[ccp4bb] Command line use of Indexing reference mtz and autosetting of resolution limits to a specific I/sigI minimum.

[Nichols, Charlie]

Hi,

I want to reprocess a large batch of mtz files from Dials using Aimless and cut 
the resolution so the outer-shell I/sigI is >=1.0
I also want them to be consistently indexed so want to specify 'Match index to 
reference' and provide a reference mtz with IMEAN used as the label for index 
matching.


So, Firstly:
I am running Aimless from command line with scripts. Is there a way to specify 
auto-setting of data output resolution cutting to a specific outer-shell I/sigI 
value?

  *   At present I've just been cutting the resolution back by 0.15A and 
grepping the I/sigI values. This mostly moves them to >=1 with a small set of 
high-anisotropy data where I need to examine the scaling logfile and apply a 
further cut


Secondly:
How do I specify an indexing reference file from the command line - Aimless 
documentation only seems to cover Scaling to reference not indexing to reference


Thanks for your help,
Take care, Charlie.






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[ccp4bb] Fwd: Position open in the HILIFE Instruct-FI cryoEM unit for a research technician - please distribute

[Kajander, Tommi A]

Daer All,

FYI, we have a job opening in CryoEM for research technician in Helsinki.

Best,
Tommi


Tommi Kajander, Ph.D.
Head of Unit, Protein crystallisation
INSTRUCT-HiLIFE
Institute of Biotechnology
University of Helsinki
Viikinkaari 1 (P.O. Box 65)
00014 Helsinki, Finland
p. +358-50-4480991
http://www.helsinki.fi/kajanderlab



From: "Butcher, Sarah" 
mailto:sarah.butc...@helsinki.fi>>
Subject: Position open in the HILIFE Instruct-FI cryoEM unit for a research 
technician - please distribute
Date: 16. June 2023 at 10.58.16 EEST
To: "Lak, Behnam" mailto:behnam@helsinki.fi>>, John 
Dolan mailto:j...@instruct-eric.org>>, 
"finstruct...@helsinki.fi" 
mailto:finstruct...@helsinki.fi>>, 
"tuesday-biophys...@helsinki.fi" 
mailto:tuesday-biophys...@helsinki.fi>>, 
"cryo...@scilifelab.se" 
mailto:cryo...@scilifelab.se>>, 
"michael.elb...@weizmann.ac.il" 
mailto:michael.elb...@weizmann.ac.il>>, 
"sharon.w...@weizmann.ac.il" 
mailto:sharon.w...@weizmann.ac.il>>, Celia Romao 
mailto:cmro...@itqb.unl.pt>>

Dear all,
we have an opening for a laboratory technician in the HILIFE Instruct-FI cryoEM 
unit, University of Helsinki, Finland. Deadline for applications 27.6.23. 
Please advertise further.
 
https://jobs.helsinki.fi/job/Laboratory-technician%2C-cryogenic-electron-microscopy-service/773176102/?feedId=350602&utm_source=CareerSite_UniversityOfHelsinki

 Best regards

Sarah
_
Prof. Sarah Butcher, Ph.D.
Molecular & Integrative Biosciences Research Programme
Faculty of Biological and Environmental Sciences
&
Helsinki Life Science Institute-Institute of Biotechnology
room 2405
P.O. Box 56 (Viikinkaari 9)
FIN-00014 University of Helsinki
Finland
office: +358 2941 59563
cell: +358 50 4155492

https://researchportal.helsinki.fi/en/persons/sarah-butcher
https://blogs.helsinki.fi/butcher/
https://www.helsinki.fi/en/infrastructures/integrated-structural-cell-biology/cryoem
https://www.vibrant-itn.eu/
https://www.itqb.unl.pt/impact







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Re: [ccp4bb] Adding metal ions

[Krieger, James M]

Charmm-gui can add copper ions and lots of other ones.

They seem to have removed the option of adding specific ions by numbers and 
instead give a box for concentration and an option to check how many there are. 
This depends a lot on the size of the box around the protein and you can maybe 
do a rough back of the envelope calculation to get started.

You would also need to set the padding distance to zero to get the ions on or 
near the protein surface. We tend to use around 10A either side for MD 
simulations to avoid the protein seeing itself across the periodic boundary, 
maybe even more padding if we expect significant conformational changes.

They also seem to only have an option of adding them in neutral pairs so you’d 
have to remove chloride ions afterwards.

Best wishes
James

On 16 Jun 2023, at 06:00, Veerendra Kumar  wrote:


Dear All,
I want to add about 200 copper ions on protein surface randomly. Is there any 
program available to serve the purpose?

Thank you
Best regards
Veerendra

Get Outlook for Android



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[ccp4bb] CCPBioSim Industry Talk - online

[Sarah Fegan - STFC UKRI]

Hi all,

Our next industry talk is coming up soon - Wednesday 28 June 2023 at 2pm UK 
time. This online talk by Antonija Kuzmanic from Schrodinger will cover 
protein-ligand structures and drug design along with her experiences developing 
a career in industry. Please visit https://www.ccpbiosim.ac.uk/schrodinger2023 
for all the details and to register for a Zoom link.

Title: Application of molecular dynamics simulations in predicting and 
analysing protein-ligand interactions

Abstract: Many structure-based drug design (SBDD) methods, including advanced 
free energy calculations, require accurate, atomic-level detail of the target 
protein structure in complex with a member of the ligand series of interest to 
perform optimally. Consequently, the domain of applicability of SBDD is limited 
by the availability of high-resolution crystal structures of the target protein 
or its close homologues. Alternatively, low-resolution structures could also be 
of use, but they might need refining, while AlphaFold2 structures completely 
lack a bound ligand, so the subtle details of protein-ligand interactions are 
left undetermined. In this talk, I will discuss simulation-based approaches 
that allow us to elucidate the intricacies of the protein-ligand interactions 
with a focus on a recently developed workflow (IFD-MD) that can predict the 
atomic details of the protein-ligand complex structure needed for SBDD, 
starting from either the target with a different ligand in the binding site or 
from a structure of a highly homologous protein.

Best wishes,
Sarah



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Re: [ccp4bb] Command line use of Indexing reference mtz and autosetting of resolution limits to a specific I/sigI minimum.

[Phil Evans]

Thinking further about this, Aimless essentially would need to be run twice to 
do automatic resolution cutoff. I could make it an internal loop to essentially 
it twice, I suppose. But in I2 my preferred method is to use the “information 
content” from Phaser as the metric for resolution

Phil

> On 16 Jun 2023, at 09:08, Nichols, Charlie  wrote:
> 
> 
> CAUTION: This email originated from outside of the LMB.
> Do not click links or open attachments unless you recognize the sender and 
> know the content is safe.
> .-owner-ccp...@jiscmail.ac.uk-.
> 
> Hi,
>  
> I want to reprocess a large batch of mtz files from Dials using Aimless and 
> cut the resolution so the outer-shell I/sigI is >=1.0
> I also want them to be consistently indexed so want to specify ‘Match index 
> to reference’ and provide a reference mtz with IMEAN used as the label for 
> index matching.
>  
>  
> So, Firstly:
> I am running Aimless from command line with scripts. Is there a way to 
> specify auto-setting of data output resolution cutting to a specific 
> outer-shell I/sigI value?
>   • At present I’ve just been cutting the resolution back by 0.15A and 
> grepping the I/sigI values. This mostly moves them to >=1 with a small set of 
> high-anisotropy data where I need to examine the scaling logfile and apply a 
> further cut
>  
>  
> Secondly:
> How do I specify an indexing reference file from the command line – Aimless 
> documentation only seems to cover Scaling to reference not indexing to 
> reference
>  
>  
> Thanks for your help,
> Take care, Charlie.
>  
>  
>  
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 



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Re: [ccp4bb] Adding metal ions

[Artem Evdokimov]

Take a protein structure with waters, replace surface waters with Cu++ and
run some very basic MD to optimize distances. Many of the atoms will move
since Cu++ will find itself in an 'unfriendly' environment, as always
caveat emptor :)

Artem

- Cosmic Cats approve of this message


On Fri, Jun 16, 2023 at 12:00 AM Veerendra Kumar  wrote:

> Dear All,
> I want to add about 200 copper ions on protein surface randomly. Is there
> any program available to serve the purpose?
>
> Thank you
> Best regards
> Veerendra
>
> Get Outlook for Android 
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Save the dates: CCP4-BCA Summer School in York 19-25 August 2023

[Johan Turkenburg]

Dear All,

Registration for the 2023 Summer School in York is now open, see the link
on the website at
https://www.ccp4.ac.uk/schools/ccp4-summer-school/index.php

As you will see the BBSRC is generously funding fees for up to 10 students,
while the BCA is also providing some bursaries. And there is additional
support from generous suppliers, see the bottom of the landing page.

Come and join us for what promises to be another exciting summer school.

The organisers,
Johan Turkenburg, Jon Agirre and Paul Bond


On Fri, 2 Jun 2023 at 16:56, Jon Agirre  wrote:

> Dear all,
>
> It is a great pleasure to announce the return of the CCP4-BCA Summer
> School on macromolecular crystallography and associated techniques, to be
> held at the University of York on 19-25 August 2023.
>
> Running in-person for the first time since the COVID-19 pandemic, the
> school aims to bring together early-career scientists in the UK, Europe and
> beyond and train them in the latest advances in structural biology, with a
> primary focus on macromolecular crystallography. The school, which was
> formerly run at the University of St. Andrews for many years, has trained
> hundreds of crystallographers while also providing them with unforgettable
> collective memories. The York team aims to capture and continue the essence
> and tradition of the school, blending it with the best the City of York has
> to offer.
>
> Registration will open soon, but in the meantime feel free to check out
> our preliminary programme on our website:
> https://www.ccp4.ac.uk/schools/ccp4-summer-school/index.php
>
> The organisers,
> Johan Turkenburg, Jon Agirre and Paul Bond
> --
> Dr Jon Agirre
> Royal Society University Research Fellow (assistant professor)
> CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo (Elixir)
> York Structural Biology Laboratory, Department of Chemistry
> University of York, Heslington, YO10 5DD, York, UK
> Office: B/K065 Phone: +44 (0) 1904 32 8252
>


-- 
Dr. Johan P. Turkenburg (he/him)Senior Technical Specialist
X-ray and cryo-EM
York Structural Biology Laboratory
University of York
York YO10 5DD   UK
Phone (+) 44 1904 328251 (also when working from home)
https://orcid.org/-0001-6992-6838
EMAIL DISCLAIMER https://www.york.ac.uk/docs/disclaimer/email.htm




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[ccp4bb] Pan-structural biology sample prep workshop at ACA

[Christina Zimanyi]

Dear All,

We wanted to bring your attention to our workshop at the upcoming ACA annual 
meeting on Sample Attributes for Multiple-techniques and Principal Requirements 
for Experiments in Pan-structural biology - SAMPREP 
(https://www.acameeting.com/workshop2-sam23)


This one-day workshop will be held Friday, July 7th, the first day of the ACA 
meeting in Baltimore, MD. It will focus on how to prepare the best possible 
samples for successful use of multiple structural biology techniques, 
particularly small angle X-ray scattering, cryo-EM and X-ray crystallography. 
The content is aimed at investigators new to the practical application of 
structural biology methods or for those with experience in one technique to 
gain the knowledge they need to pursue others (or inspire you to consider those 
you haven’t used before!). There will be a strong emphasis on practical 
application: knowing how to judge sample quality and suitability for different 
techniques and how to troubleshoot during sample preparation. We will discuss 
what you can expect to learn from the different methodologies and how to set 
expectations for a successful experiment across the spectrum of commonly used 
techniques that benefit from data collection at synchrotron sources and cryo-EM 
centers.


The workshop is part of the ACA meeting (see link above) and registration 
closes June 30th. If you are already registered for the meeting, you can still 
register for a workshop until the June 30th deadline by contacting the ACA 
office. We hope to see some of you there!


Organizers:

Christina Zimanyi, National Center for CryoEM Access and Training, New York 
Structural Biology Center

Silvia Russi, Structural Macromolecular Biology Division, SSRL, SLAC National 
Accelerator Laboratory

Sarah EJ Bowman, National High-Throughput Crystallization Center, 
Hauptman-Woodward Medical Research Institute

James Byrnes, Center for Biomolecular Structure, NSLS II, Brookhaven National 
Laboratory

Kushol Gupta, Perelman School of Medicine, University of Pennsylvania & Johnson 
Foundation Structural Biology and Biophysics Core

Marco Mazzorana, Diamond Light Source, Ltd (UK)

Vivian Stojanoff, Center for Biomolecular Structure, NSLS II, Brookhaven 
National Laboratory

Thomas Weiss, Structural Macromolecular Biology Division, SSRL, SLAC National 
Accelerator Laboratory




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