[ccp4bb] RapiData at SSRL 2019

[Smith, Clyde]

Hi everyone,

Applications are now open for the 2019 edition of RapiData at SSRL. RapiData is 
a practical course in macromolecular X-ray diffraction data collection, data 
processing and structure solution. The aim of the RapiData course is to educate 
and train young scientists in data collection and processing methods at 
synchrotron beamlines, using state-of-the-art software and instrumentation. The 
course will be held at the Stanford Synchrotron Radiation Lightsource (SSRL) 
located on the SLAC National Accelerator Laboratory campus in Menlo Park, CA, 
from May 5-10 2019. Course organizers for 2019 are Silvia Russi, Clyde Smith 
and Jeney Wierman.

The course will comprise hands-on experiments at the SSRL beamlines, software 
tutorials, and lectures on the following topics:
Specimen preparation, Data collection strategies, X-ray light sources, X-ray 
detectors, Data reduction, Structure solution by MAD, SAD and Molecular 
Replacement, Complementary methods (spectroscopy and small angle scattering)

Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2019/ and use 
the links on the "registration" page to apply for the course. The application 
deadline is December 31 2018 Successful applicants will be notified early in 
January 2019 and invited to register and book accommodation at the SLAC 
Guesthouse at that time. A limited amount of travel support funding may be 
available.

Please direct questions to Silvia Russi (sru...@slac.stanford.edu), Jeney 
Wierman (jwier...@slac.stanford.edu) or Clyde Smith (csm...@slac.stanford.edu).



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Re: [ccp4bb] suggestions for cryoprotectant

[Christine Gee]

Dear Fridous

Have a look at https://www.ncbi.nlm.nih.gov/pubmed/14646118
Malonate as a cryoprotectant

Or https://www.ncbi.nlm.nih.gov/pubmed/20606259

Regards
Christine

On Fri, Oct 19, 2018 at 2:57 PM Firdous Tarique 
wrote:

> Dear members
>
> I have got beautiful crystal hits in SaltRx screens which are not
> diffracting to a good resoultion. All of them are salt based condition and
> I am not able to formulate a good cryoprotectant for these crystals. I also
> think that in my case the poor resolution is due to a poor cryoprotectant
> selection.
>
> The conditions are as follows:
>
> 1> 4M Ammonium Acetate 100mM Bis Tris Propane pH 7.0
> 2>0.5M KCN 100mM Tris pH8.5
> 3>1.5M LiSo4 100mM Bris Tris Propane pH 7.0
> 4>4M Sodium Nitrate 100mM Tris pH8.5
> 5>1.5M Sodium Nitrate 100mM Sodium acetate pH 4.6
>
> There are few more conditions but so far not able to see good diffraction
> with using lower peg and glycerol based cryoprotectants.
>
> Can anybody suggest me good cryos conditions for salt based
> crystallization conditions or anything good for SaltRx crystallization hits.
>
> Thanks
>
> Firdous
>
> --
>
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>



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Re: [ccp4bb] suggestions for cryoprotectant

[Pascal Egea]

Hi Firdous,

I noticed that conditions 2,4 and 5 are overall harsh agents (chaotropic
agents such as KSCN (probably not KCN) and Nitrate ions ), in my own
personal experience I have never been very lucky with crystals grown in
nitrate ions.
Condition 1 however looks a bit more soft with 'gentle' ions.
May I suggest trying a sodium malonate screen or seeding in such a
crystallization agent and maybe trying to cryprotect those acetate crystals
in malonate which is a cryo-friendly so-called 'magic salt'. crystals grown
in carboxylates such as citrate and malonate are usually easier to
cryo-protect.

Hope this helps

Pascal Egea

On Fri, Oct 19, 2018 at 2:57 PM Firdous Tarique 
wrote:

> Dear members
>
> I have got beautiful crystal hits in SaltRx screens which are not
> diffracting to a good resoultion. All of them are salt based condition and
> I am not able to formulate a good cryoprotectant for these crystals. I also
> think that in my case the poor resolution is due to a poor cryoprotectant
> selection.
>
> The conditions are as follows:
>
> 1> 4M Ammonium Acetate 100mM Bis Tris Propane pH 7.0
> 2>0.5M KCN 100mM Tris pH8.5
> 3>1.5M LiSo4 100mM Bris Tris Propane pH 7.0
> 4>4M Sodium Nitrate 100mM Tris pH8.5
> 5>1.5M Sodium Nitrate 100mM Sodium acetate pH 4.6
>
> There are few more conditions but so far not able to see good diffraction
> with using lower peg and glycerol based cryoprotectants.
>
> Can anybody suggest me good cryos conditions for salt based
> crystallization conditions or anything good for SaltRx crystallization hits.
>
> Thanks
>
> Firdous
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
Pascal F. Egea, PhD
Assistant Professor
UCLA, David Geffen School of Medicine
Department of Biological Chemistry
Boyer Hall room 356
611 Charles E Young Drive East
Los Angeles CA 90095
office (310)-983-3515
lab  (310)-983-3516
email pegea at mednet.ucla.edu



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[ccp4bb] suggestions for cryoprotectant

[Firdous Tarique]

Dear members

I have got beautiful crystal hits in SaltRx screens which are not
diffracting to a good resoultion. All of them are salt based condition and
I am not able to formulate a good cryoprotectant for these crystals. I also
think that in my case the poor resolution is due to a poor cryoprotectant
selection.

The conditions are as follows:

1> 4M Ammonium Acetate 100mM Bis Tris Propane pH 7.0
2>0.5M KCN 100mM Tris pH8.5
3>1.5M LiSo4 100mM Bris Tris Propane pH 7.0
4>4M Sodium Nitrate 100mM Tris pH8.5
5>1.5M Sodium Nitrate 100mM Sodium acetate pH 4.6

There are few more conditions but so far not able to see good diffraction
with using lower peg and glycerol based cryoprotectants.

Can anybody suggest me good cryos conditions for salt based crystallization
conditions or anything good for SaltRx crystallization hits.

Thanks

Firdous



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[ccp4bb] Computational cryo-EM faculty position at the Morgridge Institute for Research and UW-Madison

[Eric Montemayor]

Dear Colleagues,

A great faculty-level opportunity between the Morgridge Institute for
Research and the University of Wisconsin-Madison. We seek to hire a
tenure-track assistant/associate/full professor in the broad area of
cryo-EM centered quantitative image processing and analysis. This position
is part of a major campus cryo-EM expansion, comprising new faculty hires
in experimental and computational cryo-EM, and a facility to house four new
cryo-microscopes including Thermo Fisher’s 300 kV Titan Krios, 200 kV Talos
Arctica, 120 kV Talos L120C, and Aquilos cryo-FIB-SEM.

For more information about this post and the application process, please
click the link below. Deadline for applications is December 15, 2018.

Morgridge (computational cryo-EM) -
https://morgridge.org/job-posting/investigator-cryo-em/

For more information about the other cryo-EM related faculty positions,
please click the links below. Each search has its own deadline for receipt
of applications. The positions will remain open until filled.

Biochemistry -
http://jobs.hr.wisc.edu/cw/en-us/job/499479/biochemistry-faculty

Virology -
http://jobs.hr.wisc.edu/cw/en-us/job/499366/virus-proteinnucleic-acid-ultrastructure-imaging-cluster-hire

Bacteriology -
http://jobs.hr.wisc.edu/cw/en-us/job/499304/assistant-professor

For additional information, please contact Liz Wright (erwrig...@wisc.edu).

--
Eric J. Montemayor
Associate Scientist
Department of Biochemistry
University of Wisconsin Madison
433 Babcock Dr. Room 145
Madison, WI 53706



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[ccp4bb] 50% TA position at U. Konstanz

[Olga Mayans]

Dear colleagues,

We have a part-time opening for a technical assistant in our laboratory at the 
University of Konstanz. The position might be of interest to candidates in our 
geographical area. Please kindly bring it to the attention of suitable 
applicants in your lab.

Full details at:

https://stellen.uni-konstanz.de/jobposting/969fc6c37f577d1bbd9640926c79bcc7d86879a8

Many thanks,

Olga


===
Prof. Olga Mayans
Biophysics and Structural Biology
Department of Biology
Universität Konstanz
D-78457 Konstanz,
Germany
Tel: +49 7531 88-2212
olga.may...@uni-konstanz.de
===



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[ccp4bb] ARP/wARP-8.0 + CCP4-7.0.065 joint release

[Andrey Lebedev]

Dear CCP4 Users

We would like to announce the joint release of ARP/wARP version 8.0
and CCP4-7.0.065.

ARP/wARP 8.0 provides a considerably improved performance for X-ray
crystallographic applications and it is now also capable of interpreting
cryo-EM maps at a resolution range 2.0-3.5 Å.

Installation and compatibility
-Checks for software installation have been enhanced
-32 and 64-bit platforms on OSX and Linux are supported
-ARP/wARP is fully compatible with the latest versions of CCP4 and Refmac

Protein chain tracing
-Protein chain tracing has been made faster and its memory handling
 has been improved
-DipCheck conformational space is introduced for the selection of
 the chain path
-NCS restraints are now default at resolution 1.5 Å or lower
-Loop closure can now be provided using a new module Loopy2018

Sequence docking and building
-Side chain guess and fit can now be accomplished using a new
 module SEQQY
-Handling of large structures has been enhanced and the maximum
 number of NCS copies increased to 60
-Both mono- and hetero-multimers can now be handled

DNA/RNA building
-Nucleotide chain tracing is enhanced with the addition of the
 second algorithm for phosphate detection
-Nucleotide chain tracing now proceeds in an iterative manner, as
 for protein tracing

Identification of crystallographic ligands
-Energy estimate for protein-ligand bound state is introduced
 during identification of crystallographic ligands

Solvent building
-Building of solvent structure exploits advanced features of Refmac
 including TLS and local NCS restraints.
-Solvent update can optionally be turned off providing a tool for
 model refinement with Refmac.

Building models into cryo-EM maps
-Protein and protein-nucleic acid models are built with a minimum user input
-Map over-sharpening is handled automatically
-Partial models can be completed by sequence-docking and loop building
-Models can be refined with a combined real- and reciprocal-space protocol
-A very fast secondary structure modelling option can be used separately.



An update No 65 for the CCP4-7.0 series automatically installs
ARP/wARP-8.0 on Mac OS X and Linux computers, where ARP/wARP-7.6 has
previously been installed as a part of CCP4 installation. (The
directory arp_warp_7.6 is _not_ removed , but CCP4 i1 and i2 are
switched to version 8.0). In addition, the update No 65 brings the
following changes.
* refmac5: correction to LINK records
* contact: increase MaxSelectedResidues
* dials: inclusion of mock module
* pointless: update to 1.11.6
* rabdam: update to 1.4.1
* crank2: fixes and improvements
* documentation: correction to freerflag documentation

In addition, tarballs and bundles for CCP4 Setup Manager consisting of
CCP4-7.0.065 and ARP/wARP 8.0 are available from CCP4 Downloads:
http://www.ccp4.ac.uk/download

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4 and ARP/wARP.

The CCP4 Core Team



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Re: [ccp4bb] viewhkl : misleading intensity appearance ?

[Eleanor Dodson]

As you say, the two are related but look different, and the intensity on
the subsequent images look different too
However there are some default scaling parameters, and I have no idea what
they are..

Any alternating strong/weak pattern should generate a strong off-origin
peak in the native Patterson . Is there such a feature?

The cell dimensions are rather symmetric a~= c; beta ~= 120?
Is there an alternative Space group?

Eleanor



On Fri, 19 Oct 2018 at 08:51, Stefano Trapani  wrote:

> Hi
>
> The attached screen shots show the first ten h sections of a merged
> dataset. The sections are displayed using both the "hklview" (on the left)
> and "viewhkl" (on the right) programs.
>
> The first time I looked at the data I used "viewhkl" and I got the
> impression that odd-h sections had systematically higher intensities than
> even-h sections (see right-hand side of the pictures; I observed that for
> h ≥ 10 too).
>
> When I saw this behaviour I though I was in presence of some kind of
> crystal "pathology".
>
> However the calculated average square |F|'s did not actually show
> systematically alternate values for odd and even h values (see plot). The
> "viewhkl" display was somehow misleading (to me).
>
> On the other hand, if one looks at the "hklview" display (on the left)
> this behaviour seems to disappear (this is at least my impression).
>
> Why the two programs display intensities so differently ? Is it just my
> personal visual impression ? I am using default display parameters.
>
> Best regards
>
> --
>
> Stefano Trapani
>
> Maître de 
> Conférenceshttp://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani
> -
> Centre de Biochimie Structurale (CBS)
> 29 rue de Navacelles
> 34090 MONTPELLIER Cedex, France
>
> Tel : +33 (0)4 67 41 77 29
> Fax : +33 (0)4 67 41 79 13
> -
> Université de Montpellier
> CNRS UMR 5048
> INSERM UMR 1054
> -
>
>
> --
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[ccp4bb] EMBL Workshop "Cryo-EM in Industry & Academia", Heidelberg, 6-8 February 2019

[Christoph Mueller]

Dear Colleagues,

This is to invite you to the workshop "Cryo-EM in Industry & Academia", 
that we are organizing at EMBL Heidelberg, 6-8 February 2019. The 
workshop will focus on success stories and new technologies, but also on 
challenges industry is facing using cryo-EM. The workshop is equally 
aimed at academic researchers interested in the impact of 
state-of-the-art cryo-EM in drug discovery, and cryo-EM support staff 
that want to learn more about the specific needs of industry.  Further 
information can be found at 
https://www.embl.de/training/events/2019/CPP19-01/
Deadlines for Registration: 20 Dec 2018 and for Abstract Submission: 15 
Nov 2018.


Best wishes,
Christoph Müller

--

Dr. Christoph W. Müller
Head of Structural and Computational Biology Unit

EMBL
Meyerhofstrasse 1
69117 Heidelberg, Germany

email: cmuel...@embl.de
phone: 0049-6221-387-8320
fax: 0049-6221-387-519
http://www.embl.de
http://www.embl.de/research/units/scb/mueller_christoph/index.html
-



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