[ccp4bb] SwissFEL Call for 2024-II

[Beale John Henry]

Dear all,

Please allow me to draw your attention to the open SwissFEL call for the second 
semester of 2024. If you have any questions regarding available instrumentation 
– please do not hesitate to contact the responsible person listed below. We 
look forward to hearing from you.

Please consult the following website to obtain general information about the 
call, the status of the available instruments, and the offered setups: 
https://www.psi.ch/swissfel/calls

=

SUBMISSION DEADLINE
The deadline for the submission of beam time requests for the Swiss Free 
Electron Laser 'SwissFEL' https://www.psi.ch/swissfel will be: March 15, 2024, 
midnight (CET).
==

EXPERIMENTAL PERIOD
Herewith we call for proposals for the beam time period between:
August 1 to December 31, 2024.
=

INSTRUMENTS
The following instruments will be open for new proposals:

 SwissFEL ARAMIS Alvra: https://www.psi.ch/alvra/
 SwissFEL ARAMIS Bernina: https://www.psi.ch/bernina/
 SwissFEL ARAMIS Cristallina-MX: https://www.psi.ch/en/swissfel/cristallina

 SwissFEL ATHOS Maloja: https://www.psi.ch/en/swissfel/maloja
 SwissFEL ATHOS Furka: https://www.psi.ch/de/swissfel/furka
=

PROPOSAL-SUBMISSION
All submissions will be handled by the PSI Digital Users Office (DUO: 
https://duo.psi.ch / contact: useroff...@psi.ch).
More information is published on: https://www.psi.ch/swissfel/submission
==

CONTACTS
New users are kindly asked to contact the beamline scientist before submitting 
a proposal to discuss instrumental options and technical feasibilities.

 SwissFEL ARAMIS Alvra: Dr. Camila Bacellar, 
camila.bacel...@psi.ch
 SwissFEL ARAMIS Bernina: Dr. Henrik Lemke, 
henrik.le...@psi.ch
 SwissFEL ARAMIS Cristallina-MX: Dr. John Beale, 
john.be...@psi.ch

 SwissFEL ATHOS Maloja: Dr. Kirsten Schnorr, 
kirsten.schn...@psi.ch
 SwissFEL ATHOS Furka: Dr. Elia Razzoli, 
elia.razz...@psi.ch
 ===


_
Paul Scherrer Institut
John Beale (he/him)
SFX Beamline Scientist
WSLA/224
Forschungsstrasse 111
5232 Villigen PSI
Schweiz

Telefon: +41 56 310 4715
Locofon: +41 79 281 87 14

Home Office: Monday morning
Office hours: Tuesday, Wednesday, Thursday, Friday
Bürozeiten: Dienstag, Mittwoch, Donnerstag, Freitag



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Re: [ccp4bb] Coot SSM Superpose Problem

[Paul Emsley]

On 16/02/2024 01:45, zx2...@connect.hku.hk wrote:

Dear all,

Hello Xin,


I encountered an issue while attempting to calculate the RMSD between 
two PDB files (each containing 4 ASUs)


do they really though?


using the SSM Superpose tool in Coot. Unfortunately, the tool was 
unable to superpose all ASUs accurately.



That's because you have mismatched bundles. It seem to me that you need 
some "Symm Shift Reference Chain Here" action.



Paul.




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[ccp4bb] Structural Biology Workshop, June 10-12 2024

[Myles, Dean A A]

Dear All,

We would like to bring to your attention  the 2024 Neutrons in Structural 
Biology workshop.  This workshop will highlight the need for next-generation 
instruments and toolsets for structural biology, with a focus on neutrons and 
other complementary techniques, and the development of integrated experimental 
and computational frameworks that connect them.



Neutrons in Structural Biology - Challenges & Opportunities,

June 10-12th 204

Sheraton Pentagon City Hotel, Arlington, VA.



For details and registration see: Neutrons in Structural Biology - Challenges 
and Opportunities (10-June 12, 2024): Overview * ORNL Neutron Sciences 
Conferences (Indico) (sns.gov)



The workshop will include a 1-day satellite training workshop (June 10, 2024) 
to educate graduate students and postdoctoral researchers in the application of 
neutron techniques in structural biology.
A limited numbers of travel awards are available to support graduate students 
and post-doctoral fellows attendance at the workshop (see link above)
The travel award application deadline is April 12, 2024.




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[ccp4bb] Postdoctoral position is available in the laboratory of Dr Igor Barsukov (University of Liverpool UK)

[Antonyuk, Svetlana]

Postdoctoral Position in Structural Biology of Cell-Matrix Adhesion

We are currently recruiting for a 3-year postdoctoral position in the field of 
Structural Biology of Cell-Matrix Adhesion at the Biochemistry and Cell Biology 
department of Liverpool University, UK. This position is funded by the BBSRC 
and offers a unique opportunity to contribute to cutting-edge research in the 
laboratory of Dr. Igor Barsukov.

As a successful candidate, you will have a strong background and expertise in 
either protein NMR spectroscopy or X-ray crystallography. Your primary focus 
will be on studying the structure and function of protein complexes involved in 
the formation of cell-matrix fibrillar adhesions, which play a crucial role in 
tissue formation, integrity, and regeneration. Recent research in our 
laboratory has highlighted the regulatory role of the adaptor protein tensin in 
fibrillar adhesions, particularly through its interactions with integrins and 
other proteins within the adhesion complexes. However, the precise mechanisms 
underlying this regulation, particularly the ability of tensin to form 
molecular condensates through phase separation, are not fully understood. In 
this position, you will utilize a wide range of biophysical techniques and 
advanced protein modifications to investigate the molecular details of tensin 
condensation and its interaction with integrin and other adhesion proteins.

Our department offers a supportive and technology-rich research environment for 
structural biology and biochemistry. This includes access to state-of-the-art 
facilities such as a High-Field NMR facility equipped with 600, 700, and 800 
MHz spectrometers with high-sensitivity cryo probes. We also have a Barkla 
X-ray crystallography facility with regular access to powerful synchrotron 
radiation facilities, as well as a protein analysis facility with advanced 
instruments for studying protein interactions.

To be considered for this position, you should hold a PhD degree in Biological 
Sciences or Chemistry. The post is available for a duration of 3 years. For 
more information, please contact Dr. Igor Barsukov at i...@liverpool.ac.uk.

To apply for this position and for more detailed information, please visit 
http://tinyurl.com/5e35csak. The closing date for applications is 15-Feb-2024





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Re: [ccp4bb] About Staraniso

[Clemens Vonrhein]

Dear Pavel & CCP4bb readers,

On Wed, Feb 14, 2024 at 08:28:03PM -0800, Pavel Afonine wrote:
> What follows below is not very specific to the particular program
> (STAIRSANISO) nor the original questions, but nonetheless, I believe it is
> relevant.

Thanks for joining the discussion: always good to have different viewpoints
or opinions made visible - especially for less knowledgeable users and
readers of the CCP4bb.

And apologies to anyone getting tired of "another long post" here, but
some remarks do require follow-ups that hopefully will help keep the
discussion at a level useful to all readers.

> In the past, performing any adjustments to the diffraction data intended
> for solving and refining atomic models was more or less considered taboo.

That is a very broad statement that I have trouble making sense of: what do
you mean with "adjustments" and what do you mean with "diffraction data"?
If we are truly looking at diffraction data as it comes out of our
experiment, we are looking at the raw images, right?  Those are then
handled roughly as follows (as an example for MX):

  * initial integrated intensities (simplifying 3D pixel data)
  
  * profile fitting of integrated intensities

  * scaling (with various parametrisation models)

  * selection of data (excluding image ranges due to radiation damage or
because a crystal moves out of the beam, excluding/handling ice-ring
contamination, selecting datasets in SSX etc)

  * adjustment of error model (to get "meaningful" error estimates,
i.e. sigma values)

  * outlier rejection (based largely on those sigmas)

  * merging (inverse-variance weighted)

Maybe all those "adjustments to the diffraction data" are not what you are
referring to in your remark above? So let's assume you are referring to the
merged intensity data after all of the above steps as being "the
diffraction data" ... and what we are doing after that:

  * conversion from intensities to amplitudes (using different methods and
priors) which most often will include an adjustment of weak and
negative intensities (e.g. via the French & Wilson method [1]).

  * decision what reflections to use for subsequent steps

- defined by geometric constraints (we can only use those that hit the
  detector)

- defined by some significance criterion

resulting in an adjustment of the dataset (not the values themselves)
coming out of the raw diffraction data.

Maybe this is still not what you are referring to as "adjustments to
the diffraction data"? Let's see what additional "adjustments to the
diffraction data" might happen further along ...

  * anisotropic scaling of the diffraction data /without/ the use of any
atomic model, as provided e.g. by

- the UCLA Anisotropy Server [2,3], using the anisotropy analysis
  from Phaser [4]

- STARANISO [5], using its own analysis

  * relative anisotropic scaling of the diffraction data and the current
model in refinement, e.g. in

- REFMAC [6,7]

Note: this includes writing a set of observed amplitudes into the
output MTZ file that have been corrected using the model-based
overall anisotropy factors (as far we know and at least up to
version 5.8.0352). So any "structure factor" deposition using only
the output reflection data from such a run will have anisotropy
corrected observed observed data in the PDB archive. Our
aB_deposition_combine tool described below detects and undoes this
(when combining the reflection mmCIF data from processing with the
reflection data after refinement) to ensure that data exactly as
used as /input/ to the refinement program is deposited.

- CCTBX [8] and Phenix [9,10]

- SHELX [11,12,13]

- BUSTER [14]

  * classification and rejection of model-based outlier reflections

- in Phenix [15] (still default?)

  * DFc completion for missing observations in 2mFo-DFc electron density maps

- default in REFMAC (into single FWT/PHWT by default as far as we know)

- default in Phenix (into an additional set of map coefficients?)

- default in BUSTER (into two additional sets of map coefficients,
  2FOFCWT_iso-fill/PH2FOFCWT_iso-fill using a sphere and
  2FOFCWT_aniso-fill/PH2FOFCWT_aniso-fill using the anisotropic cut-off
  information from STARANISO).

Which of all of the above are you referring to as being "considered taboo"?
It would be helpful if you could clarify this so that we can then focus on
that particular point in our discussion.

> When cryo-EM emerged as a competitor to x-ray crystallography, the paradigm
> began to shift. In cryo-EM, manipulations applied to the data (the map) are
> a standard practice. The map can be boxed, filtered (sharpened, blurred,
> etc.), modified (e.g., setting something outside the molecular region), and
> so forth; you name it. One might wonder why the same isn't done to x-ray data.

I don't think it is true that 

Re: [ccp4bb] problems with pandda.inspect / coot

[Tobias Krojer]

Hi Ruth,

I can’t help you with pandda.inspect, but I wrote a plugin for COOT which is 
kind of a lightweight version of it: You can download it here:
https://github.com/tkrojer/pandda_inspect_tools

Let me know in case you have problems with it.

Best,
Tobias

From: CCP4 bulletin board  on behalf of Ruth Brenk 

Date: Thursday, 15 February 2024 at 17:50
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] problems with pandda.inspect / coot
Hi,

I am trying to run Pandda. I could run pandda.analyse on the provided
dataset for the tutorial without any issues.

But I don't manage to run pandda.inspect. Coot opens, but I don't get
the Pandda interface. The last message I get from coot is:
/scratch/software/ccp4-8.0/coot_py2/libexec/coot-bin: option `--script'
requires an argument

Any ideas what's going wrong?

Ruth

--
Prof. Dr. Ruth Brenk
University of Bergen
Department of Biomedicine

ruth.br...@uib.no
+47 55586070


Visitor address: Mail address:
Jonas Lies vei 91Postboks 7804
5020 Bergen  5020 Bergen
Norway   Norway



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[ccp4bb] problems with pandda.inspect / coot

[Ruth Brenk]

Hi,

I am trying to run Pandda. I could run pandda.analyse on the provided 
dataset for the tutorial without any issues.


But I don't manage to run pandda.inspect. Coot opens, but I don't get 
the Pandda interface. The last message I get from coot is: 
/scratch/software/ccp4-8.0/coot_py2/libexec/coot-bin: option `--script' 
requires an argument


Any ideas what's going wrong?

Ruth

--
Prof. Dr. Ruth Brenk
University of Bergen
Department of Biomedicine

ruth.br...@uib.no
+47 55586070

 
Visitor address: Mail address:

Jonas Lies vei 91Postboks 7804
5020 Bergen  5020 Bergen
Norway   Norway



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Re: [ccp4bb] Combating disinformation in science and other areas

[David J. Schuller]

"Who is to be the arbiter of what is true and what is “misinformation”?


The way to uphold the integrity of science is with a free exchange of ideas, 
not an app or document that decides which publication or which interpretation 
of the data is real science and which is misinformation."


The problem with this approach is that not all participants are acting in good 
faith.

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

From: CCP4 bulletin board  on behalf of Daniel M. 
Himmel, Ph. D. 
Sent: Wednesday, February 14, 2024 10:40 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Combating disinformation in science and other areas


Dear all,


That’s a very nice idea to have an app to combat misinformation that can 
undermine the integrity of science and foster mistrust of scientific inquiry.  
But to launch such an app raises the obvious question:


Who is to be the arbiter of what is true and what is “misinformation”?


The way to uphold the integrity of science is with a free exchange of ideas, 
not an app or document that decides which publication or which interpretation 
of the data is real science and which is misinformation.


Thanks go to Bryan Lepore for pointing out that the work of Herbert Marcuse (a 
strong advocate of a brand of Marxism once popular in Germany) led to much 
violence in the USA.  Violent revolutions are how a great deal of science has 
been lost during the last several thousand years of human history, which is why 
we’re first determining atomic and near-atomic resolution structures in the 
20th and 21st centuries, not eons ago.


So, my humble request:  Can we stick to crystallography and allied fields of 
structure determination on this e-mail list, and not digress into divisive 
politics, please?


Respectfully submitted,

Daniel



[https://ci3.googleusercontent.com/mail-sig/AIorK4yaaDCOito7kuxLPC8Vy7HwqDw5i6DzTzprxgG0ijHkV1cwNX6leSeq_9r7EK46_M0TzQrRM-c]

Daniel M. Himmel, Ph. D.

Principal, Himmel Sci Med Com, LLC

E-mail:  danielmhim...@gmail.com

URL   :  https://himmelscimedcom.com



On Wed, Feb 14, 2024 at 7:52 AM Bryan Lepore 
mailto:bryanlep...@gmail.com>> wrote:
The idea of "Global Sustainability" can be found in the documents for the noted 
projects, so the United Nations "Sustainable Development Goals" appear to be 
worth reviewing as background - even though it appears the UN or UNESCO (below) 
is irrelevant to them :


“Transformation is the red thread running through all the Sustainable 
Development Goals, the United Nations’ agenda for responding to global 
challenges facing humanity and the planet. Setting our world on a more 
sustainable course requires radical shifts in current development paradigms 
that are exacerbating inequalities and imperilling [sic] our common future. 
This transition is dependent on new knowledge, research and competences that 
only higher education institutions are in a position to provide, rooted in 
their historic role of service to society.”

[...]

“In 1964, inspiring the 1968-student revolt a couple of years later, Herbert 
Marcuse wrote a key text against “one dimensional man”, urging universities and 
campuses around the world to become places that resisted reductionism. ”


Source:


Parr, et. al.

“Knowledge-driven actions: transforming higher education for global 
sustainability”

2022
UNESCO
https://doi.org/10.54675/YBTV1653



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[ccp4bb] British Biophysical Society: 2024 Biennial meeting - save the date!

[Mads Gabrielsen]

I would like to draw your attention to the upcoming meeting. This meeting
covers a range of biophysical methods, including structural biology. 

 

 

 

The British Biophysical Society (BBS) Biennial Meeting 2024

University of Swansea Bay Campus

11-13 September, 2024

 

 

We'll look forward to seeing you there!

 

 

Mads Gabrielsen MSc PhD Cert PStat (He/Him)

British Biophysical Society Committee

Technical Lead

 

Integrated Protein Analysis Facility

 

Room B4-13

Joseph Black Building

University of Glasgow

G12 8QQ

 

+44 141 330 6447

 

 

 

  mads.gabriel...@glasgow.ac.uk

 

 

https://www.gla.ac.uk/researchinstitutes/biology/research/structuralbiologyb
iophysicalcharacterisationfacility/

 

I am a Community Co-lead for the University's Research Culture Commons.
 Join the network here. Find out
more about how the University is working towards
 our five Research
Culture Priorities. Tell us what makes a thriving research culture via this
 anonymous comment form.

 




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