wrote:
...
>This might be a silly question, but I do not know the answer: After refinement
>in P1 how do I distinguish which axis is crystallographic and which one in
>non-crystallographic?
>
>Vaheh
##
Hi Marco:
short comments (I sent you also a private mail):
- the stats in CORRECT.LP look ok, but I'd like to know what ISa is, and what
the number of outliers is ("misfits"). Seeing the delta-CC1/2 stats as a
function of frame number is also useful for judging e.g. the radiation damage -
this
Hello Marco,
this sounds to me like there is space group confusion in the sense that if you
use the output model from Phaser, it may say space group P22121 (with a wrote:
>Hello Todd, I get the best solution for p22121 space group after MR with an
>LLG score of 640 from phaser. and the Rfree is
Hi Maggie,
I have CCP4 version 8.0 on my Mac and it does have the file
/Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2/bin/i2run
If I run it without arguments, it says
CCP4 /Applications/ccp4-8.0
ccp4i2 version 1.1.0
ccp4i2 source revision 6539
F
Dear readers of CCP4BB,
for various reasons I don't feel inclined to reply to this.
I'm really sorry,
Kay
On Tue, 13 Feb 2024 15:25:03 +, Gerard Bricogne
wrote:
>Dear Kay,
>
...
To unsubscribe from the CCP4BB list,
Dear Arpita,
I'll try to answer below -
On Mon, 12 Feb 2024 13:57:28 +0530, Arpita Goswami wrote:
>Dear all,
>
>Greetings to all! Apologies if the below query seems very naive!
>
>This is to query on the consensus to use Staraniso for pdb submission. We
>have solved a structure previously at 2.
Dear Gottfried,
after cad, you need to
uniqueify -f FREER
Hope this helps!
Best wishes,
Kay
On Fri, 9 Feb 2024 18:54:25 +0100, Palm, Gottfried
wrote:
>Dear all,
> I have problems preparing my experimental data (XRD) for
>deposition. I have two mtz files, which work well for refmac5, wit
e to
http://www.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi does not respond
- "othercell" is also useful but for other purposes, and it is in CCP4
thanks to all who responded so quickly!
Kay
On Wed, 27 Dec 2023 18:38:15 +, Kay Diederichs
wrote:
>Dear all,
>
>I seem to remember a
Dear all,
I seem to remember a tool called "nearestcell", a command-line equivalent of
the Oxford Nearest-Cell web server which appears to be offline.
However I cannot locate that tool in CCP4 nor elsewhere. Can anyone point me to
it or give alternatives, please? (I did try the PDB's advanced se
0 and Centos7 logfiles in the attachment.
Your Best,
Zhihong xin
From: Kay Diederichs
Date: 2023-12-19 02:35:50
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] contrast missing issue>Dear Zhihong Xin,
am I understanding correctly that you get very different output, using CentOS7
Dear Zhihong Xin,
am I understanding correctly that you get very different output, using CentOS7
versus using Windows10, for the exact same calculation? In that case, it seems
surprising (to me at least) that it is only the contrast value that is affected.
There is not much to work on, from your
Hello Devbrat,
your project is difficult and there is no magic bullet to solve its problems.
Your approach is good because it always pays off to process
the data carefully.
In this respect, let me make a few comments.
1) you don't say why you call the diffraction patterns "multi-lattice". What
Hi Sam,
What you write does not sound good to me.
Did you have Phaser check "all possible [spacegroups] in same pointgroup" (this
is how it is called in ccp4i)? P321 is quite rare, compared to P3121 and P3221.
If you miss a screw axis, you will not find a solution.
An R-factor of 50% does not at
Hi Mandar Bhutkar,
ok now that new table shows that your data are at least reasonable.
Nevertheless it pays off to optimize the data processing, and the high
resolution cutoff ...
Is it publishable? Not possible to say from your table. If I were a reviewer,
I'd want to see the raw data and the
Hi Mandar Bhutkar,
the data statistics (Rmerge, I/sigma, CC1/2) appear to be poor.
So you may want to check the data processing; try with different programs, and
perhaps with help from experienced people in your group.
You could ask for help here, but you should give more details - what exactly
Dear Jorge,
the plots available from XDSGUI in the "statistics" tab are helpful in this
respect (see https://journals.iucr.org/j/issues/2023/05/00/yr5110/index.html
and in particular Fig 4). In particular, delta-CC1/2 and R_d are sensitive to
radiation damage.
Pls note that sometimes a few ite
There is one more - https://mxrdr.icm.edu.pl/
HTH,
Kay
On Wed, 18 Oct 2023 19:23:06 +0300, JEROME JOHNSON wrote:
>Hello all,
>
>As the subject says, I am looking for an open online database to store
>unprocessed diffraction data. Does such a database exist? Essentially we
>would like our diffr
If you export the images in XDS format, then you get .pck files that MOSFLM
certainly can read, plus a XDS.INP with the geometry parameters.
Hope this helps,
Kay
On Tue, 10 Oct 2023 10:47:51 +0530, Vyankatesh Rajmane
wrote:
>Dear all,
>We have collected diffraction data on a Rigaku FR-X machi
Dear Zhen Gong,
Installation of XDS and associated programs is documented in the "Installation"
article in XDSwiki.
If I google "XDSwiki installation article", it is the first hit.
Your PATH is probably different when you double-click XDSGUI to start it,
compared to what it is on the command li
Hi Alex,
What is your operating system? Linux or Mac? Version?
Best, Kay
On Thu, 18 May 2023 23:21:47 +, Alex Aleshin
wrote:
>This morning I've discovered that I cannot type any character (numbers are
>fine) into CCP4I command windows. I've upgraded the package to a 8.0.011
>version, but
Dear Armando,
besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign
(https://zhanggroup.org/US-align/).
In my tests, THESEUS sometimes crashed in different ways. USalign is very
robust; SUPERPOSE is fast.
HTH,
Kay
On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert wrote:
>Dear all,
>
Dear Gyuhyeok,
I have no first-hand experience with CARELESS.
But my understanding is that CARELESS gives you normalized structure factor
amplitudes; this "normalization" roughly corresponds to a removal (subtraction)
of the Wilson B-factor from conventionally processed structure factor
amplit
Hallo Abhilasha Thakur,
(I am not a Gromacs user, but I'll nevertheless try to answer)
You'll have to identify the Amber99 forcefield topology file, and read it to
find out the naming of RNA atoms in that file.
The error message asks you to change (e.g. using an editor) the atom names in
your
2022 10:25:17 +0200, Demetres D. Leonidas
wrote:
>Dear Kay,
>
>you are right and I do apologize for the misunderstanding. Point 1 and 2
>are sufficient.
>
>best
>
>Demetres
>
>On 11/29/2022 10:00 AM, Kay Diederichs wrote:
>> Dear Demetres,
>>
>> sou
s the memory. It was fulling rapidly. The workaround was to:
>
>1. unzip the cbf files prior to processing
>
>2. use maximum number of jobs 1
>
>3. use number of processors 4
>
>4. run xds_par
>
>Many thanks for all your help
>
>Demetres
>
>On 11/29/2022 9:
Dear Demetres,
I agree with what James says: this is the operating system trying to to
prevent, in an over-zealous way, the
forking of too many or too big (in terms of memory) processes.
In other words, XDS hasn't changed, but the operating system changed - it
applies different limits to its pr
On Tue, 8 Nov 2022 15:25:03 -0800, James Holton wrote:
>Thank you Ian for your quick response!
>
>I suppose what I'm really trying to do is put a p-value on the
>"geometry" of a given PDB file. As in: what are the odds the deviations
>from ideality of this model are due to chance?
>
>I am leanin
Dear Gerard,
I'm not going to comment on what others said in this (new) thread; just trying
to make a few remarks about what you write below -
On Tue, 4 Oct 2022 17:01:10 +0100, Gerard Bricogne
wrote:
>Dear all,
>
> First of all, apologies for breaking the threads entitled "PAIREF -
>War
Hi Matt,
you cite the message "WARNING: There are only 40 < 50 free reflections ..." but
in the next sentence you write "This error ...".
Being a program developer myself, I'd like to point out that there is a
difference between a warning and an error. An error typically makes the program
stop
I believe you need to establish the "environment" before running certain CCP4
programs.
Something like
source /where/ever/ccp4-8.0/bin/ccp4.setup-sh
HTH,
Kay
On Mon, 26 Sep 2022 21:32:42 +0100, Zhen Gong wrote:
>Dear CCP4 developers and users,
>
>I am trying to run CCP4 sc but encountered an
Hi Robert,
you are welcome.
It seems that you own (rgampe.rgampe) the directory /software/ccp4-8.0 . You
should revert the ownerships in /software/ccp4-8.0 from root.root with
sudo chown -R rgampe.rgampe /software/ccp4-8.0
so that in the future you don't need sudo for updates.
Your real probl
Hi Robert,
hmm, more ideas:
a) check if CCP4 directory is writable, and who the owner is:
mount | grep software
sudo touch /software/ccp4-8.0/deleteme
ls -ld /software/ccp4-8.0
ls -l /software/ccp4-8.0/deleteme
sudo rm /software/ccp4-8.0/deleteme
b) try
sudo su
ccp4um
c) try
sudo -i
ccp4um
Hi Robert,
two points -
a) before you tried to update, did you
source /where/ever/ccp4/bin/ccp4.setup-sh
? The above applies to bash; for (t)csh you need to
source /where/ever/ccp4/bin/ccp4.setup-csh
That sets the PATH environment variable such that you don't always have to
specify the absolut
Hi Robert,
Concerning PROBLEM 1: have you tried
sudo ccp4um
or
sudo ccp4i
?
HTH,
Kay
P.S. didn't find Andrey Lebedev's reply on August 30 that you refer to
On Fri, 16 Sep 2022 14:11:34 +, Robert Gampe wrote:
>Hello Marcin Pedro and the CCP4 community,
>
>
>
>PROBLEM 1: I have the same st
Dear Deepak,
I guess that the spacegroup in the MTZ file that you use for refinement is
wrong.
I think you should carefully check the output of PHASER, and in particular the
PDB file that it wrote. The correct spacegroup is given there (and it may also
be P4122 or P4222 or P4322, because like
Dear Pavel,
I have seen this in very high-resolution models of triclinic lysozyme but I
don't remember the PDB ids.
Best wishes,
Kay
On Tue, 23 Aug 2022 15:02:07 -0700, Pavel Afonine wrote:
>Dear community,
>
>
>
>I’m looking for an example of a crystal structure where a large group of
>atoms
Dear Sayan,
On Thu, 28 Jul 2022 15:12:30 +0530, Sayan Saha wrote:
>Dear Sir,
>
>1. There are no ice-rings. However, diffraction spots seem to be
>overlapping. This can be seen during the data processing, as the space
>group (C2 or P222) varies even in the consecutive frames.
spot overlap result
indexing ambiguity.
Best wishes,
Kay
On Fri, 22 Jul 2022 19:02:19 +0100, Eleanor Dodson
wrote:
>Surely once you have indexed one crystal, you can use the facility to check
>the next ones indexing against the reference - aka pointless?
>
>On Fri, 22 Jul 2022 at 16:20, Kay Diederichs
>
Hi Monika,
in June we had a summer school at MaxIV, and one of the topics was serial
crystallography - with lectures and tutorials. Maybe you can talk to the people
who attended the course, and the organizers, Ana Gonzalez and Thomas Ursby, and
ask them for help.
It is more difficult to determ
Dear Jorge,
what you write makes sense to me, and I cannot answer your questions. This is
just to say that the situation you encounter is not completely uncommon,
although most crystallographers would abandon such a crystal form, I guess.
The technical term that describes this 4-fold twinning is
Hi Henrike,
I use CCP4's "contact" program:
#!/bin/bash
# find bad contacts: list all CA-CA distances < 3.8A between non-adjacent
residues
# in a well-folded protein, these should be very rare (1 contact in 1000
residues)
# KD 20.12.21
grep CA $1 > /tmp/temp.pdb
contact xyzin /tmp/temp.pdb < wr
Hi Patrick,
I have not seen similar reports.
The 2nd error message has
~/Desktop/dectris-neggia.so, 258): image not found
so maybe the ~ is not understood; try to specify more explicitly
LIB=/Users/ploll/Desktop/dectris-neggia.so
or whatever the name of your $HOME is.
Could you try durin-plugin
Dear Eleanor,
there appears to be a bug. See the sourcecode of sftools near line 11700:
do l=1,ndatasets
if (xname(l)(1:lenstr(xname(l))).eq.tmp_xname .and.
$ dname(l)(1:lenstr(xname(l))).eq.tmp_dname) then
dwavel(l) = tmp_dwave
endif
Dear Petr,
a map needs amplitudes and phases. In the case of the usual maps (2Fobs-Fcalc
and Fobs-Fcalc) calculated for twinned data, one can either
detwin the amplitudes, or take twinning into account in the Fcalc term.
When calculating the anomalous map, I believe that detwinning of anomalou
Hello Mudassar ali Khan,
these R-values after refinement rather indicate a failure of Molecular
Replacement.
Did you see in aimless.pdf:
"WARNING: the L-test suggests that the data may be twinned
so the indicated Laue symmetry may be too high
Rough estimated twin fraction alpha from cumul
On Wed, 2 Mar 2022 22:56:28 +0800, fu wrote:
>Dear Colleagues,
> I get two solutions after running SHELX C/D. In both results, the
> coordinates of the heavy atoms are centrosymmetric. Why there are two
> solutions?
>
>Best wishes,
>Fu Xingke
>Institute of Physics CAS
Hello Fu,
SHELXD write
On Wed, 2 Mar 2022 22:56:28 +0800, fu wrote:
>Dear Colleagues,
> I get two solutions after running SHELX C/D. In both results, the
> coordinates of the heavy atoms are centrosymmetric. Why there are two
> solutions?
>
>Best wishes,
>Fu Xingke
>Institute of Physics CAS
Hello Fu,
SHELXD write
On Tue, 1 Mar 2022 18:06:34 +0800, fu wrote:
>Dear Colleagues,
>I have two question.
>The first question is, in SHELXD, they use XPREP to calculate the
> correlation coefficient(CCano) between the signed anomalous differences at
> different wavelengths? What’s the meaning? And how to ca
I have updated Ubuntu on notebooks a couple of times from one LTS release to
the next. This works well (and is tested) for those packages that are part of
the old release, but it does not necessarily work well for packages outside the
distribution.
apt-mark showmanual
should show those manually
I have the same problem - https://www.ccp4.ac.uk/download/ is not accessible.
Kay
On Fri, 28 Jan 2022 09:46:17 +0100, Julian Nomme wrote:
>Hi,
>
>I'm still facing the same issue today.
>I just can't get access to the download section, the rest of the website
>being accessible.
>I'm getting the f
Dear academic users of XDS,
there is an updated version available at https://xds.mr.mpg.de/ . Since the old
(current) version will expire in March, it is advisable to download and test
the updated version before that.
The biggest change is the availability of binaries for the Apple M1 processor.
Hi Reza,
the term "validation" as used by e.g. crystallographers - namely by checking
geometric parameters of a structure derived from experiment(s) - is euphemistic
since realistic geometry is a required but not sufficient property of a model -
it can be completely wrong even if it has good ge
arlier descriptions of the
>problem, but this sounds worrying.
>
>I think you're trying to say the same thing here, Kay. Is that right?
>
>Best wishes,
>
>Randy
>
>On 21 Oct 2021, at 08:51, Kay Diederichs
>mailto:kay.diederi...@uni-konstanz.de>> wrote:
>
&
d to the hardware pixels, they can be any arbitrary subdivision of
>the detector surface.
>
>Best wishes
>
>-- Ian
>
>
>On Tue, 19 Oct 2021 at 12:39, Kay Diederichs
>wrote:
>
>> James,
>>
>> I am saying that my answer to "what is the expectation and vari
on is NOT Gaussian, but rather
>exponential. And that means adding variances may not be the way to
>propagate error.
>
>Is that right?
>
>-James Holton
>MAD Scientist
>
>
>
>On 10/18/2021 7:00 AM, Kay Diederichs wrote:
>> Hi James,
>>
>> I'm a
Hi James,
I'm a bit behind ...
My answer about the basic question ("a patch of 100 pixels each with zero
counts - what is the variance?") you ask is the following:
1) we all know the Poisson PDF (Probability Distribution Function) P(k|l) =
l^k*e^(-l)/k! (where k stands for for an integer >=0
If you write/analyze/improve a data-reduction program in crystallography, then
these questions are important: how to estimate the intensity of a Bragg spot by
evaluating the counts in the pixels of the signal area, and those of the
background area? When calculating mean and standard deviation of
Biology, University of Gothenburg
>Box 462, 40530 Göteborg, Sweden
>Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910
>Web: http://katonalab.eu, Email: gergely.kat...@gu.se
>
>From: CCP4 bulletin board On Behalf Of James Holton
>Sent: 15 October, 2021 18:06
>
Dear Wim,
on my M1 Macbook Air, coot 0.9.6 (latest from CCP4) works smoothly/fast. What
is your XQuartz version? I have 2.8.1 .
HTH,
Kay
On Thu, 16 Sep 2021 15:40:53 +0800, WENHE ZHONG
wrote:
>Dear CCP4 community,
>
>The COOT is not running smoothly on my M1 chip Macbook. For example, when
>
Dear Eleanor,
Thanks for pointing out that CCP4 FreeRflag selects the test set in the highest
possible symmetry for the crystal class! I didn't know that.
The following sentences (which are somewhat difficult to understand for me) in
https://www.ccp4.ac.uk/html/freerflag.html appear to document
;did you have something else in mind Kay?
>
>Cheers,
>
>Andrew
>
>> On 30 Aug 2021, at 13:59, Kay Diederichs
>> wrote:
>>
>> Hi Jon,
>>
>> generally I agree that the accuracy of the data is inversely related to the
>> danger of overfitting,
Hi Jon,
generally I agree that the accuracy of the data is inversely related to the
danger of overfitting, and that selection in shells is not necessary.
But if twinning is suspected, as here, and/or a choice between high and low
symmetry spacegroup has to be made, one has to make sure that
pote
Hi Jeffrey,
good question. Both twinning and NCS may couple reflections across free and
working sets, and this should be avoided by proper selection - otherwise Rfree
is biased towards Rwork. Selecting thin shells should be a good option, and can
be done in SFTOOLS (or DATAMAN, or SHELXPRO).
H
rly indicates one (and just on!) orientation for
>> the 5th chain. Thank you all for your suggestions.
>>
>> Have a nice evening,
>> Peer
>>
>> -"CCP4 bulletin board" <mailto:CCP4BB@JISCMAIL.AC.UK%0b>> <mailto:CCP4BB@JISCMAIL.AC.UK>> s
Dear Peer,
I suspect that the true spacegroup has lower symmetry than P3221, and that
there may be twinning masked by tNCS.
Subgroups of P3221 are C2 and P32 (
https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_g
Proteopedia (https://proteopedia.org/wiki/index.php/Main_Page) can be used for
commenting individual PDB entries. See also
https://proteopedia.org/wiki/index.php/Retractions_and_Fraud and
https://proteopedia.org/wiki/index.php/Proteopedia:Comments_on_Published_Structures
best wishes,
Kay
On S
has a similar file size as of 093757merged_9)
When I used your compiled generate_adx (that you provided kindly via personal
email), I don't see newly generated files.
Best,
Doo Nam
--
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.
Hi Doo Nam,
it seems that your frames do not have an extension (like .cbf or .img or.xyz).
Maybe this is related
to the fact that the program does not properly add the extension .adx ? It is
puzzling for me since
I made an attempt to take this possibility into account:
if (index(frmna
Hi James,
have never seen this ... could you try the solution at
https://community.snowflake.com/s/article/Snowsql-installed-via-RPM-fails-with-Cannot-open-self-usr-lib64-snowflake-snowsql-snowsql
i.e. exclude from prelink?
HTH,
Kay
On Mon, 28 Jun 2021 11:51:19 -0700, James Holton wrote:
>Gre
Hi Almudena,
if it is a packing problem, you need to find the correct subgroup of P6522
(179).
Take a look at
https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups
.
Subgroups of 179 are 20, 153, 154, 170, a
try to use NVidia
driver from ELRepo.
Time being I will use the one bundled with CCP4-7.1.
Once again thanks for the help.
With regards
Karthik
On 22-04-2021 02:18 pm, Kay Diederichs wrote:
Dear Karthikeyan Subramanian,
which processor does your computer have? Look at the output of e.g.
Dear Karthikeyan Subramanian,
which processor does your computer have? Look at the output of e.g. "head -20
/proc/cpuinfo". What is "model name"?
To my understanding, the main problem is
> >*./coot: line 264: 5365 Illegal instruction (core dumped) $coot_bin
This means that the compiler, w
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