Re: [ccp4bb] CCP4 v9 installation issue

Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornel

[ccp4bb] ONE WEEK LEFT TO APPLY: DLS/CCP4 data analysis workshop 2024

Well, just under one week left... Applications close Monday 16 September and will be evaluated shortly after. Best wishes, David On Mon, 2 Sept 2024, 09:36 David Waterman, wrote: > Hi folks, > > This is your two week notice before the closing date for applications to > the DLS/C

[ccp4bb] TWO WEEKS TO APPLY: DLS/CCP4 data analysis workshop 2024

Hi folks, This is your two week notice before the closing date for applications to the DLS/CCP4 workshop. Get your applications in soon to avoid missing out! Best wishes, -- David On Wed, 14 Aug 2024 at 14:07, David Waterman wrote: > Hi folks, > > Here's a reminder that applica

Re: [ccp4bb] Coot 1.* in CCP4 9

hings Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: Paul Emsley Sen

Re: [ccp4bb] Coot 1.* in CCP4 9

hings Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: Paul Ems

[ccp4bb] Coot 1.* in CCP4 9

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

Re: [ccp4bb] error in error message

erve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: CCP4 b

[ccp4bb] error in error message

t" is erroneous. === All Things Serve the Beam === David J. Schuller modern man in a post-modern world

Re: [ccp4bb] DLS/CCP4 data analysis workshop 2024

ishes, -- David On Fri, 26 Jul 2024 at 09:59, David Waterman wrote: > We are pleased to announce that applications are now open for the 11th > joint Diamond-CCP4 Workshop on MX data collection and structure solution! > Bringing together leading experts in the field of MX to teach best prac

[ccp4bb] DLS/CCP4 data analysis workshop 2024

on. - The course homepage: https://www.ccp4.ac.uk/schools/DLS-2024/ -- David (on behalf of the organisers) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=

Re: [ccp4bb] Presence of negative density in Sim Omit map

difference peak filling the void. I am more than happy to be corrected, though. Best, Dave -- Dr David C. Briggs CSci MRSB (he/him) Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK Working hours: Mon-Fri 0900-1700

Re: [ccp4bb] how to create a figure of a blob

Hi Andrea, Either CCP4mg or ChimeraX (with the Clipper plugin) can read .mtz files directly and create maps to output publication-quality blob pictures. Best, Dave Dr David C. Briggs CSci MRSB Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick

[ccp4bb] PhD position available in biochemistry and crystallography in Grenoble (France)

hamed.a...@cea.fr) and Philippe Carpentier (philippe.carpent...@esrf.fr) Sincerely, David Flot. -- Dr David FLOT Beam-Line Operation Manager Tel : (+33) 4 76 88 17 63 Structural Biology GroupFax : (+33) 4 76 88 26 24 ESRF e-mail : david.f...@esrf.fr h

[ccp4bb] CCP4-BCA Protein Crystallography Summer School (1st – 6th Sept 2024) hosted by the John Innes Centre – deadline extended to 24th June

-summer-school-2024/ Best wishes Dave --- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk<mailto:david.

Re: [ccp4bb] Ligand identification in X-ray density

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

[ccp4bb] CCP4-BCA Protein Crystallography Summer School (1st – 6th Sept 2024) hosted by the John Innes Centre

apply: https://www.jic.ac.uk/event/ccp4-bca-protein-crystallography-summer-school-2024/ Best wishes Dave --- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk

[ccp4bb] CCP4-BCA Protein Crystallography Summer School (1st – 6th Sept 2024) hosted by the John Innes Centre

--- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk<mailto:david.law...@jic.ac

Re: [ccp4bb] update manager

=== David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: CCP4 bulletin board on behalf of David

Re: [ccp4bb] update manager

part of the reason or not. I have version 8.0.017. === All Things Serve the Beam === David J. Sch

[ccp4bb] Fwd: Sixth ESRF-INSTRUCT workshop on sample preparation for cryo-EM, May 28-30, 2024

- Dear all, Quick reminder that the last date to register for the ESRF-INSTRUCT hands-on workshop on sample preparation for cryo-EM is approaching (7th April). The registration link is below. https://survey.esrf.fr/index.php/849989?new

Re: [ccp4bb] request for applications

On Mon, Apr 01, 2024, James Holton wrote: My question for the BB is: what would YOU do if you had $1e12 USD for your science? No non-scientific proposals please. There are plenty of other forums for those.  This BB is about biological structural science, so please stay on-topic.  OK?  And now

Re: [ccp4bb] Room temperature change from 25ºC to 20ºC

=== David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: CCP4 bulletin board on behalf of Nukri Sanishvili

Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

Hi Fred, CCP4 distributes the shelxl binary on Linux. I've not checked yet, but perhaps it is also part of CCP4 on Windows? Cheers -- David On Tue, 12 Mar 2024 at 09:38, Fred Vellieux wrote: > Hello and thanks for the reply. > > My input file came from my checking SHELX man

Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

? Cheers -- David On Tue, 12 Mar 2024 at 09:01, Fred Vellieux wrote: > Hi folks, > > I have a simple question: is there an electronic bulletin board for > small-molecule crystallography? I have checked the list of CCP projects > and there is no CCP-project for small molecule crystal

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

erial/Datareduction2015.pdf Cheers -- David On Fri, 23 Feb 2024 at 10:17, Harry Powell < 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi Graeme (I may well have mentioned this when we shared an office) et al > > I’ll add something from my small-molecule crystallography days,

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

David On Fri, 23 Feb 2024, 10:40 Huw Jenkins, < 288da93ae744-dmarc-requ...@jiscmail.ac.uk> wrote: > > On 23 Feb 2024, at 09:58, Winter, Graeme (DLSLtd,RAL,LSCI) < > 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > > > > so strictly it is possible and cor

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

uot; The problem with this approach is that not all participants are acting in good faith. === All Things Serve the Beam ===

Re: [ccp4bb] Truncate / ctruncate / moments of E etc.

Norman Stein's article at the back of this newsletter is the one I like! https://legacy.ccp4.ac.uk/newsletters/newsletter47/newsletter47.pdf -- David On Wed, 14 Feb 2024 at 15:14, Winter, Graeme (DLSLtd,RAL,LSCI) < 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > Good

[ccp4bb] Structural Biology Facility Manager vacancy at the John Innes Centre, Norwich UK

-time For further details, please visit our website http://jobs.jic.ac.uk or contact the Human Resources team on 01603 450814 or nbi.recruitm...@nbi.ac.uk quoting reference 1004561. Best Wishes, Dave Lawson --- Prof. David M. Lawson Department of Biochemistry and Metab

Re: [ccp4bb] SAXS models and data

Hi Gloria, There are repositories of SAXS data. https://www.sasbdb.org/ For example. Hth, Dave Dr David C. Briggs CSci MRSB Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == about.me/david_briggs<http://about

Re: [ccp4bb] Problem running CCP4I2 in CCP4 8

to do next." === All Things Serve the Beam === David J. Schuller modern man in a p

Re: [ccp4bb] Problems updating CCP4 via CCP4i

=== All Things Serve the Beam === David J. Schuller modern man in a post-modern world

Re: [ccp4bb] Resolution Discrepancy in Data Set

See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8248825/ Hope this helps, Dave Dr David C. Briggs CSci MRSB Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == about.me/david_briggs<http://about.me

Re: [ccp4bb] Alternatives to X

who you see in your local various feeds. You can post about whatever takes your fancy. I realise that this particular phrase has certain Brexity connotations, but Mastodon's democratisation/decentralisation of social media really allows one to "take back control" 🫠 Best, Dave

Re: [ccp4bb] Alternatives to X

Speaking of, Dave, did you mean at_fediscience_dot_org for this last instance? Both! -- Dr David C. Briggs CSci MRSB (he/him) Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK Working hours: Mon-Fri 0900-1700 == about.me

Re: [ccp4bb] Alternatives to X

struc...@a.gup.pe) that acts a bit like a distribution list. Hth, Contact me off list if I can help get you started. Dave @xtald...@xtaldave.net (Apologies if anyone got this twice - the original was pinged back as it tripped the spam filter, presumably the list of servers) Dr David C. Briggs CSci

Re: [ccp4bb] Fragile Crystals

3360-3369 === All Things Serve the Beam === David J. Schuller modern man in a post-mo

[ccp4bb] Structural Biology Facility Manager vacancy at the John Innes Centre, Norwich UK

-time For further details, please visit our website http://jobs.jic.ac.uk or contact the Human Resources team on 01603 450814 or nbi.recruitm...@nbi.ac.uk quoting reference 1004561. Best Wishes, Dave Lawson --- Prof. David M. Lawson Department of Biochemistr

Re: [ccp4bb] [OFF TOPIC] On Ni-NTA resin TEV cleavage

me of exposure to low pH by eluting the protein straight into some 1M Tris or HEPES to bring the pH back up to something more neutral. Hth, Dave Dr David C. Briggs CSci MRSB Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute Londo

Re: [ccp4bb] Issues in diffraction image export compatible to iMosflm

Hi, The latest version of DIALS may be able to read this format. If you can send me an image off-list I would be happy to check. Once in DIALS, it also may be possible to export the dataset in CBF format. Best wishes David On Tue, 10 Oct 2023, 06:28 Vyankatesh Rajmane, wrote: > Dear

[ccp4bb] DEADLINE APPROACHING: DLS/CCP4 data analysis workshop 2023

Hi folks, Please be reminded that the deadline for applying to attend this year's DLS/CCP4 workshop is *Monday 9th October at 17:00 UK time*. Best wishes, -- David On Tue, 26 Sept 2023 at 17:07, David Waterman wrote: > We are pleased to announce that the 10th joint Diamond-CCP4 Wor

[ccp4bb] DLS/CCP4 data analysis workshop 2023

previously collected datasets) will be given priority in selection. - The course homepage: https://www.ccp4.ac.uk/schools/DLS-2023/ - Apply at the Diamond website: https://www.diamond.ac.uk/Home/Events/2023/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2023.html -- David (on behalf of the

Re: [ccp4bb] Regarding RNA AMBER OL3 Force field

On Thu, Sep 21, 2023, Abhilasha Thakur wrote: If anyone is using the AMBER OL3 force field kindly send it to me. I am working on RNA str prediction. I think the official source of OL3 parameters is here: https://fch.upol.cz/ff_ol/ This will cite the correct references. OL3 is based on earli

Re: [ccp4bb] Outlawed PDB files, what should a muggle do

Of course the proper answer should be to fix dimple to read mmCIF (for which I would also recommend gemmi) -- David On Wed, 20 Sept 2023 at 16:35, David Waterman wrote: > gemmi convert --shorten 7qgf.cif foo.pdb > > ? > -- David > > > On Wed, 20 Sept 2023 at 15:57, Winte

Re: [ccp4bb] Outlawed PDB files, what should a muggle do

gemmi convert --shorten 7qgf.cif foo.pdb ? -- David On Wed, 20 Sept 2023 at 15:57, Winter, Graeme (DLSLtd,RAL,LSCI) < 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > Looks like PDB files have been outlawed because mmCIF > > But dimple needs PDB files > > cif2pdb sa

[ccp4bb] PDBe Coordinator Position at EMBL-EBI

via PDBe data resources, tools and services. The closing date for this post is 22nd September 2023. For more information and to apply, visit: https://www.embl.org/jobs/position/EBI02160 Kind Regards, David -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute

Re: [ccp4bb] re-open the results from a previous DIALS User Interface session in CCP4 cloud?

Hi both, Thanks for the suggestions. I will see if I can find a workable solution based on what you say. Best wishes Dave --- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web

[ccp4bb] re-open the results from a previous DIALS User Interface session in CCP4 cloud?

s not possible? Any suggestions? Many thanks Dave ------- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk<mailto

Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]

Thanks both! Dave --- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk -Original Message- From

[ccp4bb] Introducing ‘Covalently Linked Components’ and enriched ligand information at PDBe

ve our data infrastructure and user accessibility. Thankyou for your continued support. Kind Regards, David -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge

Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]

Hi Paul, Just wondering where we are with this fix. Is it safe to apply the latest CCP4 updates? Many thanks Dave --- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https

[ccp4bb] PDBImages: A new, open-source macromolecular structure imaging pipeline

** *Dear all,* * The PDBe team, in collaboration with David Sehnal (NCBR, Masaryk University, Czech Republic), has developed a new data pipeline for generating images of macromolecular structures. The new tool, PDBImages, provides more consistent and scalable visualisation for a range of

[ccp4bb] Job Advert: Drug Discovery Project Research Scientist position, Francis Crick Institute, London, UK.

mcdon...@crick.ac.uk). Application Deadline: 1st Sept 2023. For more details about the role and the application process, please see: https://crick.wd3.myworkdayjobs.com/External/job/London/Postdoctoral-Project-Research-Scientist---Signalling-and-Structural-Laboratory_R1245-1 -- Dr David C. Briggs

[ccp4bb] 3D-Beacons update: Search for structural models by protein sequence

quence Kind Regards, David -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK To

Re: [ccp4bb] Dry shipper in limbo

advice on that. === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cor

Re: [ccp4bb] real space refinement broken in COOT 0.9.8.8 EL?

Hi Eugene, Many thanks – that’s sorted it! Best wishes Dave --- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law

[ccp4bb] real space refinement broken in COOT 0.9.8.8 EL?

Dave --- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk<mailto:david.law...@j

[ccp4bb] Clustering of distinct protein conformations across the whole PDB archive

r would like further details, please feel free to contact the team at pdbeh...@ebi.ac.uk. Kind regards, David -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton C

Re: [ccp4bb] AI and cis-peptides

This is very much anecdotal - in my experience, AF2 tends to put the Cys residues in the disulfide bridge adjacent to each other, sometimes with roughly the correct side chain orientation. It doesn't build/refine the S-S bond, becuase I don't think it knows how to. Best, Dave

Re: [ccp4bb] BUSTER on CCP4 Cloud

uite early here). Perhaps someone else can help with that? (please reply to the list because I'd like to know as well!) Best, Dave -- Dr David C. Briggs CSci MRSB (he/him) Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute Londo

[ccp4bb] cryo-electron tomography experiments at the ESRF CM01 cryo-EM facility

ai.kand...@esrf.fr <mailto:eaazhisai.kand...@esrf.fr> -- Dr David FLOT Beam-Line Operation Manager Tel : (+33) 4 76 88 17 63 Structural Biology GroupFax : (+33) 4 76 88 26 24 ESRF e-mail :david.f...@esrf.fr http://www.esrf.eu Room: 30.1.13 Physical address

Re: [ccp4bb] Error in xdsgui: you have to install generate_XDS.INP in your path

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

[ccp4bb] A new process for aggregating and naming assemblies in the PDB

complexes that are relevant to their research. Find out more at https://www.ebi.ac.uk/pdbe/news/new-process-aggregating-and-naming-assemblies-pdb Kind Regards, David -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology

Re: [ccp4bb] About the A in AI

e not supported by the data. The authors' experiments do not provide any direct evidence that PsiX is a trimethylating enzyme, and they do not provide any information about the mechanism of the methylation reaction. Based on these criticisms, I recommend that the paper be rejected. thumb_upthumb_down uplo

Re: [ccp4bb] choosing an NMR structure from PDB

wer to your question, the above process should help in filtering the options. Kind Regards, David On 03/05/2023 11:45, Harry Powell wrote: Hi folks I was wondering. If there is a UniProt entry (for example, P01132, but there are plenty of others) for which I want the “best” (whatever that mi

Re: [ccp4bb] Unknown electron density

Anomalous data might have been helpful. Zinc has an edge at 1.2837 A. === All Things Serve the Beam === David J. Schuller

[ccp4bb] Removal of ls-lR index file from the PDB archive

/holdings/released_structures_last_modified_dates.json.gz> in /pub/pdb/holdings/. Please contact i...@wwpdb.org with any questions. -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge

Re: [ccp4bb] To Trim or Not to To Trim

On Tue, Mar 28, 2023, James Holton wrote: Members of an ensemble spread out over a supercell are equivalent to a conventional multi-conformer model, but only when it comes to the density derived from the coordinate atoms alone.  They are not the same when it comes to bulk solvent and also not

[ccp4bb] Updated pipeline for small molecule data processing at PDBe

://www.ebi.ac.uk/pdbe/news/updated-pipeline-small-molecule-data-processing-pdbe <https://www.ebi.ac.uk/pdbe/news/updated-pipeline-small-molecule-data-processing-pdbe> Kind Regards, David Armstrong * -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EM

[ccp4bb] Helping improve AlphaFold DB - survey on similarity searches

our time and interest! As we progress on this project, we will keep the community updated. * -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge

[ccp4bb] Job opening for a post-doctoral research fellow in the cryo-EM facility of the European Synchrotron, ESRF, France

Forwarded Message Subject: Job opening for a post-doctoral research fellow in the cryo-EM facility of the European Synchrotron, ESRF, France Date: Fri, 3 Mar 2023 09:28:36 +0100 From: Eaazhisai KANDIAH Organization: ESRF To: cc...@jiscmail.ac.uk Dear Collea

[ccp4bb] Diamond User Committee nominations

have a separate committee. If you have any questions before considering standing, please do not hesitate to contact me. Best wishes, and good luck! Dave -- Dr David C. Briggs CSci MRSB Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick

[ccp4bb] 5th ESRF-INSTRUCT workshop on sample preparation for cryo-EM, May 23-24-25, 2023

after the deadline. For more information, please consult <https://www.esrf.fr/cryo-em1-2022>https://www.esrf.fr/home/events/conferences/2023/instruct-cryo-em-workshop.html This is an in-person workshop and is funded by INSTRUCT (IBS). Best regards, Isai (on behalf of the organizing committee)

Re: [ccp4bb] Unidentified density

Hi Zeya, Did you cryoprotect with glycerol perhaps? Dave --- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law

[ccp4bb] Enriched chemical component files at PDBe

generated using RDKit in these updated CCD files. Kind Regards, David Armstrong -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK

[ccp4bb] Continued issues with CCP4BB

ce update is on their webpage: https://www.jiscmail.ac.uk/. Please bear with us for the time being while they resolve the current issues. Best wishes, -- David To unsubscribe from the CCP4BB list, click the follow

Re: [ccp4bb] Is this Spam? This looks like Spam.

will be done for us by Jisc or if those subscribers should re-subscribe themselves. Of course, deleted subscribers will not see this message... Cheers -- David On Tue, 10 Jan 2023 at 23:11, Bernhard Rupp wrote: > I got unsubscribed from ccp4em yesterday with a similar message for

[ccp4bb] Test message

This is a test message to explore issues reported about automatic removals from the BB. -- David To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&a

[ccp4bb] Reminder: AlphaFold DB bioinformatics training role at EMBL-EBI - deadline 15th Jan

licly represent AlphaFold DB at various training events. There is the option for a part time role in this position. Deadline: 15th January 2023 For more information on this role and to apply, visit https://pdbe.org/jobs. Kind Regards, David Armstrong * -- David Armstrong Outreach and Training

[ccp4bb] Software Infrastructure Engineer role available at PDBe

-KB services remain firmly placed on a sustainable footing. Deadline: 29th January 2023 For more information on this role and to apply, visit https://pdbe.org/jobs Kind Regards, David * -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European

[ccp4bb] AlphaFold DB bioinformatics training role available at EMBL-EBI

and publicly represent AlphaFold DB at various training events. There is the option for a part time role in this position. Deadline: 15th January 2023 For more information on this role and to apply, visit https://pdbe.org/jobs. Kind Regards, David Armstrong * -- David Armstrong Outreach and Tra

Re: [ccp4bb] TEV vs HRV3C

f one over the other, but having both in your freezer means you can cleave off tags sequentially as needed by your purification strategies. HTH, Dave Dr David C. Briggs CSci MRSB Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute Londo

Re: [ccp4bb] hydrogens?

On 11 Nov 2022, 19:46, Murpholino Peligro wrote: Can hydrogens be added in a pH/pka-dependent manner? Something like this (https://server.poissonboltzmann.org/) but get a pdb file ready for phenix.refine/buster/refmac? You might want to try http://newbiophysics.cs.vt.edu/H++/. It outputs an u

[ccp4bb] Another folding AI

e Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@corne

Re: [ccp4bb] EDR (Sophos) and CCP4 compatibility

Hi Mark, Our IT admin has mandated various AntiVirus software on OSX, including Sophos, and I have never encountered a problem installing and downloading CCP4, Phenix, Coot, Chimera , etc etc HTH, Dave Dr David C. Briggs CSci MRSB Principal Laboratory Research Scientist Signalling and

[ccp4bb] Jenkins?

gs Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University sch

[ccp4bb] JOB IN SCIENTIFIC ILLUSTRATION AT THE MRC LABORATORY OF MOLECULAR BIOLOGY (LMB), CAMBRIDGE

UBED1=CCP4BB&A=1 LMBVisLab_SciIllustratorAnimator.pdf Description: Adobe PDF document __Dr. David BarfordStructural Studies DivisionMRC Laboratory of Molecular BiologyFrancis Crick AvenueCambridge CB2 0QH, UK.e.mail: dbarf...@mrc-lmb.cam.ac.ukTel. +44 (0)1223 267075079

[ccp4bb] CLOSING SOON: DLS/CCP4 data analysis workshop 2022

Hi all, The application period for the DLS/CCP4 workshop closes 17:00 (UK time) on Tuesday the 20th. Don't leave it to the last minute to apply! :) Cheers -- David On Tue, 13 Sept 2022 at 12:02, David Waterman wrote: > Hi folks, > > A reminder: there is one week left to apply f

[ccp4bb] ONE WEEK TO APPLY: DLS/CCP4 data analysis workshop 2022

Hi folks, A reminder: there is one week left to apply for this year's DLS/CCP4 workshop. Please see below for details. Best wishes -- David On Tue, 6 Sept 2022 at 13:31, David Waterman wrote: > We are pleased to announce that the 9th joint Diamond-CCP4 Workshop on MX > data col

Re: [ccp4bb] PDBx-format utilities

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

[ccp4bb] DLS/CCP4 data analysis workshop 2022

-Structure-Solution-Workshop-2022.html -- David (on behalf of the organisers) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message

[ccp4bb] Multiple AlphaFold DB jobs available at EMBL-EBI

part time role in this position. Deadline: 26th September 2022 For more information on all these job roles and to apply, visit https://pdbe.org/jobs. * -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wel

Re: [ccp4bb] Checking X-ray sequence (no more protein).

Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: CCP4 bulletin board on behalf of Robbie Jo

[ccp4bb] Improved EM validation with Q-score at the PDB

map+model, EM map-only, and EM tomograms. If you have any questions or queries about wwPDB validation, please contact us at validat...@mail.wwpdb.org. Best regards, James Tolchard -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular

Re: [ccp4bb] Unidentified electron density

t was in the crystallisation conditions (thinking specifically about cations - any Mg2+, Ca2+?) Good luck! Dave -- Dr David C. Briggs CSci MRSB Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == about.me/david_b

Re: [ccp4bb] Off-topic: Mol* Viewer re-centring hack

entation at PDBe and queries about the use of the viewer. Kind Regards, David Armstrong On 28/06/2022 10:36, Read, Jon wrote: I have been using Mol* recently which looks like a really nice tool for basic model viewing. When you click off an atom (which is the normal action for clearing a select

Re: [ccp4bb] Regarding R factor value (R Free)

header, or recover this information using the PDB accession codes. I suspect this can be done relatively easily through the API, but others can better advise you on how to do this. HTH, Dave Dr David C. Briggs CSci MRSB Principal Laboratory Research Scientist Signalling and

[ccp4bb] Reminder: Data Visualisation Software Engineer position at PDBe

regards, David -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544

[ccp4bb] Reminder: Bioinformatician/Scientific Programmer position at PDBe

user-facing web pages for PDBe and PDBe-KB. The closing date for this post is 3rd May 2022. For more information and to apply, visit: https://www.embl.org/jobs/position/EBI02000 Kind Regards, David Armstrong -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute

[ccp4bb] Bioinformatician/Scientific Programmer position at PDBe

more information and to apply, visit: https://www.embl.org/jobs/position/EBI02000 Kind Regards, David Armstrong -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton

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