A couple of extra comments on top of Bob's rather comprehensive
recommendations, based purely on actually looking at Pilatus data (I
mean *looking*)
When you are inspecting the images looking at them at 100% size is
important: spots are small relative to pixels and the point spread is
essentially
Dear Rain Field,
The current release is indeed unable to work with the newest versions
of XDS and a new version should be available before the end of the
week, which will be advertised on the blog. However this requires
either a new nightly build of phenix or an unreleased cctbx build, as
bits of
Dear Rain Field,
A new xia2 release is now available please see:
http://xia2.blogspot.com
for details. This version should be included in the next CCP4 update.
Once again apologies for the inconvenience.
Best wishes,
Graeme
On 4 July 2013 08:18, Graeme Winter graeme.win...@gmail.com wrote
integration software.
For further information please contact Graeme Winter (
graeme.win...@diamond.ac.uk) or Dave Hall (david.h...@diamond.ac.uk) though
for applications please use the link above.
The closing date is the end of September.
Best wishes,
Graeme and Dave
You could try putting this into the Zanuda server
http://www.ysbl.york.ac.uk/YSBLPrograms/
which will search for possible correct spacegroups given the coordinates
and structure factors. There are however no reasons why you can't have a
pseudo-cubic monoclinic lattice, however unlikely it is.
Usually this means that you have relatively high multiplicity, which
give-or-take improves the I/sig(I) by sqrt(m) where m is the multiplicity,
but also increases the Rmerge.
For any given narrow shell of reflections,
Rmerge ~ 0.8 / unmerged(I/sig(I))
merged(I/sig(I)) ~ sqrt(m) *
Hi Folks,
A xia2 user wrote in asking where to find
'observed criterion sigma(F)' and 'observed criterion sigma(I)'
in the xia2 logs (i.e. from Scala or Aimless or XSCALE)... I have no idea
what they are so will struggle to give a helpful answer ;o) and
surprisingly google was not a lot of use
what Scala does.
On 25 Nov 2013, at 09:21, Graeme Winter graeme.win...@gmail.com wrote:
Hi Folks,
A xia2 user wrote in asking where to find
'observed criterion sigma(F)' and 'observed criterion sigma(I)'
in the xia2 logs (i.e. from Scala or Aimless or XSCALE)... I have no idea
what
Hi All,
A major opportunity with Pilatus detectors is the chance to redistribute
the dose in reciprocal space i.e. measure a lot more data, with less dose /
frame, then decide in hindsight where you probably should have cut off the
data set.
It is certainly true that strategies such as 0.2 s/0.2
signal-to-noise and to turn your
sentence you may get better data into you will get better data. I
think this would be worth implementing at beamlines - do you know if
anything in this direction is on its way?
Best,
Tim
On 05/01/2014 09:25 AM, Graeme Winter wrote:
Hi All,
A major
Dear Tony,
Sorry to hear you are having trouble - I have never seen this message
before. Please could you send me (off list) the output of the last XDS job
ran before this one and (ideally) the XDS.INP file in the offending area?
There must be something very odd going on here.
Thanks best
Dear Tony,
OK, clearly Tim's suggestion is spot on, to remove the offending images
from processing (this is easily done by splitting your input xinfo or the
automatically generated one, I will copy an example below)
I suspect that the memory error results from
IMAGE IER SCALE NBKG NOVL
Hi Folks,
Colleague of mine here at Diamond just pointed out a neat EU funded way of
publishing raw data which generates a digital object identifier as part of
the process:
http://zenodo.org
Worked through it myself to see if it works and apparently it does:
doi:10.5281/zenodo.10271
Thought
Hi Folks,
Following some bug reports I spent a few minutes over the weekend wrangling
with regular expressions to digest image file names - the dismantling of e.g.
foo_bar_001.img to foo_bar_###.img, 1 etc. I think now that the scheme I have
should work for everything, however what I could
in questions_answers:
answer = template_regex(filename)
assert answer[0] == questions_answers[filename]
On 30 April 2012 09:19, Graeme Winter graeme.win...@gmail.com wrote:
Hi Folks,
Following some bug reports I spent a few minutes over the weekend wrangling
with regular
Hi Ed,
If you use XDS for integration then all of the reflections are full
(they are summed by the program during the integration), so there are
no partials from which to determine an estimate of the mosaic spread
in Scala.
Mosflm 0 mosaic spread is a different issue, but has been much
improved
Hi Phil,
Usually with something like this I use:
Data line--- bins 20
Data line--- resolution 2.80
Data line--- run 1 batch 1 to 900
Data line--- resolution run 1 high 2.80
Data line--- name run 1 project AUTOMATIC crystal DEFAULT dataset SAD
Data line--- scales constant
Data
Hi Antony,
Using xia2 with a reference dataset for both indexing and R-free seems to
work fine, apart from the fact that the resulting mtz file, now contains
R-free labels for reflections that have no observations… i.e. taken from the
higher resolution reference dataset; see output below.
Thanks indeed Eleanor, when I get a moment I will add this too to the xia2
cad script!
Best wishes,
Graeme
On 5 November 2012 11:37, Antony Oliver antony.oli...@sussex.ac.uk wrote:
Thanks Eleanor - guess I should have plumbed the depths of the CAD manual
a little further.
Works perfectly.
.
best wishes,
Graeme
On 5 Nov 2012, at 15:13, Graeme Winter wrote:
Thanks indeed Eleanor, when I get a moment I will add this too to the xia2
cad script!
Best wishes,
Graeme
On 5 November 2012 11:37, Antony Oliver antony.oli...@sussex.ac.uk wrote:
Thanks Eleanor - guess I should
Dear All,
Sorry, finally have released an updated version where this problem has gone
away: xia2.blogspot.com has the details.
Best wishes,
Graeme
On 6 November 2012 10:31, Graeme Winter graeme.win...@gmail.com wrote:
Well there's a funny thing. It seems that this is already in xia2
The XDS CORRECT step will also (by default) do scaling - if I
understand correctly the same scaling as in XSCALE, but for a single
sweep and with no zero-dose.
If what you want is merging statistics, I find it helpful to write out
the data unmerged and then use pointless -c and aimless to merge
Hi Sebastiano,
If they hand you an *unmerged* mtz file containing scaled data you can
do this, by remerging the data with Scala or Aimless. Equivalently the
unmerged output of scalepack or XSCALE (or XDS CORRECT)
If however you have merged data then you have lost this information,
though
Hi Folks,
To follow up Harry's comments. We have a Pilatus 300K on I19 here at
Diamond which is used from time to time for small molecule work.
Processing with XDS has proved to be successful (I can send an example
XDS.INP but you will need to make sure you have a good knowledge of
the
Dear Eugene,
Personally I have a habit of using bzip2 for archival of data.
Negative points: very slow. Positive points: universally supported,
lossless. I have lots of data. To be honest most of it I keep in the
native format.
I expect to see plenty of comments of lossless vs. lossy compression
Dear Saleem,
To compute one manually I take it you mean by hand with commonly
available software as opposed to via e.g. automated beamline methods?
If so:
start up imosflm
index your image(s) and estimate mosaic spread
select strategy, auto-complete, go
XDS has XPLAN equivalently, though you
Suspect most people would be looking for painless though I would
guess that should be a program to tell you the right crystallization
conditions...
On 3 May 2013 00:15, Jacob Keller j-kell...@fsm.northwestern.edu wrote:
Nevertheless?
JPK
On Thu, May 2, 2013 at 2:18 PM, Roger Rowlett
Hi Sajid,
The crosshair on the images is the tile join between the four
tapers, and is a standard feature on all ADSC 4-tile detectors. I am
certain HKL2000 should know about these - certainly mosflm will simply
ignore the image there.
Any image from the same detector should have the same
Hi Dave,
That is very odd - oh, I have just found something - I am using the
ppc version ;o)
The ppc version works file on intel machines (some complex spell
casting that macs do I guess) so you may be better off downloading and
using that one:
file `which pointless-1.2.16`
Hi Roni,
Changing the spacegroup within a pointgroup in this way is fine. If
you want to change the pointgroup you should take the sorted
reflection file you put into Scala and reindex it and re-scale/merge -
this will give you the correct number of reflections and is the
correct thing to do
Hi Folks,
Following on from this, does anyone have a copy of the information on
how to get coot working in intel mac 10.5.x? I downloaded the linked
disk image and coot tarball, planning to print the instructions the
following day.
As Homer would say, D'Oh!
Just the place you are supposed to
Hi David,
There is a clipper utility called cphasematch which will do exactly
this. More info here:
http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html
or you can get the updates against ccp4 6.0.2 through the ccp4 downloads pages.
Cheers,
Graeme
2008/8/6 David Waterman [EMAIL
Hi Folks,
If anyone wants to do this on an Intel mac you will need a fortran
compiler, which is not installed by XCode. There is a compatible
gfortran here:
http://r.research.att.com/tools/
which in my experience works fine, though is completely incapable of
producing static binaries.
There
Hi James,
You are the victim of an epic command line. This has been fixed in the
6.1.1 release, but you will find that using a shorter path (i.e.
noniso rather than non-isomorphism c.) will pull the command line
down to something more sensible.
CCP4i writes this out to allow the job to be rerun
Hi Frank,
I would have assumed that the purpose of the experiment would have
been defined in the publication associated with the deposition - not
to trivialize your point, which is very important, but to put it in
context. I would also assume that the sequence and ligands are as per
the
Hi James,
This isn't a direct answer to your question, but you can assign these
on the Scala command line input, thus:
name run 1 project AUTOMATIC crystal DEFAULT dataset WAVE1
name run 2 project AUTOMATIC crystal DEFAULT dataset WAVE2
I am assuming that this would be your next step anyhow.
Dear Nick,
In XDS.INP, set
TRUSTED_REGION=0.0 1.41
This will integrate to sqrt(2) * radius of the inscribed circle,
provided that the resolution ranges are set appropriately.
Best wishes,
Graeme
On 10 June 2010 12:09, Nicholas Keep n.k...@mail.cryst.bbk.ac.uk wrote:
Sorry this is off topic.
Dear Tim,
There are instructions on how to build cctbx against your system
Python (which I assume is the one used by PyMol) here:
http://cctbx.sourceforge.net/current/installation.html#manually-building-from-sources-under-unix
From there you can also install other Python modules e.g. Numpy in
'libtbx.scons install' after everything was built?
Cheers, Tim
On Wed, Jun 23, 2010 at 03:27:32PM +0100, Graeme Winter wrote:
Dear Tim,
There are instructions on how to build cctbx against your system
Python (which I assume is the one used by PyMol) here:
http://cctbx.sourceforge.net/current
Hi Murugan,
One useful indicator of raw anomalous signal is the ANOMPLOT graph
from Scala - this shows the differences between reflections compared
with the expected differences. If the gradient of the plot is 1
there's no more differences that you would expect. If the gradient is
more than one
Dear Anna,
Something I find useful is to convert the output of XSCALE (unmerged) to MTZ
format using pointless (pointless -c xdsin SCALED.XDS hklout sorted.mtz)
then to merge the reflections with Scala:
scala hklin sorted.mtz hklout scaled.mtz eof
run 1 all
scales constant
anomalous on # or off
Hi Tim,
Is it as easy as
reindex hklin a.mtz hklout b.mtz eof
symm P43212
eof
This will simply (and correctly) reassign the symmetry operations. Is
this what you meant?
Best wishes,
Graeme
On 30 September 2010 10:49, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
Hello,
we are currently
Dear Evette,
You can still get this analysis with Scala even after scaling with
scalepack. If you output the measurements unmerged (no merge original
index) you can convert them to MTZ using pointless, then remerge the
data as follows:
scala hkiin from_pointless.mtz hklout merged.mtz eof
run 1
Dear ccp4bb,
I had an interesting question from a xia2 user last week for which I
did not have a good answer. Here's the situation:
- spacegroup is P212121, which was specified on the command-line
- xia2 processes this as oP, assigns the spacegroup as P212121 before
running scala - generates
Hi James,
May I just offer a short counter-argument to your case for not including
weak reflections in the merging residuals?
Unlike many people I rather like Rmerge, not because it tells you how good
the data are, but because it gives you a clue as to how well the unmerged
measurements agree
Hi Folks,
Before I try to write a new program, I thought I would check what I want to
do can't be done
I have many unmerged but scaled summed MTZ files from scala (output
unmerged) for which I would like to simply change the DNAME. I tried CAD,
but it complains about the multi-record nature
assessment of CAD and MTZUTILS. In principle, the
functionality should be in mtzutils, but I doubt that it would be easy
to add.
m
On Fri, 2011-03-18 at 09:43 +, Graeme Winter wrote:
Hi Folks,
Before I try to write a new program, I thought I would check what I
want to do can't be done
...@lbl.gov wrote:
REBATCH
On 3/18/2011 2:43 AM, Graeme Winter wrote:
Hi Folks,
Before I try to write a new program, I thought I would check what I want
to do can't be done
I have many unmerged but scaled summed MTZ files from scala (output
unmerged) for which I would like to simply
Dear Petr,
Here at Diamond we have a version of HKL2000 which works for Pilatus detectors.
Best wishes,
Graeme
On 20 July 2011 12:25, Petr Leiman petr.lei...@epfl.ch wrote:
Dear all,
What is the status of Denzo/HKL2000 availability/support for the Pilatus 6M
detector?
Thank you,
Petr
Hi Eleanor,
So far I have managed to lurk on this one - keeping an eye on things
but not getting involved. However this has prompted me to respond!
Has anyone raided the point that while archiving is good, it will only be
generally useful if the image HEADERS are informative and use a
Hi James,
Just to pick up on your point about the Pilatus detectors. Yesterday
in 2 hours of giving a beamline a workout (admittedly with Thaumatin)
we acquired 400 + GB of data*. Now I appreciate that this is not
really routine operation, but it does raise an interesting point - if
you have
Hi Ed,
Ok, I'll bite: I would be very interested to see any data sets which
initially were thought to be e.g. PG222 and scale OK ish with that but
turn out in hindsight to be say PG2. Trying to automatically spot this
or at least warn inside xia2 would be really handy. Any
pseudosymmetric
HI James,
Regarding the suggestion of lossy compression, it is really hard to
comment without having a good idea of the real cost of doing this. So,
I have a suggestion:
- grab a bag of JCSG data sets, which we know should all be essentially OK.
- you squash then unsquash them with your
Dear Herbert,
Sorry, the point I was getting at was that the process is one way, but
if it is also *destructive* i.e. the original master is not
available then I would not be happy. If the master copy of what was
actually recorded is available from a tape someplace perhaps not all
that quickly
17:06, Antony Oliver antony.oli...@sussex.ac.uk wrote:
Dear CCP4 developers,
Forgive the posting here, but I can't find the correct contact details for
Graeme Winter…
I have just downloaded the latest version of XIA2 (0.3.3.3 build 3479) and
tried to integrate a dataset. The program fails
report.
Graeme
On 15 November 2011 17:06, Antony Oliver antony.oli...@sussex.ac.uk wrote:
Dear CCP4 developers,
Forgive the posting here, but I can't find the correct contact details for
Graeme Winter…
I have just downloaded the latest version of XIA2 (0.3.3.3 build 3479) and
tried to integrate
Dear Ping,
You need the unmerged data for this - for instance the output from
Mosflm or the XDS INTEGRATE step. Pointless works by comparing
potentially symmetry related measurements.
Best wishes,
Graeme
2011/11/17 Ping Wang wangping...@sina.com:
Dear all,
I have a dataset with spacegroup
can I get the unmerged data or in
which step to get the data I need?
Thanks!
- 原始邮件 -
发件人：Graeme Winter graeme.win...@gmail.com
收件人：CCP4BB@JISCMAIL.AC.UK
主题：Re: [ccp4bb] pointless problem
日期：2011年11月17日 15点34分
OK, feel like I need to comment on this one. In terms of general
programming you could use whatever you like, perl (if as was said
above you like write-only programs) tcl, python, c++ etc.
However if you would like to do crystallographic calculations, I can
recommend that Python + CCTBX is
Hi Jacob,
I think a lot of people do use I/sigma :o)
However sigma is in some cases poorly defined, and the merging
residuals you refer to are calculated only from the I values and are
related to I/sigma anyhow... Of course the R values are sometimes also
poorly defined for low multiplicity
Dear Nick,
If you're happy to keep on using xia2, you can just put both of the
data sets in a single directory and run
xia2 -3dii /heres/where/the/data/went
And wait a little while.
To comment on your analysis of the statistics: inside xia2 the scaling
is switched off as far as possible in the
Dear Theresa,
My answer would be - it depends.
If you are in the business of learning crystallography, then I would
absolutely suggest you start from doing everything by hand. Indeed, if
you really want to get stuck in I would suggest starting with the
programs you need (mosflm, scala, truncate
Dear Steve,
Thanks for getting in touch. It seems that for some reason the ccp4i
interface to xia2 is not currently working correctly. I will look into
this and get back to you with a fix, it currently has me confused.
Best wishes,
Graeme
On 17 February 2012 12:54, Stephen Carr
On 17 February 2012 15:44, Graeme Winter graeme.win...@gmail.com wrote:
Dear Steve,
Thanks for getting in touch. It seems that for some reason the ccp4i
interface to xia2 is not currently working correctly. I will look into
this and get back to you with a fix, it currently has me confused.
Best
Hello Lu,
I would usually suggest using mtz2sca (f you have an MTZ with
intensities) to get a scalepack format file, which you may have
already. Then I would use shelxc to generate the .ins and .hkl file
for shelxd.
You can do this through ccp4i from an MTZ file, or write a script as
detailed
Mosflm works fine with our Pilatus 2M at DLS - however you do need to
be using the beta-test version.
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/betas/
best wishes,
Graeme
On 12 March 2012 19:57, Dean Derbyshire dean.derbysh...@medivir.com wrote:
Hi again, it's the 2M detector I'm having
Hello Deng,
Process them as usual with e.g. Mosflm, then sort them together (you
may need to rebatch one of the runs) and do one Scala run - this will
put all of the measurement on a common scale and write out data
suitable for refinement. For pointgroups with ambiguous origin choices
(e.g. P4)
... presuming of course the automated software got this resolution limit right.
If for whatever reason you would like to cut the limit mtzutils will
do this nicely:
mtzutils hklin blah_free.mtz hklout blah_lower.mtz eof
resolution 1.8
eof
(say) - I am sure there are other ways within the suite
of your data e.g. with pointless (I/sigI 2.0 is a good marker)
and reprocess the data to that limit. If you integrate the whole
detector area and the outer parts contain only noise, the noise has a
negative effect on the real data.
Tim
On 03/19/12 15:25, Graeme Winter wrote:
... presuming
detector area and the outer parts contain only noise, the noise has a
negative effect on the real data.
Tim
On 03/19/12 15:25, Graeme Winter wrote:
... presuming of course the automated software got this resolution limit
right.
If for whatever reason you would like to cut the limit mtzutils
Hi Matt,
We use module here at Diamond, so will be happy to provide a file. I
guess it would be helpful to have these on a wiki somewhere :o)
I do however need to update it a little and tidy up before sharing! If
anyone else is interested, please shout and I will send it to you
too... (i.e. not
Hi Rana,
You could use cphasematch to put the two maps on the same origin. To
do this you will need to CAD the two data sets together then give
cphasematch the phase columns to use. Typing cphasematch on the
command-line should tell you how to do this. It's a tool from the
clipper library, so
Hi David,
If the data compression is carefully chosen you are right: lossless
jpeg2000 compression on diffraction images works very well, but is a
spot slow. The CBF compression using the byte offset method is a
little less good at compression put massively faster... as you point
out, this is the
Hi Ben,
There's an example in the JCSG archive (2PBL, 47717) which exhibits
the same phenomenon, as a result of non crystallographic symmetry. For
example (from xtriage)
Acentric reflections
I^2/I^2:3.669 (untwinned: 2.000; perfect twin 1.500)
F^2/F^2:0.504 (untwinned: 0.785;
Dear Miguel,
You may find that replacing the ipmosflm binary with the one from
Harry's web page may be more reliable - typically these sorts of
things come down to gfortran or g77 being a little keen in
optimization.
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/
Cheers,
Graeme
2009/9/30 Miguel
Hi Jan,
Always worth a try is to process the data in P1 then assigning the
symmetry in CORRECT - that way the cell constants can refine to what
they want to. It also means you can check that the symmetry actually
is cubic.
For the majority of data sets in my experience it makes little
difference
Hi Andy,
If you have a recent CCP4 installation (i.e. 6.something I think)
there's diff2jpeg, which does exactly what you want. Otherwise there
are also spells to use Mosflm for this which allows a little more
control over the greyscale settings.
Cheers,
Graeme
2009/10/21 Andy Torelli
Hi Francois,
SCALEIT in CCP4 sounds like the tool you want - this is for scaling
e.g. native and derivitive data sets together. You will need to cad
together the two files first though.
This is illustrated in the tutorials here:
,
Graeme
On 12 March 2010 09:27, Francois Berenger beren...@riken.jp wrote:
Graeme Winter wrote:
Hi Francois,
SCALEIT in CCP4 sounds like the tool you want - this is for scaling
e.g. native and derivitive data sets together. You will need to cad
together the two files first though.
My
Hi Folks,
I have seen this when you take data from XSCALE to merge in Scala -
the former puts I's on the scale I=F^2 making for very large numbers.
I typically undo this scaling factor using pointless -c and the
multiply keyword. Multiply by 1/the value reported in XSCALE output.
Pointless is
Dear Jurgen,
Thanks for your interest in DIALS - we are working hard at the moment on
testing the software and finding bugs (and fixing them!) and I would say
right now it's not quite ready for the general user, but we do plan to make
an alpha release of the software before the end of the year.
Dear Kay
Just to comment on (e) since you say you don't know why anyone would want
to do this, yet this is exactly what xia2 -3d does :o)
I use AIMLESS to merge data already scaled by XDS CORRECT or XSCALE as a
way to get a report on the merging statistics which includes all of the
AIMLESS
the misunderstanding spreads, which is then why
I get asked can CORRECT scale a data set? and other misunderstandings
along these lines ...
best,
Kay
On Thu, 13 Nov 2014 08:15:12 +, Graeme Winter graeme.win...@gmail.com
wrote:
Dear Kay
Just to comment on (e) since you say you don't know why
)252-0667
rsanishv...@anl.gov
--
*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Graeme
Winter [graeme.win...@gmail.com]
*Sent:* Thursday, November 13, 2014 2:15 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] To scale or not to scale
of the home source ones. See docs. You can specify explicitly I think
Phil
Sent from my iPhone
On 17 Nov 2014, at 09:44, Graeme Winter graeme.win...@gmail.com wrote:
Dear Nukri,
The following is my opinion which I think is worth discussion, and are
based on my understanding of what XDS does
Dear All,
dxtbx.print_header /path/to/image should work
Graemes-MacBook-Pro:~ graeme$ dxtbx.print_header
data/i04-BAG-training/th_8_2_0001.cbf
=== data/i04-BAG-training/th_8_2_0001.cbf ===
Using header reader: FormatCBFMiniPilatusDLS6MSN100
Beam:
wavelength: 0.97625
sample to source
Dear Jacob,
There are a multitude of directions you can go from here - a few comments
spring to mind:
- are repeated observations of the same reflection on the same part of the
detector really independent?
- for the wide phi sliced vs. fine sliced discussion the detector type
matters a great
Hi Nathan,
While what you observe does sound like a bug I would not like to comment
whether this is right or wrong. However a CCP4 alternative to this which
I find easier to use is pointless -
pointless -c xdsin XDS_ASCII.HKL hklout sorted.mtz
This will give an unmerged MTZ which can be used in
Looking at PAD images is something we have had to get used to at Diamond,
and sometimes it takes some tweaking to get a really good idea of what the
images actually look like. This is a challenge if you measure the data
properly with fine slicing low dose...
One thing which really helps is to
Dear All,
Starting from here I would just use the generate_XDS.INP script developed
by Kay Diederichs:
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP
It will make the necessary input files from just the image headers.
best wishes Graeme
On Thu, May 7, 2015 at
you there!
Best wishes,
Graeme Winter, David Waterman Gwyndaf Evans
When? August 23rd, 2015 (Sunday), 10:00 AM – 3:30 PM
Where? Rovinj (Red Island), Hotel “Istra”, Huetterot congress hall
Registration fee: EUR 20,00 (Registration through the registration system
of the ECM29).
Number
is not relevant, percentage is.
Approximate consensus (i.e. what I will look at doing in xia2) - probably
follow Randy Read recipe from ccp4wiki as this seems to (probably) satisfy
most of the criteria raised by everyone else.
On Tue, Jun 2, 2015 at 11:26 AM Graeme
Hi Folks
Had a vague comment handed my way that xia2 assigns too many free
reflections - I have a feeling that by default it makes a free set of 5%
which was OK back in the day (like I/sig(I) = 2 was OK) but maybe seems
excessive now.
This was particularly in the case of high resolution data
Dear Mohamed
You can get the equivalent of frame.CBF by using the duals image viewer
with datablock or experiments.json and integrated.pickle. this will allow
you to step through the frames looking at the actual integration boxes.
Best wishes Graeme
On 21 May 2015 17:02, Mohamed Noor
Dear Ivan
This is not a xia2 error, rather something very unhappy with ccp4i - you
should be getting this error from almost any ccp4i session? I expect more
ccp4i expert people will be able to help here.
It is also possible (indeed, easier) to run xia2 from the command line, for
more
of the better ways through
which we can ensure preservation (or at least another backup) of our most
important diffraction images?
- Ally
ps I should also say that I originally learned of Zenodo from Graeme Winter
at Diamond.
-
Allister Crow
Department of Pathology
University o
in model refinement" Skubak P, Murshudov GN,
Pannu NS. Acta Cryst. 2004 D60: 2196-2201 "REFMAC5 dictionary: organisation
of prior chemical knowledge and guidelines for its use." Vagin, AA,
Steiner, RS, Lebedev, AA, Potterton, L, McNicholas, S, Long, F and
Murshudov, GN. Acta Cryst. 2004 D60: 2
Dear Wolfram
For
“I was looking for a well-defined, stable interface for scripting in python“
You can do much worse than using cctbx i.e.
>>> from iotbx import mtz
>>> m = mtz.object('scaled.mtz')
(then play with m i.e. help(m) to discover capabilities) – I use this all over
the place in
From:
http://www.ccp4.ac.uk/ccp4bb.php
“CCP4bb is an electronic mailing list intended to host discussions about topics
of general interest to macromolecular crystallographers. Any
crystallographic-related item is acceptable, and doesn't have to be directly
related to CCP4. The bulletin board
Dear Smith
F is some structure factor amplitude, probably half of a map coefficient. Fobs
is presumably related to some intensity observation. Important point though:
you can name the columns in an MTZ *whatever you like* i.e. F1, F2, F_Hg, … so
beyond some conventions adopted by CCP4 programs
1 - 100 of 143 matches
Mail list logo
