Dear Smita,
You need only do a format conversion I expect, no processing required. For this
you will want either f2mtz -
http://www.ccp4.ac.uk/html/f2mtz.html
or pointless - here use the -c option to copy rather than performing the
analysis on the data
helsinki.fi<mailto:tommi.kajan...@helsinki.fi>]
Sent: Monday, July 16, 2018 10:55 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] data processing with split/bad crystals
Dear All,
I was wondering what would be the best software nowadays to try to proces
helsinki.fi<mailto:tommi.kajan...@helsinki.fi>]
Sent: Monday, July 16, 2018 10:55 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] data processing with split/bad crystals
Dear All,
I was wondering what would be the best software nowadays to try to proces
lf of Kajander,
> Tommi A [tommi.kajan...@helsinki.fi]
> Sent: Monday, July 16, 2018 10:55 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] data processing with split/bad crystals
>
> Dear All,
>
> I was wondering what would be the best software nowadays to try to process
>
A [tommi.kajan...@helsinki.fi]
Sent: Monday, July 16, 2018 10:55 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] data processing with split/bad crystals
Dear All,
I was wondering what would be the best software nowadays to try to process data
from crystal that clearly is split or
has a secondary set
>
>
> From: CCP4 bulletin board on behalf of Andreas
> Förster
> Sent: 16 July 2018 22:14:49
> To: ccp4bb
> Subject: Re: [ccp4bb] data processing with split/bad crystals
>
> Dear Tommi,
>
> DIALS is good with multiple lattices. It mi
wishes Graeme
From: CCP4 bulletin board on behalf of Andreas Förster
Sent: 16 July 2018 22:14:49
To: ccp4bb
Subject: Re: [ccp4bb] data processing with split/bad crystals
Dear Tommi,
DIALS is good with multiple lattices. It might not have given you best
results
CrysAlisPro would be my best bet. It has an option for multicystals and
twinning. Also it offers a very good visual tools to see any relationships
between multiple lattices, if they have.
Rangana
On Mon, 16 Jul 2018 at 22:16 Andreas Förster wrote:
> Dear Tommi,
>
> DIALS is good with multiple
Dear Tommi,
DIALS is good with multiple lattices. It might not have given you best
results as part of the Diamond pipeline, but give it a try with the
max_lattices=2 parameter during dials.index and see where it takes you.
That said, you'll end up with worse statistics if you have two
Dear Tommi,
saint (Part of the Bruker APEX/Proteum suite) can integrate with, I think, up
to five orientation matrices at a time. It integrates smoothly with twinabs.
Saint seems quite sophisticated in modelling the reflection profiles from the
different lattices.
EvalCCD (Eval15?) may be able
Dear All,
I was wondering what would be the best software nowadays to try to process data
from crystal that clearly is split or
has a secondary set of lattice points (close, poor data) in the raw data - data
can be processed with XDS (2.9-2.8 Å) but Rmerge tends to be
bit high at low
Thank you very much for useful suggestions! :-)
Best,
Almu
2014-05-20 9:44 GMT+02:00 Kay Diederichs kay.diederi...@uni-konstanz.de:
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.
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 all,
I am looking for some suggestions here. I have lately collected some
datasets but the spots are very very weak... it is very difficult to
process them. At times it looks like XDS is stalled or at times it just
says that it can not interpret the lattice parameters... also while running
Hi Almudena
Have you tried Mosflm (since this is the CCP4 BB...)?
On 19 May 2014, at 17:18, Almudena Ponce Salvatierra wrote:
Dear all,
I am looking for some suggestions here. I have lately collected some datasets
but the spots are very very weak... it is very difficult to process them.
De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Almudena Ponce
Salvatierra [maps.fa...@gmail.com]
Envoyé : lundi 19 mai 2014 18:18
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] data processing with XDS
Dear all,
I am looking for some suggestions here. I have lately collected some
Hi Everyone,
Just wanted to let everyone know that i was able to process this dataset
with XDS ( and lots help from experts !)
Thanks again
Mahesh
On Mon, Aug 19, 2013 at 5:07 PM, Petri Kursula petri.kurs...@oulu.fiwrote:
I have often processed images like this with XDS. Of course, you
Thank you experts for your valuable suggestions. I think Ill try to solve
it by proper data collection strategy the next time as i am unable to
process my current data even with the tricks that were mentioned here.
Thanks again
Mahesh
On Fri, Aug 16, 2013 at 2:04 PM, Bosch, Juergen
Hi Mahesh,
TESTGEN START 1 END 120 ANGLE 0.5
moving the detector further back or using 2theta and collecting more frames.
When you started shooting at your image you should have checked for overlaps
ahead of time.
I assume this to about 1.8 Å - maybe it would have been wiser to collect a 2.5
Å
doesn't necessarily looked twinned to me.
Rather it looks like you have a trigonal or hexagonal cell with a long c-axis.
On image 2 it seems you may have systematic absences along l, although it is
hard to tell the order. Perhaps P31, P32, P62, P64 or spacegroups with these
symmetries plus
PS For future data collections, try to get the long c-axis roughly along the
crystal rotation axis if possible.
On 16 Aug 2013, at 16:38, Mahesh Lingaraju wrote:
Hi CCP4 folks
I have a data set which is looks twinned ( see the image-1 - I zoomed on to
the image so that one can spot the
Hi Mahesh
In addition to what Mark and Juergen have written, it looks to me like you have
very high mosaicity in one direction - the first image shows no distinct lunes;
I suspect that may have something to do with the failure to process - but what
do you mean when you say you cannot process
This is clearly a case of a crystal with a very long unit cell; a case
which should be approached mindfully.
HKL2000 has a default search for indexing solutions such that diffraction
along the longest unit cell will be resolved, with the assumed spot size.
The problem with such diffraction has 2
for #2)
I'd suggest get some of those Mitigen loops that are titled. I assume you have
hexagonal plates as crystals and you really want to shoot along the thin area
of the crystal down the sixfold. With normal loops it's an art to get that
crystal to sit upright in the loop but not impossible
This is clearly a case of a crystal with a very long unit cell; a case
which should be approached mindfully.
HKL2000 has a default search for indexing solutions such that diffraction
along the longest unit cell will be resolved, with the assumed spot size.
The problem with such diffraction has 2
This is continuation of the previous message, which was sent prematurely.
In case of crystals with one, very long unit cell data collection strategy
needs to be carefully chosen.
Ad. 2) What would be a better way to collect data in the future?
First, the detector needs to be placed far back
tilted is what I meant at an angle of e.g. 30 or 60 degrees. Works fine with
most SSRL beamlines except of the 12-2 microfocus - but that might have been
fixed in the meantime.
Jürgen
On Aug 16, 2013, at 1:57 PM, Bosch, Juergen wrote:
for #2)
I'd suggest get some of those Mitigen loops that
Hi there,
Thank you for all your suggestions and generous help, I tried some methods
you guys mentioned and learned something new . I really appreciate it.
With Kay's help,(after exclusion of the ice rings he found that the data are
P1, not P2(1). ) I got my structure solved, there are four copies
6:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] data processing problem with ice rings
Hi ChenTiantian,
the R-factors and I/sigma are bad even at low resolution where the first
icering does not influence the results.
Thus, the problem with your data processing has little to do
Hi ChenTiantian,
the R-factors and I/sigma are bad even at low resolution where the first
icering does not influence the results.
Thus, the problem with your data processing has little to do with the
icerings. I guess that the indexing is not correct.
My suggestion:
1) using adxv or a similar
Hi
I'd agree with Kay here - I would think that the original indexing is
incorrect.
One thing I notice on the original image as posted - there's a red
cross on it - if that's supposed to mark the beam position, I think
it's about 4mm or so away from the true position.
So -
(1) check
Hi,
I agree with other people. You must have a wrong index here. Can you tell us
what is the unit cell for this crystal from your determination? I can see
very close spots in the high resolution shell from your image, which are
overlapped into one spot in the low resolution shell. Try to use other
First of all, are you sure those are ice rings? They do not look typical. I
think you might have salt crystals from dehydration *before* freezing.
Otherwise, I think your freezing went well. Maybe try a humidity controlled
environment when you freeze.
Second, I'm not so sure the bad stats come
Your main problem is not the ice rings but a wrong lattice/indexing solution. R
factors are very high for even low res shells and I/sigma very low. To me this
tells you are not finding your diffraction spots at all.
First thing to try: Take more images for the indexing step and use only the
Hello ,
Can any one send me pdf of this paper as its a old paper and not
accessible here .
M.F. Perutz, Preparation of haemoglobin crystals. *J. Cryst. Growth*
, * 2 * (1968), pp. 54–56.
On Fri, Oct 14, 2011 at 10:42 AM, ChenTiantian
chentiantian2...@gmail.comwrote:
Hi
These rings are nanocrystalline cubic ice (ice Ic, as opposed to the
usual ice Ih). It is an interesting substance in that noone has ever
prepared a large single crystal of it. In fact, for very small crystals
it can be hard to distinguish it from amorphous ice (or glassy
water). The three
try a frozen xtal ...
On Fri, 14 Oct 2011 13:12:12 +0800
ChenTiantian chentiantian2...@gmail.com wrote:
Hi there,
I am processing a dataset which has bad ice rings (as you
can see in the
attach png file).
I tried both XDS and imosflm, and got similar results, it
seems that adding
: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Md. Munan Shaik
[munanbt2...@yahoo.com]
Sent: Tuesday, May 17, 2011 12:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Data processing
Dear all,
Can anybody give me some suggestion about data processing with mosflm. I want
to
process one dataset with defining the cell parameter.
I collect two dataset of the same crystal but when I am trying to index and
integrate then i saw some differences in the cell parameter.
I also
Labelit can act as a front end for Mosflm data processing. It has the
ability to use the same cell orientation when indexing the second data wedge
from the same crystal. Please follow the
labelit.store_crystal_orientation link at http://cci.lbl.gov/labelit for
instructions. Labelit is bundled
The program Pointless in CCP4 (Data reduction - Find symmetry) will combine
the files and average the unit cells. If they are very different you might have
to increase the tolerance, though you should then worry about whether it's
sensible to combine them
Phil
On 16 May 2011, at 22:40, Md.
Hi all,
Thank you all how have replied for their kind suggestions and diagnosis of
collected data.
sincerely
Debajyoti
On Sat, 26 Mar 2011 04:44:42 +0530 wrote
Hi all,
I have collected one iodine soaked data in our home source, and processing the
data using HKL2000. Exposure time
Hi all,
I have collected one iodine soaked data in our home source, and processing the
data using HKL2000. Exposure time per frame is 5min/1 degree.
While processing I have noticed that the Chisq values, cell parameters and
rotation change Vs frame are deviating like anything. Please find the
The most likely explanation is that you have a cracked crystal or your
crystal has split from radiation damage around the frame 70.
If you had a cracked crystal from the start, the spot overlap between
crystals would change when the sample was rotated. In such cases, it may
happen that the
Dear All,
I have the problem in processing the data with imosflm. The data was
collected with 2.5A resolution about 300 images. Auto index found the space
group P222 with unit cell a= 40.2; b= 79.2; c= 194.7 and α=b=γ = 90.0. For
this cell, the penalty is 7. I feel this penalty is good enough to
Have you picked from multiple images and do you have more than 1000 reflections
to index from?
You might also want to limit the resolution manually to perhaps 3 first.
Before processing your data you should refine your cell by using multiple
wedges of 10 degrees.
Check out the manual for
Hi Sampath
That message should never appear during refinement; the popup is called
from the autoindexing code in iMosflm, and once that process is completed
successfully there is no way the code can call it - so there's obviously
something very odd happening. Indexing appears to have succeeded
I would like to draw your attention to an upcoming free webinar series
that will cover several of the most widely used X-ray diffraction data
processing packages. This series is part of a larger webinar program that
focuses on topics 'near and dear' to the crystallographic community.
The
Criswell angela.crisw...@rigaku.com
To
CCP4BB@JISCMAIL.AC.UK
cc
Subject
[ccp4bb] Data processing webinars
I would like to draw your attention to an upcoming free webinar series
that will cover several of the most widely used X-ray diffraction data
processing packages. This series is part
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