Re: [ccp4bb] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy

he model), then they automatically balance themselves with the data likelihood. If the data are less sensitive to changes in the model than the restraints are, the restraints will win, and vice versa. Best wishes, Randy On 10 Oct 2024, at 06:34, Frank von Delft <bcb385fe5582-dmarc-requ...@jisc

Re: [ccp4bb] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy

! But the battle for the "Last Angstrom" is far from over. -James Holton MAD Scientist On 10/9/2024 10:25 AM, Frank von Delft wrote: So Randy, what should we be saying/using, and where do we find it... and (not least!), /when/ in the experiment-to-final-model process? By "wha

Re: [ccp4bb] Nobel prize for Alpha fold and protein design!

Oh, we can just badge ourselves as what the LHC is to Peter Higg's Prize. On 09/10/2024 14:06, Subramanian, Ramaswamy wrote: Dear All, I am sure many of you saw the announcement of the Nobel Prizes. I am glad for the recipients. This would not have been possible but for PDB and the other str

Re: [ccp4bb] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy

So Randy, what should we be saying/using, and where do we find it... and (not least!), /when/ in the experiment-to-final-model process? By "what" I mean, the specific words - since as Ian points out, the words "resolution limit" and "diffraction limit" are quite different, whatever we thoughtl

[ccp4bb] Antiviral Open Science Forum: 19 June 4pm BST

Hello, for those of you interested in line-of-sight to clinic, the next Antiviral Open Science Forum should be particularly interesting: https://asapdiscovery.org/forum/#2024-jun Weds 19 June @ 4pm BST (11am EST). Sign up to get the link. * *John Pottage, Jr.

Re: [ccp4bb] Crystal optimization

Usually, you should try to push up the protein concentration, often quite a lot (30, 50, even 100 mg/ml), and decrease precipitant (might have to be really low, eg <3% PEG is not unthinkable). To get the protein up, you may need to find a new buffer solution - there are screens for this, and DS

Re: [ccp4bb] AlphaFold3 Transparency and Reproducibility

What we really need is a tweet from Nature, declaring their embarrassment at having been suckered into becoming DeepMind's advertising arm. On 14/05/2024 01:56, Paul Adams wrote: The letter may have had (or helped have) an impact already: On X today from Pushmeet Kohli @ DeepMind "We love

Re: [ccp4bb] Rescale merged data?

Is it easy/non-arcane or indeed automatic for non-experts to add these loops?  Because that's the only way this will be achieved systemically. Presumably ccp4i2 can be wrangled into making it happen magically. (Apologies if it does already, if so, a comment here would help the discussion...)

Re: [ccp4bb] request for applications

Oh dear, your prime number oversupply crashed the crypto Ponzi scheme market. Will you accept $10e2 proposals now? Sent from tiny silly touch screen From: James Holton Sent: Monday, 1 April 2024 08:01 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] request for appli

Re: [ccp4bb] Crystallizing a tough target

Don't forget to try pure water. On 05/02/2024 10:44, Savvas Savvides wrote: Dear Kavya, we encountered this issue for a protein complex at 95 mg/mL involving Human Serum Albumin (HSA) and a designed protein binder (Alphabody) as described in Pannecoucke et al. 2021 Sci Adv 7 (13), DOI:10.112

Re: [ccp4bb] PDBe Unveils New Streamlined FTP Structure and Enhanced Ligand Data Files

14:15, Frank von Delft wrote: Hi Deborah - sounds great, well done! Are you yet harvesting and serving up the restraints used in refinement?  If not, that remains a huge gap, in my view.  (The chemists tend not to be aware that's even a thing, I keep discovering.) Frank On 31/01/2024 13:5

Re: [ccp4bb] PDBe Unveils New Streamlined FTP Structure and Enhanced Ligand Data Files

Hi Deborah - sounds great, well done! Are you yet harvesting and serving up the restraints used in refinement?  If not, that remains a huge gap, in my view.  (The chemists tend not to be aware that's even a thing, I keep discovering.) Frank On 31/01/2024 13:57, Deborah Harrus wrote: *Dear

[ccp4bb] Recruiting: Science Coordinator - antiviral discovery (14 Jan)

cience intimately, like organising and writing, but don't want to follow the postdoc ("bench-scientist") route.  If that resonates, take a look at the job description in the link above. Do email me if you have specific questions, that aren't answered in the documentation. Ch

Re: [ccp4bb] [pe...@leadszone.live: CCP4 Study Weekend-2024] (fwd)

I mean, who'd actually want that list anyway?! On 15/12/2023 13:23, Gerard Bricogne wrote: Dear all, I just received this a moment ago, and it looks most suspicious. Can any action be taken, other than warn people not to follow up? Best wishes, Gerard - Forwarded mes

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

That's a press release, not a tool that can be tested. On 01/12/2023 12:19, Roberto Steiner wrote: Great paper indeed! However quite significant progress seems to have been achieved with ligands as well (and not only)… https://deepmind.google/discover/blog/a-glimpse-of-the-next-generation-of

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

Wonderful paper, well done! On 30/11/2023 21:35, Tom Terwilliger wrote: Hi Structural biologist colleagues! Our article that helps you make the case that the experiment is still very much needed is now out: https://www.nature.com/articles/s41592-023-02087-4 "AlphaFold predictions are valuab

[ccp4bb] Posts in advancing fragments: biophysics, informatics

Hello - I'm recruiting to posts to develop better ways to progress fragments to potency.  They're both connected to our antiviral big discovery programme , and part of the XChem team. _*Biophysics*_: Can we make sensor-based

Re: [ccp4bb] in memoriam of Raimond Ravelli

My word that was a shock to read.  Farewell Raimond, what an amazing scientist and person.  Frank On 05/07/2023 19:54, a.perra...@nki.nl wrote: Dear all, It is with profound sadness I announce the passing of Raimond Ravelli, one of most remarkable and beloved members of our scientific commun

Re: [ccp4bb] how to get mol files from PDB and restraint CIF?

on doesn't take place and I have no idea why. HTH, Fred. On 5/19/23 11:28, Frank von Delft wrote: Hello - as in the subject line, does anybody know of, or have, code that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the restraints CIF file used in refinement, and generate

[ccp4bb] how to get mol files from PDB and restraint CIF?

Hello - as in the subject line, does anybody know of, or have, code that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the restraints CIF file used in refinement, and generate a .mol (or .sdf) file? OpenBabel apparently does not. I thought the PDB processing tools would, but my

[ccp4bb] Fwd: Register for the Antiviral Drug Discovery (AViDD) Open Science Forum virtual meeting Wed 15 Feb 11.00A ET

Hello all - slightly off-topic, but many BB readers will find the talks at this forum of direct or indeed indirect interest. They will run monthly, for as long as the AViDD awards run (currently middle 2025), and will cover topics of antiviral drug discovery and development, from early discove

Re: [ccp4bb] Future Diffraction Methods

Whether cross-pollination happens depends on the session chairs, and the remit they're given, and the instructions given to the speakers:  if early on everybody sets the tone, to inform as much as advertise, then it could be a rip-roaringly interesting meeting. At least, I've never encountered

Re: [ccp4bb] Future Diffraction Methods

Shoot... that sucks. Yes, we do need something! "Structural Biology Methods"? More interesting question:  does it need the GRC to host?  What about reimagining the CCP4 study weekend - the question keeps coming up there anyway. That's one for CCP4 WG1 to discuss - they're meeting straight

Re: [ccp4bb] Another folding AI

Great, now we have two random number generators. On 03/11/2022 12:10, David J. Schuller wrote: https://www.biorxiv.org/content/10.1101/2022.07.20.500902v2 Evolutionary-scale prediction of atomic level protein structure with a langu

Re: [ccp4bb] PAIREF, Anisotropy and STARANISO

Gerard, that's fascinating, thanks for the explanation. I conclude in summary:  nobody (including you) yet knows whether any refinement program properly extracts the high-resolution signal when there's anisotropy. My (similar) question a few days ago was: /"Is that because of the practicalit

Re: [ccp4bb] issues running PANDDA with anisotropic data

Hi Charlie - that's quite a technical question, so I suggest you ask the question on the xchembb (use The Google to find it), in case someone has that script to hand. (But if you need to do any scripting, chances are you'll need to spend a few days on the Google anyway, even if someone can sen

[ccp4bb] Recruiting XChem postdocs for antivirals

will include close work with my and other groups at Oxford's Centre for Medicines Discovery <https://www.cmd.ox.ac.uk/> (CMD). Vacancy link is here <https://vacancies.diamond.ac.uk/vacancy/postdoctoral-research-associate-antiviral-xchem-496546.html>; closing date is Sept

Re: [ccp4bb] Yes, there are now 214 *million* structures in the AlphaFold Protein Structure Database

Gerard, Sameer - that is highly impressive indeed About that Editorial (nice read!), it frames these developments as a "crisis" that heralds "the end of structural biology" - or at the very least, you're responding to people having said that.  I remain puzzled that such stuff receive any

Re: [ccp4bb] open review?

I suspect funders will worry about it becoming even harder to find reviewers - they're already hard to flush out, if I'm not mistaken, and might become even more reclusive if they run the risk of being pilloried in public. If that sounds theoretical:  even in this community, for all its colle

[ccp4bb] Doctoral studentship: Fragments to Field

As part of this PhD studentship, the candidate will have the opportunity to spend 3 months at Syngenta, a unique opportunity to get an insight into industrial research and to build a professional network. Prof Frank von Delft Professor for Structural Chemical Biology Principal Beamline Scientist: I04-1

Re: [ccp4bb] High-order oligomers vs robust crystals - references?

g students, looking for something *actually useful* to write a review about! Frank On 12/11/2021 14:52, Frank von Delft wrote: Hello all Two decades ago, I remember (!) much talk about a reason that bacterial proteins crystallize "more easily" is that they tend to come as oligome

[ccp4bb] 2021 Moonshot Webinar - 16 Dec 4pm GMT

Dear BB It's been 20 months since we broadcast on this BB (and elsewhere) for help to develop a SARS-CoV-2 Mpro inhibitor from XChem fragments.  The thing is still going strong, and in the open, with funding up to clinic. Please do sign up if you're interested in drug discovery and developme

[ccp4bb] High-order oligomers vs robust crystals - references?

Hello all Two decades ago, I remember (!) much talk about a reason that bacterial proteins crystallize "more easily" is that they tend to come as oligomers (dimers and up), and that this internal symmetry made them happier to crystallize. Did anybody ever publish hard evidence?  Or even, is

Re: [ccp4bb] am I doing this right?

big "consequence of getting it wrong" is embarrassing myself by re-making a 200-year old mistake I am not currently aware of. I am confident a solution exists, but only recently started working on this.  So, I figured ... ask the world? -James Holton MAD Scientist On 10/17/2021 1:51 AM,

Re: [ccp4bb] am I doing this right?

James, I've been watching the thread with fascination, but also the confusion of wild ignorance. I've finally realised why. What I've missed is: what exactly makes the question so important? I've understood what brought it up, if course, but not the consequence of getting it wrong. Frank Sen

[ccp4bb] XChem proposals: NEXT WEDS (Oct 6)

s/Mx/Fragment-Screening/XChem-Applications.html> Looking forward to your applications! Frank Prof. Frank von Delft Professor for Structural Chemical Biology Principal Beamline Scientist: I04-1/XChem Diamond Light Source +44 1235 778997 (o) +44 7471 026103 (m)

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

Thanks Andrea for this! One more for crystallization: Ng JT., Dekker C., Kroemer M., Osborne M., von Delft F., (2014), Acta D, 70, 2702 - 2718 On 03/08/2021 12:43, Thorn, Dr. Andrea wrote: Dear colleagues, I have compiled a list of papers that cover the application of AI/machine learnin

Re: [ccp4bb] pictures in emails

Ahem.  Ed, Tim - the 90s called, they want want their disk space and email clients back. As a co-perpertrator of vast volumes of detector data, and religious proponent of text /formatting/ as inseparable part part the message, I disagree that in the year 2021, your suggestion still conforms to

[ccp4bb] XChem recruiting: Beamline Scientist

Hello all We're recruiting a Beamline Scientist to the XChem facility at Diamond;  the advert and details are below: If you're wondering if it's for you:  the best ways to make a guaranteed impact in science is (a) to teach lots of smart young people and/or (b) work at a facility that accele

Re: [ccp4bb] Arcimboldo

That paper is jaw-dropping... On 03/07/2021 10:33, Randy John Read wrote: If there isn’t already a suitable model, this looks like a good opportunity to try out the powerful new RoseTTAFold deep learning algorithm by Minkyung Baek in David Baker’s lab. It can be used through the Robetta serv

Re: [ccp4bb] Co crystalization with less soluble ligand.

And then of course, you need to decide whether you at all care to know anything about a compound that is so insoluble that it needs that kind of treatment :) On 23/06/2021 09:52, hoh wrote: Hi As total insolubility does not exist, I regularly use another method, which is to deposit a gr

Re: [ccp4bb] Should Rmerge be reported?

Or just boycott the journal...?? On 10/06/2021 14:02, Tim Gruene wrote: Hi Graeme, could you explain why Rmeas does not serve the same purpose as Rmerge? I guess Manfred (and others) have no objection to reporting Rmeas just instead of Rmerge. @ Christy: If one of my manuscript were rejected

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

ymol: https://pymolwiki.org/index.php/BiologicalUnit/Quat <https://pymolwiki.org/index.php/BiologicalUnit/Quat> 4. BiologicalUnit in pymol: https://pymolwiki.org/index.php/BiologicalUnit <https://pymolwiki.org/index.php/BiologicalUnit> (CCP4bb is amazing) Frank On 25/05/2021

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

ders.com/> From: Debanu Das Sent: Tuesday, 25 May 2021 20:55 To: Frank Von Delft Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file Hi Frank, PISA is your friend here. Thanks, Debanu On Tue, May 25, 2021 at 12:44 PM Fran

[ccp4bb] writing coordinates of full biomol into one (PDB) file

Hello all - this presumably has a really simple solution: For a PDB file with a (correct) biomolecular assembly record (REMARK 350), what program do I use to generate and write out the coordinates of the biomolecular assembly (or one of them). Thanks Frank ###

Re: [ccp4bb] The weekly nonsense

It's certainly a real problem they're writing about. Or at least, one that some people say we should be worrying about. Sent from tiny silly touch screen From: Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> Sent: Saturday, 23

Re: [ccp4bb] Open position - data management in biophysics

For me as hiring PI, what's repeatedly dismaying is that it's our funders and universities that set the terms, and only with extreme creativity can one shift the dial, and only on indidual recruitments, certainly not the high politics of the system as a whole. No, I don't know what will break

Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

I guess that also means that AlphaFold has learnt the crystal-structure-ness that older homology methods never achieved - which is why (anecdotally?) a "better" homology model tended to give worse MR performance than the "worse" template? (Or something like that, I'm parrotting what I remember

[ccp4bb] Help us help you: write support for Ultra-XChem beamline in Diamond-II

s so many discplines, you can probably send to just about everybody you work with... Thank you for your help! Frank Prof Frank von Delft Professor for Structural Chemical Biology Principal Beamline Scientist: I04-1/XChem Diamond Light Source Principal Investigator: Protein Crystallography Cent

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

I believe Paul is trying to make the caffeine materialise directly in your bloodstreams. He seems to have forgotten that people actually like harvesting and roasing the coffee beans and folding the paper cup - so even if he figured out how to simulate the burning sensation in your throat as th

Re: [ccp4bb] metal coordination at low resolution - restraints

Surely an opportunity for machine learning to make a real difference?  There's enough data in the PDB by now, that you can conceive of a classifier generating the most likely set of restraints appropriate given an OMIT map. On 09/09/2020 11:37, Eleanor Dodson wrote: I know how difficult it i

Re: [ccp4bb] RES: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

Thanks Stephen for reminding me there's a point no-one raised at the time: There are two sets of people that have agency in this:  1) the organisers, and 2) the ones that get the invites. Group 1 already have a tough job:  organising a meeting is a pile of work - so go easy on them.  (Or orga

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

Gerard, fantastic proposal - let's call it "abundancy"!!! Which developer will be the first to change their logfile? On 30/06/2020 16:38, Gerard Bricogne wrote: Dear Phil, I would like to make an attempt to not let this question get mired in exchanges of well-researched linguistic argum

Re: [ccp4bb] 2fofc maps from refmac twinned refinement - clarify?

pical result of small-molecule refinements.  I expect that is why they are not nearly as afraid of twinning as we are. -James Holton MAD Scientist On 4/28/2020 2:19 PM, Frank von Delft wrote: > Hi all - feel free to point me to the docs if it's already clear

Re: [ccp4bb] disinfecting keyboards

Make your users wear masks. Sent from tiny silly touch screen From: David Schuller Sent: Wednesday, 29 April 2020 21:03 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] disinfecting keyboards If you are going that route, it would make sense to locate the UV lamps

[ccp4bb] 2fofc maps from refmac twinned refinement - clarify?

Hi all - feel free to point me to the docs if it's already clear somewhere: When refmac generates 2mFo-DFc maps after twinned refinement, are they the "untwinned" view of the electron density?  I.e. with the twinnig convoluted out by his statistical magic? I remember Garib mentioning the ambi

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!

the competitor and you still do not have the data. An alternative may be to ask an academic friend who also works on sausage esterases to inquire with the authors… Good luck with your decision! Herman *Von:* CCP4 bulletin board *Im Auftrag von *Frank von Delft *Gesendet:* Dienstag, 7. Ap

Re: [ccp4bb] on-topic: your opinions requested!

Write to the editor - that's their job. Though they may also see it as their job to ignore emails like yours because that's far easier than dealing with them. Alternatively, go the Rupp Route:  Name and Shame! ;) On 07/04/2020 16:08, Artem Evdokimov wrote: Dear CCP4ers, I would like to sol

Re: [ccp4bb] COVID-19 protease inhibitors - 2nd call for designs - Thurs midnight

deadline. Will there be additional design rounds?  Thanks again for making all this data available and it really is inspirational what your team is doing to confront collaboratively this global crisis. Best, Nick On Wed, Apr 1, 2020 at 10:16 AM Frank von Delft mailto:frank.vonde...@sgc.ox.ac.u

Re: [ccp4bb] COVID-19 protease inhibitors - 2nd call for designs - Thurs midnight

For those that wish to play with an advanced tool: BioSolveIT have made it easy to get a relevant licence, link on that webpage. Sent from tiny silly touch screen From: Jurgen Bosch Sent: Wednesday, 1 April 2020 16:19 To: Frank Von Delft Cc: CCP4BB

[ccp4bb] COVID-19 protease inhibitors - 2nd call for designs - Thurs midnight

All - last week's call for compound designs to the CoV-2 main protease (https://covid.postera.ai/covid) elicited an astonishing response...  (I confess I was quite taken aback.) I just realised I should let this BB know the second call for designs is now open. *Deadline is tomorrow 23:59 PST (A

Re: [ccp4bb] Paired refinement proves data quality goes beyond the spatial limits of the detector

That is awesome.  It means we can add data up to a kilometer out, and start modelling quarks? I urge the community to deposit all raw data to a virtual detector of 1km in size - I'm sure Google will happily stump up for the storage costs, the business case is unarguable. On 01/04/2020 05:

[ccp4bb] COVID-19 - help design protease inhibitors - 1st round Thurs midnight

so on the forums on that page *** If you want to use the data for anything else - PLEASE DO - we were anxious to push it out ahead of PDB release cycle or getting preprint written. Frank -- Prof Frank von Delft Professor for Structural Chemical Biology Principal Beamline Scientist: I04-1 and

Re: [ccp4bb] [3dem] Which resolution?

Belatedly, but since the thread is still alive: Thank you Colin for answering my request - super informative, as were the later posts on B-factor and sharpening. It all reinforces my prejudice: we need to turn to interpretability, i.e. the next step (modelling), to inform the question of info

Re: [ccp4bb] What resolution - X-ray diffraction round this time

Tell the editor to find a new reviewer.  And cite Kay's paper, the one Graeme linked to. On 28/02/2020 08:22, dusan turk wrote: > Hi, > > Browsing through the recent discussion on EM data resolution cutoff it > occurred to me that the X-ray diffraction community isn’t that unanimous > either. >

Re: [ccp4bb] MX data processing with GPUs??

Since Kay asks: Do all of us really want and need to collect from thousands of crystals every synchrotron day? Are all of us really producing that many crystals? Who is? I can't help to respond: even if not "all of us", we certainly are! https://www.diamond.ac.uk/Instruments/Mx/Fragment-Scr

Re: [ccp4bb] Remember the turkey?

I daresay, large segments of humanity might not consider that "unfortunate". But since we're straying into political territory, I conclude that a number of subscribers have recently been on holiday and thus had the luxury of only far-off deadlines ;) Sent from tiny silly touch screen __

Re: [ccp4bb] Remember the turkey?

Those authors raise a fair point though, don't they:  if nothing else, "suppremacy" is an utterly daft word to use in any scientific context, since it brings nothing technical to the table. Before geek triumphalism became the rage (or maybe before the need for grant-gaining hyperbole?), we migh

[ccp4bb] Position at Diamond: XChem Beamline Scientist

s the 15th Dec 2019, and we wil linterview on 17th Dec (i.e. before Xmas). If you have questions, contact me or Alice Douangamath <mailto:alice.douangam...@diamond.ac.uk>, who heads the facility. Frank -- Frank von Delft Professor for Structural Chemical Biology Principal Beamline Scien

Re: [ccp4bb] A grumble

Eleanor, whom are you grumbling at? If it's at the depositors, here's a counter-grumble: How would a depositor even know * know that it's "wrong" * know what definition of "wrong" to work towards * know that someone somewhere will care about this particular "wrongness" * kno

Re: [ccp4bb] design specs/tolerances for crystallization rooms?

29 41 32 Lab pages: http://pharm.kuleuven.be/Biocrystallography<http://pharm.kuleuven.be/anafar> From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of Frank Von Delft <mailto:frank.vonde...@sgc.ox.ac.uk> Sent: Wednesday, September 25, 2019

Re: [ccp4bb] design specs/tolerances for crystallization rooms?

My colleague Opher Gileadi gave us an excellent tip when we were designing our 4C harvesting room, over a decade ago: set it to 7C. The crystals are unlikely to mind, but it's SO much more comfortable to be in for hours. I seem to remember he mentioned something like a comfort inflection point

[ccp4bb] XChem fragment screening - call for proposals - 2nd October 5pm

Dear all, This is a reminder that Diamond Light Source is accepting proposals for its XChem fragment screening facility, for the allocation period April to September 2020. The deadline is Wednesday 2nd October at 5pm (2 weeks from now). Details on how to apply are here - we're oversubscribed, so

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Better Beamline suggestion!

We also described how to bend the loops in this article: http://doi.org/gcb8j3 Figure 4 specifically. On 21/08/2019 18:21, Edwin Pozharski wrote: In the absence of such you can resort to carefully bending the loop or bending the pin (Jim Holton made a nifty device for bending the pin) while

Re: [ccp4bb] not solely pdb issue: need someone to officially settle the pdb dispute

If A had deposited it to the PDB immediately, he'd have had been able to claim the kudos and help lots of scientists besides B. How is it that we structural biologists still are so precious about our coordinates? Or more to the point, that the supervisors still don't teach their students that

Re: [ccp4bb] AW: need someone officially settle a pdb dispute for a publication

Structural genomics efforts have been putting PDBs in the public domain for almost 2 decades - precisely so they'd be used. That's the whole point of the PDB, and open repositories: set the data free, so it can make science happen. "A" should be delighted that their work have actually been use

Re: [ccp4bb] challenges in structural biology

1.1  Getting many diverse conformations routinely into well-diffracting crystals;  and knowing how to interpret them biologically. On 15/07/2019 20:44, Holton, James M wrote: > Hello folks, > > I have the distinct honor of chairing the next Gordon Research > Conference on Diffraction Methods in S

[ccp4bb] Has anybody put CCP4 into a singularity container?

Hi all - see subject line. If they have, or have tried and failed, can they get in touch, please?  (Or more specifically, email Conor, conor.w...@oriel.ox.ac.uk.) Thanks! Frank To unsubscribe from the CCP4BB list, click

[ccp4bb] 2 positions around XChem-related compound design

lidation of the newly designed compounds with collaborating scientists in order to progress them towards potent molecules. / Cheers Frank -- Prof Frank von Delft Associate Professor Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 6

Re: [ccp4bb] High Rfree in last Shell

Jan, tell your reviewer to join us all in the 21st century. Diederichs and Karplus, Science, about 2 decades ago.  (Technically, 2012 , but it really is a long long time ago now.) On 16/04/2019 18

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

You can use sftools to set a shell of reflections to MNF - then Refmac will fill those in with DFc, and that'll presumably be much better than having very wrong reflections. Whether that will fix your Rfactor is a different story. phx On 04/04/2019 11:05, Eleanor Dodson wrote: You cant exclu

[ccp4bb] Call reminder: XChem fragment screening, NEXT WEDNESDAY

ratory access ("Tier 1") * BAG access:  several labs and collaborations have requested increased flexibility, and several have been assigned Block Allocation Groups.  If you wish to submit this route, I suggest you also email me directly. Happy screening! Frank -- Prof Fra

Re: [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

Or do sitting drop, it's much easier all round. Frank Sent from tiny silly touch screen From: Minmin Yu Sent: Thursday, 31 January 2019 21:42 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallizat

Re: [ccp4bb] VERY old mtz file..

Congratulations, CCP4bb, you have just witnessed the longest thread on JISCMAIL.  38 messages (and counting, presumably). Now we know how to troll the BB:  not even that old evergreen of where to cut resolution generates a fraction of this traffic. phx On 14/11/2018 15:54, Robbie Joosten wr

Re: [ccp4bb] Very strange LINK cards appearing in recent structures

Sorry, that was menat to be:  "... force us _to deposit_ /full details/" On 12/11/2018 09:49, Frank von Delft wrote: While you're at it, can you force us /full details/ of restraints used, whether it's the particular CCP4 library release, the CIF of the ligand, or th

Re: [ccp4bb] Very strange LINK cards appearing in recent structures

While you're at it, can you force us /full details/ of restraints used, whether it's the particular CCP4 library release, the CIF of the ligand, or the non-standard links? As far as I understand refinement, they're as least as important a determinant of the final structure as the observed data

Re: [ccp4bb] CC work / free

Does any refinement software automatically do the CC* resolution exploration ("paired refinement") that Kay did in the original paper?  Now that /would/ be fantastically useful. On 08/11/2018 12:44, Pavel Afonine wrote: Clément, I'm guessing this is because it isn't clear what CCwork/CCfree c

Re: [ccp4bb] help needed with a rabbit-head-shaped blob

It's more a Pacman ghost, innit?? Sent from Nine From: Deborah Harrus Sent: Friday, 2 November 2018 21:25 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] help needed with a rabbit-head-shaped blob Dear all, I came across an unidentified ra

[ccp4bb] Deadline for Diamond XChem proposals next Wednesday

cess ("Tier 1") * BAG access:  several labs and collaborations have requested increased flexibility, and they can now apply as Block Allocation Groups.  If you wish to submit this route, I suggest you also email me directly. Happy screening! Frank -- Prof Frank von Del

[ccp4bb] Recruiting fragment/XChem crystallographers

p;p_process_type=&p_applicant_no=&p_display_apply_ind=Y>, and deadline is in two weeks (October 5th). Frank -- Prof Frank von Delft Associate Professor Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 617583 (office: W,F) Princi

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

nthalpy driven. The models differ only in how > they explain the source of the entropy loss." > > Best > > Stefano > > > > Le 2018-09-19 14:41, Frank von Delft a écrit : >> >> Hi Stefano - could you elaborate? >> >> Certainly the medicin

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

wrote: Le 2018-09-19 11:59, Frank von Delft a écrit : I believe medicinal chemists do indeed talk about "enthalpic interactions".  Frank Not a good choice either (à mon avis ...) The Real Reason Why Oil and Water Don't Mix Todd P. Silverstein Journal of Chemical Educ

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

I believe medicinal chemists do indeed talk about "enthalpic interactions".  Frank On 19/09/2018 10:40, Stefano Trapani wrote: Le 2018-09-18 19:31, Daniel M. Himmel, Ph. D. a écrit : (where hydrophobic interactions result from van der Waals forces in an aqueous environment). Hi I am not

[ccp4bb] Vacancy at Diamond: Senior Support Scientist (I04-1, XChem)

The ad is here: https://vacancies.diamond.ac.uk/vacancy/senior-support-scientist-356961.html Frank -- Prof Frank von Delft Principal Beamline Scientist: I04-1 Diamond Light Source +44 1235 778997 (office: M,T,T) +44 7471 026103 (mobile) Associate Professor Principal Investigator: Pr

Re: [ccp4bb] Should we still keep copies of all raw data?

Are the LHC researchers that analyse the detector readout on the fly without ever storing the data also guilty of malpractice? Hardcore. Just a few more years, a few more Eiger detectors, a few more serial beamlines, a few more clusters and clouds, and a few more DIALS-style programmers, befor

Re: [ccp4bb] PanDDA error revisiting old run

Hi Chris - that said, it is probably a better idea to repeat the old analyses with the new version, even if that costs more time. Frank On 20/06/2018 11:42, Pearce, N.M. (Nick) wrote: Hi, Yes, it is the case that newer pandda version may not be compatible with old pandda analyses. You’ll ha

Re: [ccp4bb] Compound with flexible conformation but nM Kd

Long alkyl chains tend to bad things to hang onto any compound, if it's to be biologically useful.  Go consult your friendly local medicinal chemist, chances are they'll freak out. Anyway, long alkyl chains LOVE binding to surfaces, which is of course exactly the sort of thing that generates

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

ueify in P212121, then you won't.  That sort of thing.  Note that it doesn't matter what the "true" space group is, it only matters what is in the mtz header when you run uniqueify. Could that be what is going on? -James Holton MAD Scisntist On 4/5/2018 3:52 AM, Frank von De

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

s.. I didnt know CAD would generate indices not in the input file, unless you asked to generate a full set of FreeR terms, when the job I thought ran uniqueify? Eleanor On 5 April 2018 at 11:52, Frank von Delft <mailto:frank.vonde...@sgc.ox.ac.uk>> wrote: Hello - can anybody shed

[ccp4bb] (arcane) How to generate complete set of indices at low res

Hello - can anybody shed light on this mystery: We need (for PanDDA analysis) a lot of datasets each to have the complete set of low resolution indices, whether measured or not. (Refmac adds the estimates as DFc, which is crucial when comparing maps.) In ccp4, there are two obvious ways to ge

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