[ccp4bb] S2C2 Modeling Workshop, 15–17 January 2020

[Dunn, Lisa B.]

S2C2 Modeling Workshop,  15–17 January 2020



Stanford-SLAC CryoEM Center (S²C²) will offer a training workshop held at SLAC 
National Accelerator Laboratory between January 15 and 17, 2020.  This workshop 
covers the basic principles and practical protocols to obtain atomic models 
based on cryo-EM density maps at near atomic resolution. This workshop will 
consist of three days of lectures and hands-on training sessions.

Speakers

· Paul Adams, LBNL

· Tom Goddard, UCSF

· Greg Pintilie, Consultant, Stanford University

· Cathy Lawson, Rutgers

There is no fee for this workshop.  If you are interested in attending in 
person please apply by December 20, 2019. 
https://cryoem.slac.stanford.edu/s2c2/training/s2c2-workshops/next-workshop


The missions of the Stanford-SLAC Cryo-EM Center (S2C2) are:

1. to provide access to state-of-the-art cryo-EM instruments for data 
collection towards atomic resolution structure determination of biochemically 
purified single particles.

2. to enable scientists across the nation to become independent cryo-EM 
investigators capable to carry out the entire workflow from specimen 
preparation to structure validation.

The S2C2 is supported by the National Institutes of Health Common Fund 
Transformative High Resolution Cryo-Electron Microscopy 
program.

See also:

Future S²C² Training 
Workshops

In-Residence Training 
Program

Project Application

Onsite Stanford Guest 
House  and  
Stanford Lodging Guide




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[ccp4bb] Two Marie Curie PhD position on structural studies of DNA helicases involved in genome maintenance

[Silvia Onesti]

We are looking for two PhD students within a MSCA-ITN grant entitled “DNA 
helicases in genome maintenance: from molecular and cellular mechanisms to 
specific inhibitors as potential drugs” (AntiHelix). The project aims to obtain 
a detailed picture of the mechanism of action and the physiological role of a 
number of DNA helicases that are implicated in human diseases, as well as 
discover specific inhibitors of those enzymes, which can then be tested as 
novel therapeutic drugs, especially for cancers. Our role will focus on the 
structural, biochemical and cellular characterization, with one studentship 
focussing on RecQ4 and the other on proteins belonging to the FeS helicase 
family. 

More info on the whole project can be found here: 
https://www.elettra.eu/AntiHelix/ 

The positions are subjected to the usual MSCA eligibility rules (not more than 
4 year from the degree that allows you to do a PhD, and transnational mobility) 
and will start in February/March 2020.

Our laboratory is located at the Italian synchrotron facility Elettra, Trieste. 
Elettra is an international research centre, hosting a large number of 
scientists and users, with a thriving programme of in-house research. The 
Structural Biology laboratory includes state-of-the-art facilities for cell 
biology, molecular biology, large scale protein expression and purification, 
crystallization and structure determination, biochemical and biophysical 
charaterization. Trieste is a beautiful, multicultural city, at the border 
between Italy and Eastern Europe and hosts numerous International research 
centres, having the highest density of scientists in the whole of Europe!
More information on the host laboratory can be found here: 
https://www.elettra.trieste.it/it/lightsources/labs-and-services/biolab/structural-biology-lab.html
 

https://www.facebook.com/Elettra-Structural-Biology-Lab-240626766554284/ 

For more information please contact Silvia Onesti: silvia.one...@elettra.eu 

-
Silvia Onesti - Head of Structural Biology

Elettra - Sincrotrone Trieste S.C.p.A.
AREA Science Park, 34149 Basovizza, Trieste ITALY

Email: silvia.one...@elettra.eu
Tel. +39 040 3758451  Mob +39 366 6878001

http://www.elettra.trieste.it/People/SilviaOnesti 

http://www.elettra.trieste.it/labs/structural-biology 

---





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Re: [ccp4bb] 8/ 2263 spots indexed XDS

[Almudena Ponce Salvatierra]

Dear all,

after a week looking more closely into the datasets, also with the help of
Manfred Weiss and Kay Diederichs, who kindly offered to look at some of
them, I come back to you to report on our findings (should this info be
useful in the future to any of you). Thank you very much everybody for your
replies. :)

I have 11 datasets, collected from 3 very small crystals (30-40 um aprox).

While the highest resolution for the "best datasets" extended to 4 or 4.5
Angstroms, two aspects that contributed to the difficulty in processing
were: radiation damage and also the presence of multiple lattices. It was
necessary to look through the images and select the wedges where there were
(single) spots at "high resolution" (often after only 180 degrees of data
collection the crystals were considerably damaged and attempts to process
the 360 degrees that were collected didn't work or resulted in extremely
poor overall statistics).

For the indexing of multiple lattices I have had the opportunity to try
programs like CrysalisPro from Rigaku and Proteum from Bruker (sorry I
didn't try DIALS yet, although I was advised to do it too!) and I can tell
that they do a fine job in finding the crystal lattice despite the ugliness
of the spots. However, since only small wedges of the data were useful and
I have a low symmetry space group, I couldn't take great advantage of their
capabilities, though. In some of the datasets, we could also see that
indexing of few frames gave ok statistics, but as more and more frames were
added to the processing (also as the presence of the second lattice became
more evident) the statistics became worse.

With the exception of 3 datasets (belonging to the same crystal), were the
spots were streaky/multiple/splitted, the others could be treated to a
greater or a lesser extent and processed with the XDS.INP file resulting
from generate_XDS.INP.

Also, the fact that many spots were selected by COLSPOT but very few were
used in the IDXREF step was due to the fact that I had some ice rings (how
could I miss that, right?) and many were picked from there. So, once again,
carefully selecting the SPOT_RANGE or defining it more than once, as well
as using the keyword EXCLUDE_RESOLUTION_RANGE where the ice rings were, or
simply cutting the resolution at 4 Angstroms, alleviated the problem in
most cases. Kay also advised me to use DELPHI=20, which is used during the
INTEGRATE step, and although its default is 5, it's good to increase its
value in instances where there are few strong reflections that can be used
for learning spot profiles (avoids geometry refinement with too few
reflections in INTEGRATE). With the data that I have, very weak, I was also
advised by Kay not to lower the MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT below 3
- but rather to increase it to 6 if my reflections were big. And if the
latter was done (MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=6) lower STRONG_PIXEL
to 3.

Although the first instinct from many of you was to think that there was
something wrong with the input, like detector distance, origin, oscillation
range, etc., all these parameters were recorded correctly. I think that the
fair way to summarize this all is "it's crappy data" (for a number of
reasons), because the programs and the synchrotron software did their job
fine.

So thank you once again everyone for helping me and participating in this
discussion, I will now go back to the lab and try to grow nicer, better
ordered, bigger crystals ;)

All the best,

Almu

El vie., 29 nov. 2019 a las 14:43, Tim Gruene ()
escribió:

> Dear Almudena,
>
> SPOT_MAXIMUM-CENTROID is probably the keyword in XDS.INP that you want to
> increase in your situation. The default is 3. Try e.g. 5, and increase
> slowly
> to make sure that the suggested solution makes sense
>
> Best regards,
> Tim
>
> On Friday, November 29, 2019 12:48:11 PM CET Almudena Ponce Salvatierra
> wrote:
> > Dear all,
> >
> > I have some data sets that don't want to be processed :p
> >
> > In one of them, when I look at IDXREF.LP I see virtually none of the
> found
> > spots were indexed and the reason is that they are "too far from the
> > expected position". The spots are smeary and elongated, so not the
> > prettiest.
> >
> > I have managed to process so far only one data set with decent statistics
> > from another crystal harvested from the same drop, where the diffraction
> > spots look better.
> >
> > I am trying to find in the xds wiki the keyword I should fine tune in
> order
> > to make those spots indexable.
> >
> > Could you help me please?
> >
> > Thank you very much in advance.
> >
> > Best wishes,
> >
> > Almu
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: 

[ccp4bb] PhD position in Structural Biology of Novel Plastic Degrading Enzymes in Portsmouth (UK)

[Michael Zahn]

Dear all,

We are looking for a motivated young research student with a strong
background in biochemistry, structural biology and/or biophysics to join
our newly established *Centre for Enzyme Innovation (CEI)* at the
University of Portsmouth (UK) to work on *Novel Plastic Degrading Enzymes*.
This position is a *fully-funded four year PhD studentship* available to UK
and EU students only to commence in *October 2020*. Application
deadline is *7th
February 2020*.
The PhD will be supervised by *Dr Michael Zahn
,
Prof John McGeehan

*
and
* Dr Andy Pickford.
*

Full job descriptions and person specifications are available on our
recruitment website:
https://www.port.ac.uk/study/postgraduate/postgraduate-research/research-degrees/phd/explore-our-projects/structural-and-biophysical-characterisation-of-novel-plastic-degrading-enzymes

Portsmouth is a harbour city on the south coast of England, 90 minutes away
by train from London with affordable living costs.

Best Regards,
Michael Zahn



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