Re: [ccp4bb] DIALS 3.11 release: graphical utilities broken

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Dear all,

Updated release at https://dials.github.io/installation.html - 3.11.1 - now 
based on Python 3.9.13 - with  working graphical utilities

Sorry to those who stubbed their toes on this, many thanks to my colleagues for 
fixing this on 1st day back :-)

All the best Graeme

On 30 Aug 2022, at 16:31, Winter, Graeme (DLSLtd,RAL,LSCI) 
<6a19cead4548-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Hello everyone including brave souls who are keen to use the latest greatest 
version of DIALS - the recently released 3.11

Sorry

Please don’t

We have had a couple of reports of issues with the graphical utilities in here 
caused by upstream changes in Python which have completely broken the graphical 
libraries on which we depend

Locally detailed at

https://github.com/dials/dials/issues/2216

For anyone who wants to see the gory details which are a side-effect of

https://github.com/python/cpython/issues/82180

As this is in our graphical interface tools it is not subject to automated 
testing and it would appear that those of us who are developing on 3.10 did not 
stumble across the problem

We will make a .1 release in the next couple of days - it would appear that the 
nightly builds are also affected by the same issue.

In the meantime I recommend people download the previous latest release 3.10.3

https://github.com/dials/dials/releases/tag/v3.10.3

I would like to emphasise that the algorithms are still fine (I believe) this 
is just an error with the viewers but fixing this in the longer term could be a 
substantial body of work.

For those who get their DIALS from CCP4 you will be fine as that is still on 
Python 3.7 or 3.8 so will not be affected by these issues.

Best wishes Graeme


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[ccp4bb] DIALS 3.11 release: graphical utilities broken

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Hello everyone including brave souls who are keen to use the latest greatest 
version of DIALS - the recently released 3.11

Sorry

Please don’t

We have had a couple of reports of issues with the graphical utilities in here 
caused by upstream changes in Python which have completely broken the graphical 
libraries on which we depend

Locally detailed at

https://github.com/dials/dials/issues/2216

For anyone who wants to see the gory details which are a side-effect of

https://github.com/python/cpython/issues/82180

As this is in our graphical interface tools it is not subject to automated 
testing and it would appear that those of us who are developing on 3.10 did not 
stumble across the problem

We will make a .1 release in the next couple of days - it would appear that the 
nightly builds are also affected by the same issue.

In the meantime I recommend people download the previous latest release 3.10.3

https://github.com/dials/dials/releases/tag/v3.10.3

I would like to emphasise that the algorithms are still fine (I believe) this 
is just an error with the viewers but fixing this in the longer term could be a 
substantial body of work.

For those who get their DIALS from CCP4 you will be fine as that is still on 
Python 3.7 or 3.8 so will not be affected by these issues.

Best wishes Graeme

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Re: [ccp4bb] DIALS error

[Fuentes-Montero, Luis (DLSLtd,RAL,LSCI)]

Dear Maria,

The files  3_experiments,expt and 3_reflections.refl nust be inside the 
directory dui_files created by dui

warmest regards,

Luiso.

From: CCP4 bulletin board  on behalf of Winter, Graeme 
(DLSLtd,RAL,LSCI) 
Sent: 11 May 2020 14:58
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] DIALS error

Dear Maria

Please could you send (off list) the 3_experiments,expt and 3_reflections.refl 
files? Happy to take a look. I expect it’s related to your experiment geometry 
(beam centre or similar)

Thanks Graeme

On 11 May 2020, at 14:22, Demou, Maria 
mailto:maria.demou...@ucl.ac.uk>> wrote:

Hello,
I am very new to DIALS, and I have been trying to index these images, however 
whatever parameters I put there is no suitable lattice. I used half the images 
as the rest I was told had radiation damage, but still there is no result.



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Re: [ccp4bb] DIALS error

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Dear Maria

Please could you send (off list) the 3_experiments,expt and 3_reflections.refl 
files? Happy to take a look. I expect it’s related to your experiment geometry 
(beam centre or similar)

Thanks Graeme

On 11 May 2020, at 14:22, Demou, Maria 
mailto:maria.demou...@ucl.ac.uk>> wrote:

Hello,
I am very new to DIALS, and I have been trying to index these images, however 
whatever parameters I put there is no suitable lattice. I used half the images 
as the rest I was told had radiation damage, but still there is no result.



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[ccp4bb] DIALS 2.0: from images to MTZ files with DIALS

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Dear ccp4bb

We are pleased to announce the release of - DIALS 2.0: a complete toolkit for 
processing of X-ray diffraction data from area detector images through to 
scaled intensities - free to all users and every line of code available for 
inspection at https://github.com/dials/dials. 

Thanks to the efforts of everyone in the team we are please to announce the 
release of DIALS 2.0 for processing of crystallographic rotation data. This 
includes a large number of changes in particular:

• symmetry determination and scaling - used by default in xia2
• flexible workflows for challenging data
• improvements in speed across for all main steps in the analysis
• more consistent output file naming
• multi-crystal analysis with cosym and xia2.multiplex
• Python 3 compatible code (experimental: will be fully supported in 
2.1)

As always we are constantly working on bug fixes and improvements so the 
current release is version 2.0.2. The binaries for download can be found at:

Downloads: https://dials.github.io/installation.html

With the tutorial documentation at:

Documentation at: https://dials.github.io 

If you have any problems please feel free to log issues at:

Issues: https://github.com/dials/dials/issues 

Or drop us a line at dials-supp...@lists.sourceforge.net. DIALS 2 will be 
included in the forthcoming CCP4 7.1 release. 

This work is only possible thanks to the support of institutions and funding 
agencies:

Diamond Light Source
CCP4 
Biostruct-X project No. 283570 (EU FP7)
Wellcome Trust (Grant No. 202933/Z/16/Z) 
US National Institutes of Health grants GM095887 and GM117126

Which in turn reflects the support offered from the community for our efforts, 
so thank you. 

Sent on behalf of the DIALS development group.
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
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Re: [ccp4bb] DIALS spot finding

[james.parkhu...@diamond.ac.uk]

Dear Yu,


If you open the images using the dials.image_viewer command you should see a 
window called "settings", a screenshot of which I have attempted to attach 
below.


At the bottoms of the settings window are a number of buttons for seeing how 
the spot finding algorithm will behave. Clicking any of these will update the 
display with the following processed image data:


  1.  image - shows the raw image data
  2.  mean - shows the local mean image
  3.  variance - shows the local variance image
  4.  dispersion - shows the local dispersion image
  5.  sigma_b - shows the dispersion threshold mask
  6.  sigma_s - shows the mean pixel threshold mask
  7.  global - shows the global threshold mask
  8.  threshold - shows the combined threshold mask


The "threshold" button shows what the spot finder will consider to be strong 
pixels on an image.


The various threshold levels can be adjusted in the settings window (sigma 
background, sigma strong, global threshold, min local, gain and kernel size). 
Without seeing an image, it is difficult to make specific suggestions; however, 
playing with these might result in better spot finding.


Finally, in dials.find_spots, some filtering is done to remove e.g. very small 
and very large spots. If your spots are composed of less than 3 pixels with 
strong signal, then they will be filtered out. If you could post the contents 
of the dials.find_spots.log file, it might be possible to see if this is the 
case.


Best wishes

James


[cid:7a94b8be-c4b3-43ee-8902-7ebe4f4bc455]



From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Zhang Yu 
<ccp4f...@gmail.com>
Sent: 10 April 2018 08:16:36
To: ccp4bb
Subject: [ccp4bb] DIALS spot finding

Dear all,

I am just switching from HKL3000 to DIALS for processing data collected at 
EIGER detectors because it is too slow for the HKL300 to handle over 1000 
images per dataset.

Our crystals are not perfect and you would expect split spots or spots of 
multiple crystals in most cases. Sometimes we are lucky enough to extract spots 
of one lattice by playing with the spot-finding parameters in HKL 3000 and find 
an solution during the index step (changing spot size, more spots, fewer spots, 
restraining the resolution, etc.). However, it seems very difficult to adjust 
these parameters in the dials.find_spots step of DIALS.

The DIALS tutorial suggest checking the spots using "dials.image_viewer" after 
the spot findin step. By inspecting the images, it seems that most split sports 
were not included into the list of "strong spots" for indexing. What options do 
you have during the step of spot finding (especially fins strong spots for 
indexing) using DIALS?

Thank you in advance.
Best,
Yu

--
Yu Zhang
HHMI associate
Waksman Institute, Rutgers University
190 Frelinghuysen Rd.
Piscataway, NJ, 08904


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This e-mail and any attachments may contain confidential, copyright and or 
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are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

[ccp4bb] DIALS spot finding

[Zhang Yu]

Dear all,

I am just switching from HKL3000 to DIALS for processing data collected at
EIGER detectors because it is too slow for the HKL300 to handle over 1000
images per dataset.

Our crystals are not perfect and you would expect split spots or spots of
multiple crystals in most cases. Sometimes we are lucky enough to extract
spots of one lattice by playing with the spot-finding parameters in HKL
3000 and find an solution during the index step (changing spot size, more
spots, fewer spots, restraining the resolution, etc.). However, it seems
very difficult to adjust these parameters in the dials.find_spots step of
DIALS.

The DIALS tutorial suggest checking the spots using "dials.image_viewer"
after the spot findin step. By inspecting the images, it seems that most
split sports were not included into the list of "strong spots" for
indexing. What options do you have during the step of spot finding
(especially fins strong spots for indexing) using DIALS?

Thank you in advance.
Best,
Yu

-- 
Yu Zhang
HHMI associate
Waksman Institute, Rutgers University
190 Frelinghuysen Rd.
Piscataway, NJ, 08904

[ccp4bb] Dials

[张士军]

Dear all

When I run dials.index it result me "Sorry: No suitable lattice could be 
found", but the other software can give me C2 space group. How could I DO with 
this situation

Best Regards

Shijun

[ccp4bb] DIALS 1.5.1 released

[Graeme Winter]

Dear All,

DIALS 1.5.1 for synchrotron data has been released - full release notes at

https://github.com/dials/dials/releases/tag/v1.5.0

The software may be downloaded from

http://dials.github.io/installation.html
http://dials.diamond.ac.uk/installation.html
http://dials.lbl.gov/installation.html

Key changes:

*** CRITICAL ***

dxtbx: Converted models into C++. Bug fixes for HDF5/Eiger files to correct a 
previously inverted axis. In some cases sign of anomalous signal was inverted.

Request: examples of data from beamlines with Eigers to allow more thorough 
testing - was spotted with data from Spring8

More info: https://github.com/dials/dials/issues/324

*** IMPORTANT ***

dials.align_crystal: numerous bug fixes and simplified output
dials.find_spots: Correctly smooth histogram, #317
dials.geometry_viewer: display of crystal basis vectors, and added fast, slow, 
normal vectors to panels in display
dials.image_viewer: new mask generation tool; performance improvements
dials.import: full specification of meta data from phil parameters; can now 
import data with different detector etc into same file
dials.index: improvements to nearest neighbour analysis used in max_cell 
estimation (optionally choose between linear and logarithmic histogram binning)
dials.reciprocal_lattice_viewer: reciprocal unit cell display
dials.refine: equal shift constraints

*** XIA2 ***

xia2.report:
 - use merged intensities for calculating second moment statistics
 - include xtriage report;
 - include analysis of distribution of multiplicity in reciprocal space
 - add plots of completeness and multiplicity vs resolution
 - optionally choose cc_half_method=sigma_tau
xia2.multi_crystal_analysis: add stereographic projection plots for crystal 
orientation analysis

If you have any problems please contact dials-supp...@lists.sourceforge.net or 
report on our issue tracker:

https://github.com/dials/dials/issues

Best wishes Graeme (on behalf of DIALS development teams at Diamond, CCP4 & LBL)

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please notify us of receipt by returning the e-mail and do not use, copy, 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
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Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

[ccp4bb] DIALS 1.3 release / xia2 0.5

[Graeme Winter]

Dear CCP4BB

The DIALS team have now released DIALS 1.3 / xia2 0.5: this includes a number 
of fixes to problems reported over the last couple of months (detailed in 
release notes) as well as useful developments, particularly for Eiger detector 
data processing & small molecule data processing.

We would like to draw xia2 users to slight changes in the program output and 
the way the program command-line options work - detailed here:

http://xia2.blogspot.co.uk/2016/07/xia2-command-syntax-now-changed.html

As always, any problems please contact 
dials-supp...@lists.sourceforge.net 
or xia2.supp...@gmail.com, or if you like feel 
free to report issues at

https://github.com/dials/dials/issues

or

https://github.com/xia2/xia2/issues

(feature requests are always welcome)

Installers for Linux, MacOS X and MacOS X 10.6 as well as a source file 
distribution are available from:

http://dials.github.io/installation.html

Best wishes, Graeme (on behalf of the DIALS / xia2 development teams)

=

Release notes

DIALS 1.3.0 (2015-07-29):

• Improved support for processing compressed images (#79)
• More efficient parallel processing in dials.find_spots (#150)
• dials.image_viewer is now more responsive to parameter changes (#166), and 
can display resolution ellipses when detector is at 2theta angle > 0 (#66). 
Image annotations work for summed images (#107).
• The distl spotfinding webserver has been updated to the most recent versions 
of apache and mod_python, and expanded to support the dials spotfinder, 
including native support for Eiger HDF5 data from Dectris. Some documentation 
is available.
• dials.two_theta_refine provides a refinement of the unit cell parameters 
against the 2theta angles of indexed reflections.
xia2 0.5.45:

• xia2 version 0.5 includes a major overhaul of the available command line 
parameters (xia2/xia2#42). xia2 is moving away from switch-like command line 
parameters (eg. -3dii) to PHIL format parameters (eg. pipeline=3dii) - the same 
command line parameter format used in DIALS. Deprecation warnings are given for 
the most used commands, including all pipeline commands. Run xia2 without any 
parameters to get a very brief overview of available parameters.
• Unit cell sizes are obtained via 2theta refinement, and reported with 
estimated standard deviations when possible (xia2/xia2#28). The command 
xia2.get_unit_cell_errors will be removed in the future.
• Bruker CCD images (.sfrm) are now supported. It may be necessary to set a 
suitable gain value as command line parameter (eg. gain=10)
• xia2 generates a crystallographic information file (xia2.cif) by default 
(xia2/xia2#27)
• Small molecule processing now uses multi sweep indexer by default when 
possible (xia2/xia2#37). High resolution data are no longer cut off when 
running small molecule processing. To return to previous behaviour, use 
keep_all_reflections=false (xia2/xia2#30). xia2.small_molecule is a new 
shortcut for xia2 small_molecule=true.
• Spotfinding results are displayed for XDS pipeline processing (xia2/xia2#20)

Source Code installation

You can compile DIALS 1.3 from scratch by running

$ wget 
https://raw.githubusercontent.com/dials/cctbx/dials-1.3/libtbx/auto_build/bootstrap.py

$ python bootstrap.py --builder=dials hot update base build

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please notify us of receipt by returning the e-mail and do not use, copy, 
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are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
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Diamond Light Source Limited (company no. 4375679). Registered in England and 
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[ccp4bb] Dials

[David Schuller]

Does this look like a suitable solution for those who like dials while 
model building?


http://petapixel.com/2015/07/07/review-palettes-modular-photo-editing-controls-are-pricey-but-powerful/

http://www.cnet.com/news/buttons-and-sliders-and-knobs-oh-my-palette-offers-a-more-physical-interface-for-pcs/

http://palettegear.com/

Palette tactile controllers - a core unit hooks up to the computer via 
USB cord. Dials, buttons and sliders can be arranged in flexible 
configurations and snap together magnetically.


They advertise compatibility for Mac and Windows. No mention of Linux. 
It looks like a lot of effort and expense went into aesthetics and this 
makes the price somewhat high.


Still, there has not been a really good solution for a control interface 
with more than one dial for a while now.


Cheers,

--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

[ccp4bb] DIALS Workshop at ECM 29

[Graeme Winter]

Dear CCP4BB,

The DIALS team will be running a workshop at ECM29 this summer - more
information can be found at:

http://www.diamond.ac.uk/Home/Events/2015/Satellite-meetings-at-the-ECM.html

and is copied below. Registration is through the usual ECM registration
process. We look forward to seeing 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 of participants is limited to 30 and they will be accepted on a
first-come-first-served basis.

Applicants are kindly asked to book their own accommodation in Rovinj.
Registration fee includes lunch box and refreshments.

Website: http://dials.sourceforge.net

DIALS (Diffraction Integration for Advanced Light Sources) is a new
integration package being developed as a collaboration between Diamond
Light Source, CCP4 and Lawrence Berkeley National Laboratory, with
significant input from the MRC-LMB and funding from Biostruct-X workpackage
6. The aim of this workshop is to introduce new users to the package, with
a view to using the software for X-ray diffraction data processing from
macromolecular samples. Since the software is completely free and open
source the workshop attendees will have the opportunity to bring their own
laptop computers to have the software installed, and will need to do so to
run the tutorials.

[ccp4bb] DIALS-I workshop on X-ray Diffraction Data Analysis

[Gwyndaf Evans]

[Just to correct a few issue with my earlier announcement here it is again with 
subject line!]

Dear All,
I would like to draw your attention to the DIALS-I workshop on X-ray 
Diffraction Data Analysis to be held at Diamond Light Source on June 12th/13th 
2012.

For information about the programme and how to register for the workshop please 
go to  http://www.diamond.ac.uk/Home/Events/DIALS-1.html.

A more detailed programme will appear soon.

For any further information about the scope and purpose of the meeting please 
contact Gwyndaf Evans 
(gwyndaf.ev...@diamond.ac.ukmailto:gwyndaf.ev...@diamond.ac.uk).

The number of places on the workshop is limited so please register as soon as 
possible.

Regards,
The Organisers

Gwyndaf Evans, Graeme Winter, Alun Ashton and David Waterman