[ccp4bb] AsCA 2018/CRYSTAL 32: Registration Open!

[Christopher Squire]

[https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-public/d231daa0bdac4db99817bc87d65a4b98]


Registration for the AsCA 2018/CRYSTAL 32 Conference (2 - 5 December 2018 at 
the University of Auckland, New Zealand) is now open!

Please follow this link to register http://asca2018.org/registration/

Workshop registration is not yet open, however please use the voting function 
here to advise which of the four potential 
workshops would be of most interest to you.

Finally, a reminder that submissions are now open. Please visit the Call for 
Abstracts page for more information 
and to submit an abstract.

Should you have any queries regarding the AsCA 2018/CRYSTAL 32 Conference, 
please do not hesitate to contact us using the email address listed below.

Kind regards,

Event Services
University of Auckland
Email: asca2...@auckland.ac.nz



[https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-public/74ff1f66f2454a1badc85ad293b9e939]

[ccp4bb] Issues with update manager in ccp4 updates 52 and 53

[Andrey Lebedev]

Descriptions are now available online:
http://www.ccp4.ac.uk/updates/
If your update manager does not start, look at No 3 and 4 - they may
relate to your case.
Best wishes
Andrey

[ccp4bb] Postdoctoral position at the University of Toronto, Canada

[Jinrong Min]

 A postdoctoral position is immediately available in the group of Jinrong Min 
in the Structural Genomics Consortium at the University of Toronto. My lab aims 
to characterize protein-protein, protein-DNA and protein-RNA complexes by X-ray 
crystallography in combination with other biochemical and biophysical 
techniques. More details about our research can be found at the  
http://www.sgc.utoronto.ca/Chromatin or 
https://www.ncbi.nlm.nih.gov/pubmed/?term=min%20jinrong.

Applicants should have a Ph.D. in structural biology, biochemistry, or 
molecular/cell biology with 0-3 years postdoctoral research experience.  
Interested candidates are invited to send their CV with 3 references to Dr. 
Jinrong  Min by email: jr@utoronto.ca. 

 Jinrong Min 
Principal Investigator, Structural Genomics Consortium 
Associate Professor, Department of Physiology University of Toronto 
101 College St., Toronto On M5G 1L7, Canada 

[ccp4bb] CCP4i2 on Windows: issue with update 52

[Andrey Lebedev]

Dear CCP4 Users,

The has been an issue with the CCP4 Update 52 released on 28 Feb 2018.

This will only affect I2-interface users on Windows with there CCP4
installation at version 7.0.052. (The version is shown at the very top
of the interface window). To apply new updates you will have to use
(only once) the old interface or to type "ccp4um" in CCP4-Console
window (the icon should be on your Desktop).

Apologies for any inconvenience caused and best wishes

Andrey

[ccp4bb] Beamtime @ SLS

[Meitian Wang]

===
SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT SLS
===

Proposal application deadline: Sunday, April 15, 2018

Periods:
July 1, 2018 - December 31, 2018 (Normal / Test proposals)
July 1, 2018 - June 30, 2020 (Long-term proposals)

Proposal submission:
http://www.psi.ch/sls/px-beamlines-call-for-proposals 


Travel support is available via CALIPSOplus (http://www.calipsoplus.eu/ 
)

What's New (http://www.psi.ch/sls/pxi/pxi ) 
- X06SA
Fast beam size changing from 5 x 5 to 80 x 80 micron^2, one-micron beam 
available
EIGER 16M detector (133 Hz)
Continous grid scan (100Hz)
Serial crystallography with automated data processing and merging
- X06DA
Rapid access mode for experimental phasing, especially native-SAD 
(contact directly vincent.olie...@psi.ch )
- Sample changer
30 second sample exchange time

Beamline characteristics and features
X06SA Beamline (http://www.psi.ch/sls/pxi/pxi )
X06DA Beamline (http://www.psi.ch/sls/pxiii/pxiii 
)
X10SA Beamline (http://www.psi.ch/sls/pxii/pxii 
)

Best regards,

The MX group at SLS
__
Meitian Wang
Swiss Light Source at Paul Scherrer Institut
CH-5232 Villigen PSI - http://www.psi.ch/sls/ 
Phone: +41 56 310 4175

Re: [ccp4bb] biological molecule?

[Carter, Charlie]

Many thanks Joel and others.

There is a download button that is so obvious but has no options; I never 
explored the new layout of the menu bar. 

Charlie
> On Apr 9, 2018, at 5:59 PM, Joel Tyndall  wrote:
> 
> Hi Charlie,
> 
> I just visited the RCSB PDB website and looked up a random structure. You can 
> still download the biological unit in pdb format from the download files 
> pulldown
> 
> J
> 
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Carter, Charlie
> Sent: Tuesday, 10 April 2018 9:56 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] biological molecule?
> 
> I knew this would happen one day. I loathed the cif versions of the 
> coordinates, but fortunately, I’ve never had to use a .cif file. 
> 
> Now, the pdb no longer offers anything but…
> 
> I cannot find in the .cif file where the instructions are to generate the 
> biological molecule from the asymmetric unit. How does one do this please?
> 
> Thanks,
> 
> Charlie

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  on behalf of Zhang Yu 

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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[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