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

[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] 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

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] 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] 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] [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

[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] 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 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] 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

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] 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] 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

[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] 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

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] [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] 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] 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] [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

[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] 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

Re: [ccp4bb] number of cycles in refmac

Hi Ian (Yes, your technical point about semantics is correct, I meant over-fitting.) To pin down your points, though, you're saying: 1) Don't use Rfree, instead look at LLfree or Hamilton Rfree. 2) Compare only the final values at convergence when choosing between different parametriz

Re: [ccp4bb] UV imaging of crystals

A while ago I was trying to be cheap, so we played around with it quite a bit in the lab. After rediscovering some of the basics of signal-to-noise and microscope transmission efficiency and that sort of rot, I realised that the commercial systems may not be all that ridiculously overpriced af

Re: [ccp4bb] Ramachandran plot difference between Coot and Morprobity (or Phenix)

Oh god no don't ask Procheck , its Rama plot is a complete disaster zone - for one thing, it's * ancient*. Doesn't discriminate between amino avoid types. Grrr. To be avoided at all costs. Sent from tiny silly touch screen - Reply message - From: "Edward A. Berry" Date: Fri, Sep 30, 20

Re: [ccp4bb] IUCr committees, depositing images

On the deposition of raw data: I recommend to the committee that before it convenes again, every member should go collect some data on a beamline with a Pilatus detector [feel free to join us at Diamond]. Because by the probable time any recommendations actually emerge, most beamlines will ha

Re: [ccp4bb] IUCr committees, depositing images

soon (collectively) stop being able to care about the original dataset or how to reproduce analysis number 2238 from 2 years ago. (No, I'm not convinced this question is relevant only to structural genomics.) phx. On 16/10/2011 19:38, Frank von Delft wrote: On the deposition of

Re: [ccp4bb] IUCr committees, depositing images

ed this question is relevant only to structural genomics.) phx. On 16/10/2011 19:38, Frank von Delft wrote: On the deposition of raw data: I recommend to the committee that before it convenes again, every member should go collect some data on a beamline with a Pilatus detector [fee

[ccp4bb] buccaneer_pipeline failure (ccp4 6.2.0)

Hi, we got around to switching to ccp4 version 6.2.0, but now buccaneer fails from the GUI. Below is what shows up if you view the com file before execution; and below that the logfile. Seems to me it's using the wrong python executable; the first one on my path is certainly nothing to do wi

Re: [ccp4bb] buccaneer_pipeline failure (ccp4 6.2.0)

is modified around line 231 in $CBIN/include/ccp4.setup My python binary is /usr/bin/python, and I have used buccaneer without errors. Tim On 10/17/2011 09:30 PM, Frank von Delft wrote: Hi, we got around to switching to ccp4 version 6.2.0, but now buccaneer fails from the GUI. Below is what

Re: [ccp4bb] buccaneer_pipeline failure (ccp4 6.2.0) (SOLUTION)

usr/local/ccp4/6.2.0/ccp4-6.2.0/share/python/CCP4pipeline.py (on our installation, the mode is actually 755, but I suppose 644 should be sufficient). You can set PYTHONVERBOSE to 1 or higher in the shell you start ccp4i from to see what python is doing ('man python'). Tim On 10/18/2011 11:

Re: [ccp4bb] IUCr committees, depositing images

Since when has the cost of any project been limited by the cost of hardware? Someone has to /implement /this -- and make a career out of it; thunderingly absent from this thread has been the chorus of volunteers who will write the grant. phx On 25/10/2011 21:10, Herbert J. Bernstein wrote:

Re: [ccp4bb] IUCr committees, depositing images

e CCP4bb. Yours sincerely, John and Tom John Helliwell and Tom Terwilliger On Wed, Oct 26, 2011 at 9:21 AM, Frank von Delft wrote: Since when has the cost of any project been limited by the cost of hardware? Someone has to implement this -- and make a career out of it; thunderingly absent from

Re: [ccp4bb] Archiving Images for PDB Depositions

"Loathe being forced to do things"? You mean, like being forced to use programs developed by others at no cost to yourself? I'm in a bit of a time-warp here - how exactly do users think our current suite of software got to be as astonishingly good as it is? 10 years ago people (non-developer

Re: [ccp4bb] image compression

I'll second that... can't remember anybody on the barricades about "corrected" CCD images, but they've been just so much more practical. Different kind of problem, I know, but equivalent situation: the people to ask are not the purists, but the ones struggling with the huge volumes of data.

Re: [ccp4bb] crystal orientation during data collection

I believe you achieve completeness more quickly (fewer crystals) if you just take random orientations. At least, that's what I learnt from Dave Stuart. phx On 18/11/2011 04:20, Frank Murphy wrote: Yanwu, I surmise from your question that you are inquiring how to go about collecting from m

Re: [ccp4bb] image compression

(Old thread, just cleaning up, sorry...) I thought James' algorithm didn't do anything to the spots, just to the stuff in between. So one obvious way to handle this is for the data processing programs to be looking between the integrated spots as well, whether they're missing anything; the

Re: [ccp4bb] reliable/unreliable maps?

Or just print both Rfactors...? On 10/01/2012 15:21, Luca Pellegrini wrote: Hi Paul, What would you rather it say, I'm happy to change the message. "The EDS does not think that this is a reliable map, in that it is or may be inconsistent with what the authors were looking at during deposit

Re: [ccp4bb] writing scripts-off topic

What an astonishingly low bar On 24/01/2012 14:19, David Schuller wrote: On 01/24/12 00:41, Bart Hazes wrote: I have used a number of languages and have found only one I really disliked, that being perl. It is hard for me to imagine that this language was developed by a linguist yet in m

Re: [ccp4bb] Reasoning for Rmeas or Rpim as Cutoff

Hi Randy - thank you for a very interesting reminder to old literature. I'm intrigued: how come this apparently excellent idea has not become standard best practice in the 14 years since it was published? phx On 30/01/2012 09:40, Randy Read wrote: Hi, Here are a couple of links on the ide

Re: [ccp4bb] All-D World

I believe Eric is paraphrasing Genesis 3. It's all the serpent's fault. http://www.ic.unicamp.br/~stolfi/PUB/misc-misc/GenesysParody.html On 16/02/2012 02:39, Eric Bennett wrote: Jacob, I wish it were that cheery. Do

Re: [ccp4bb] How to reduce no. of overlaps

You probably have to tilt your crystal, so that the long axis is parallel to the beam. We do this routinely: cut a plastic pipette tip to have a sharp point, then push the loop where it attaches to the pin, to bend the crystal itself. You have to identify from your diffraction whether the lo

Re: [ccp4bb] How to reduce no. of overlaps

Yes... quite. Thanks! (Beam, rotation axis... how can you expect me to keep all these new-fangled inventions apart?!) On 07/03/2012 07:33, VAN RAAIJ , MARK JOHAN wrote: typo correction, you'll want the long axis parallel to the rotation axis, not to the beam. Mark Quoting Frank von

Re: [ccp4bb] How to reduce no. of overlaps

om/product_detail.aspx?cid=24&sid=136&pid=385> *From:* Frank von Delft <mailto:frank.vonde...@sgc.ox.ac.uk> *Sent:* Wednesday, March 07, 2012 1:26 AM *To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> *Subject:* Re: [ccp4bb] How to reduce no. of overlaps You prob

Re: [ccp4bb] very informative - Trends in Data Fabrication

No James, you're not alone - astonishing petty pile-on (bullying?) on this board the last few days. Wikipedia says: "In Internet slang , a *troll* is someone who posts inflammatory,^[2]

Re: [ccp4bb] problem in scaling the Zn-MAD data

Sounds then like your spacegroup is p321... It's your data (scaling) that determines that, not your preconceptions (which wasn't clear how arrived at either?) cheers Phx Sent from tiny silly touch screen - Reply message - From: "Deepthi" Date: Wed, Apr 4, 2012 22:07 Subject: [ccp4bb]

[ccp4bb] Checking in dry shippers?

Hi, what's the latest on flying with dry shippers? Until about 2009, I used to fly with dry shippers all the time: I just tossed them (dry!) on the check-in belt, and the airlines didn't mind. But that was only London-Zurich, using BA or SwissAir. Anybody know if this still works, especiall

Re: [ccp4bb] Checking in dry shippers?

Hi, thanks for all responses. Most people suggested avoiding the scenario altogether, which was cute but not the question. Answers below the original question: On 17/04/2012 15:59, Frank von Delft wrote: Hi, what's the latest on flying with dry shippers? Until about 2009, I used to fly

Re: [ccp4bb] Checking in dry shippers?

More replies below (thanks all!!). Sounds like in Europe, checking in the dry shipper is not an issue. No idea of US - I assume absence of responses means nobody's bothering to try it, presumably too much hassle. phx Ed said (bb post) that airlines are meant to be happy to take dry shipper

Re: [ccp4bb] Checking in dry shippers?

MAIL.AC.UK] On Behalf Of Frank von Delft Sent: Tuesday, April 17, 2012 9:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Checking in dry shippers? Hi, thanks for all responses. Most people suggested avoiding the scenario altogether, which was cute but not the question. Answers below th

Re: [ccp4bb] "resolution" on PDB web page

Our policy is to request the pdb to update the stated resolution limit after the deposition's gone through. That said, I suspect it did not happen for many of our structures, because: 1) it's not part of the deposition mechanism, i.e. easy to forget. 2) the various programs (especially i

[ccp4bb] ctruncate and anistropy correction

Hello, a colleague just pointed me to an innocuous sentence in the ctruncate: "CTRUNCATE looks for anisotropy in the data and performs anisotropy correction." What exactly does that involve...? phx.

[ccp4bb] viewing small mol cif & fcf files?

Hi daft question: I was sent cif and fcf files for a small molecule crystal structure - solved with Bruker software, I think. Anybody know how to display this as electron density maps? I tried coot and mg, they barfed though - not sure whether that's a file problem though. Thanks for help!

Re: [ccp4bb] diverging Rcryst and Rfree

b) very large Rmerge values: Rmerge Rwork Rfree Rfree-Rwork Resolution - 0.9990 0.1815 0.20860.0271 1.80<<< SG center, unpublished 0.8700 0.1708 0.22700.0562 1.96<<< unpublished 0.7700 0.1870 0.2297

Re: [ccp4bb] Against Method (R)

Um... * Given that the weighted Rfactor is weighted by the measurement errors (1/sig^2) * and given that the errors in our measurements apparently have no bearing whatsoever on the errors in our models (for macromolecular crystals, certainly - the "R-vfactor gap") is the weighted Rfactor

Re: [ccp4bb] Hardware question

I've been told by my (frighteningly geek-competent) colleague that the platters are identical, but the cheaper ones are those at the bottom of the Quality Control pile, which are therefore spun more slowly, and don't get any claims of reliability. (Have you checked the disk rotation speed? I

Re: [ccp4bb] Against Method (R)

Yes, but what I think Frank is trying to point out is that the difference between Fobs and Fcalc in any given PDB entry is generally about 4-5 times larger than sigma(Fobs). In such situations, pretty much any standard statistical test will tell you that the model is "highly unlikely to be correc

Re: [ccp4bb] Looking for PDB His-tag statistics

(A tad delayed) Actually, typically we set up crystal trials for both cleaved and uncleaved protein right away at the same time (if there's enough protein and the cleavage works). Cheers phx On 07/01/2011 15:10, Bosch, Juergen wrote: I vaguely remember a paper by Aled Edwards, where they did

Re: [ccp4bb] what to do with disordered side chains

I'm amazed at the pedestal people put their precious coordinates on -- isn't the first thing you learn about MX that our models are rubbish parametrizations of the actual content of the crystal? And thus they will remain as long as we have the R-factor gap, and no amount of coordinate-sigmas

Re: [ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains

This is a lovely summary, and we should make our students read it. - But I'm afraid I do not see how it supports the closing statement in the last paragraph... phx. On 31/03/2011 17:06, Zbyszek Otwinowski wrote: The B-factor in crystallography represents the convolution (sum) of two types of

Re: [ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains

On 31/03/2011 23:43, Zbyszek Otwinowski wrote: Regarding the closing statement about the best solution to poorly ordered side chains: I described in the previous e-mail the probabilistic interpretation of B-factors. In the case of very high uncertainty = poorly ordered side chains, I prefer to d

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

I'm pretty sure Coot has been displaying it all along. In the early days it displayed it much better, I must say, which is why it tended to crash. Maybe the next version of coot as well as pymol/ Raster3D could also display virtual particles. This would really flashily push the quality of ou

Re: [ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains

Hi Robbie > If it's probability you're after, if there's no density to guide you > (very common!) you'd have to place all "likely" rotamers that don't > clash with anything, and set their occupancies to their probability (as > encoded in the rotamer library). Which library? The one for all side c

Re: [ccp4bb] Hampton's adjustable cryoloop

Hi Zhijie -- With all manipulations on the goniometer, I strongly advise what I learnt from Elspeth Garman: practice, practice, practice... but not with your real crystal! Take it down, put up a dummy pin, and take the time play around. I imagine even a non-hollow pin can be bent without

Re: [ccp4bb] Fwd: Regarding Sel-Met containing proteing crystallisation

Don't forget to do seeding with the native crystals: it's often more about nucleation than growth. Phx Sent from tiny silly touch screen - Reply message - From: "Frederic VELLIEUX" Date: Mon, Jun 13, 2011 07:37 Subject: [ccp4bb] Fwd: Regarding Sel-Met containing proteing crystallisatio

Re: [ccp4bb] Milestones in Crystallography

Oh wow, talk about challenging a community to confront their own worst fears of stagnation and irrelevance! Hehe - never mind cat in the pigeons, more like a man-eating tiger in a shanty-town. Wouldn't top of the list be "dwindling budget priority"? :-) But okay, back to specifically structu

Re: [ccp4bb] Another paper & structure retracted

On 12/08/2011 00:30, David Schuller wrote: link: http://iai.asm.org/cgi/reprint/IAI.05661-11v1 Ferric C. Fang& Arturo Casadevall Retracted Science and the Retraction Index Infec. Immun. doi:10.1128/IAI.05661-11 Abstract: Articles may be retracted when their findings are no longer considered

Re: [ccp4bb] Aging PEGs

And now, does anybody know of /systematic/ data indicating how consistently all this matters? phx On 24/08/2011 21:45, Prince, D Bryan wrote: For those of us truly controlling types :), I used to make the PEG solutions and filter them over a Bio-Rad resin that filtered out all the junk ad

Re: [ccp4bb] number of cycles in refmac

Hmm, I used to think I understood this, but I'm feeling a bit dim right now. On 25/08/2011 11:07, Ian Tickle wrote: Since the target function in MX refinement is the total likelihood (working set + restraints), there's no reason whatsoever why any another function, such as Rfree & LLfree, shou

Re: [ccp4bb] Oxidation, again!

Hi Jeremiah -- the short answer is Yes You Must! Don't whether you need that high concentration generally, but if it's not too osmotically active, the crystals should be fine; test it. But when mounting SeMet crystals, it's always a good idea to add fresh DTT or TCEP or whatever, it seems to

Re: [ccp4bb] units of the B factor

I second that... are there committees that ratify these things? phx James Holton wrote: Many textbooks describe the B factor as having units of square Angstrom (A^2), but then again, so does the mean square atomic displacement u^2, and B = 8*pi^2*u^2. This can become confusing if one sta

[ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor

Hi Marc Not at all, one uses units that are convenient. By your reasoning we should get rid of Å, atmospheres, AU, light years... They exist not to be obnoxious, but because they're handy for a large number of people in their specific situations. Sounds familiar... phx Marc SCHILTZ wro

[ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor

Eh? m and Å are related by the dimensionless quantity 10,000,000,000. Vive la révolution! Marc SCHILTZ wrote: Frank von Delft wrote: Hi Marc Not at all, one uses units that are convenient. By your reasoning we should get rid of Å, atmospheres, AU, light years... They exist not to be

Re: [ccp4bb] units of the B factor

That's still only by convention. Which was the point of this thread to begin with: let's settle on a convention. I'm surprised this is contentious. phx. Ian Tickle wrote: No, just like this: 'solid angle = 1.234' (or whatever its value is). Since the conversion unit 'steradian' = 1 (i.e.

Re: [ccp4bb] Refining against images instead of only reflections

On 28/01/2010 20:20, Ian Tickle wrote: On another point you said you wanted an 'operational' definition of I(Bragg). I'm not entirely clear what you mean by that. Are you saying I believe he means something that is relevant to real life where crystals are small, diffraction weak, and backg

Re: [ccp4bb] HKL-MTZ conversion

One thing that is superior is that the scala output gives you a better feel for the data quality, especially thanks to the per-image plots, for things like B-factor decay. Or should I say: it works better for *me*. All other scaling programs are more terse than scala, but maybe I've just nev

Re: [ccp4bb] 24-well sitting-drop plates

You don't *have* to use every single one of the 96 wells on a plate, of course -- it's quite feasible to use only 24 wells and then seal it. If you buy that argument: I recommend the 3-drop plates from SwissCi because you can do multiple drops per well, you can do pretty large volumes, and yo

Re: [ccp4bb] Display x-ray images in windows

Actually, imosflm works very nicely indeed on windows, and needs no third-party package. (Unless you consider ccp4 "third-party" as opposed to essential.) phx. On 23/03/2010 19:38, James Holton wrote: I have been reminded that the front page of ADXV's website does not have a link to the "wi

Re: [ccp4bb] Phasing statistics

I fully agree, for high quality data. What though if the data are not impeccable and the structure necessarily ropey? E.g. 4A phases and anisotropic diffraction. By what metrics do we then judge the results? (I don't know the answer, btw, but our membranous colleagues surely spend quite a

Re: [ccp4bb] Proportion of MR in PDB

Jim Pflugrath calls it "molecular substitution" -- I find this a very neat distinction. On 19/04/2010 15:50, Ian Tickle wrote: I would say it should still be classed as MR: the distinguishing feature of MR is surely that it uses an known structure as a starting model, not that it does a rotati

Re: [ccp4bb] sigma cutoff for fitting waters in model

Has anybody ever explored contouring maps using a "sigma" (i.e. rmsd) derived only from what is clearly the solvent region? Obviously that's not relevant during early phasing, but in the later stages of refinement, that would be relatively clear. And it would be fairly comparable from map to

Re: [ccp4bb] Rsym problems...maybe???

Yeah, stop worrying! Your I/sdI is all that matters. phx On 22/04/2010 18:06, Daniel Bonsor wrote: Hello again. At first I was not worry but maybe now I am. I have completed a structure and submitted to the PDB. They queried my Rsym value in the highest resolution bin, 2.5-2.37A (may I dare

Re: [ccp4bb] SUMMARY: scala and xds data

Hi, I sense a misunderstanding: Cell parameters are not relevant when scaling together datasets: what matters are intensities and (depending on algorithm) directional cosines and the like. Cell parameters are relevant, along with the other experimental parameters, for knowing where to pick

[ccp4bb] Fwd: Re: [ccp4bb] SUMMARY: scala and xds data

Well, there's one one very good reason to scale XDS data with scala: scala prints out per-image statistics, which are fantastically useful. My particular favourite: the scaling B-factor, which is as direct a read-out of dose (i.e. decay) as we have: 1A^2 per MGy. (Lots and lots of cave

Re: [ccp4bb] lossy compression of diffraction images

Just looked at the algorithm, how it stores the average "non-spot" through all the images. What happens with dataset where the "non-spot" (e.g. background) changes systematically through the dataset, i.e. anisotropic datasets or thin crystals lying flat in a thin loop? How much worse is compr

Re: [ccp4bb] Micro-g Crystal Growth and the literature

(I noticed these words of wisdom did not make it to the thread. Hereby belatedly corrected.) The relevant TLI here is ROI: for the money to put one crystallization plate in space, you can employ enough postdocs probably to solve all membrane proteins in the human genome terrestrially 3 times o

Re: [ccp4bb] updated mtz file or original one in refmac5

Hi Jay No, don't use the new one: the F's in there have been scaled by the overall anisotropic B-factors. (At least, they used to be, a few years ago.) Definitely go with the old one, every time. The output mtz has the coefficients for the maps, that's all. Cheers phx. On 17/05/2010

[ccp4bb] Where to find "novelty" of PDBids?

Hi, for an analysis I need the sequence identity of any PDBid to its closest match in the PDB *at the time it was deposited*. It seems like something somebody would have done before; any thoughts where to find it? Cheers phx

Re: [ccp4bb] Anisotropic data and an extremely long c axis

On 09/06/2010 16:49, James Holton wrote: Operationally, I recommend treating anisotropic data just like isotropic data. There is nothing wrong with measuring a lot of zeros (think about systematic absences), other than making irrelevant statistics like Rmerge higher. One need only glance at t

Re: [ccp4bb] Merohedral twining for P212121. -

My experience with pseudo-merohedral twinning (it was actually the reticular case with half the spots overlapped and the other non-overlapped half on a pseudo C-centred lattice) is that the degree of splitting varies widely over the diffraction pattern. In some places there was complete overlap,

Re: [ccp4bb] vacuum adapter for Dry shipper Cryo Dewar

They seem to have a finite life-time: we had two of these, bought at the same time, self-immolate the way you describe within months of another, after ~5 years of good service. We asked TW about it and they said it would cost more to get it fixed than just get a new one -- then again, they wo

Re: [ccp4bb] measure of anamolous signal

I've found the scala CC-anom significantly underestimates the anomalous signal, relative to e.g. xprep. I don't know why that is, but the latter seems to agree with what shelxd is happy with. Cheers phx On 29/06/2010 10:35, Graeme Winter wrote: Hi Murugan, One useful indicator of raw ano

Re: [ccp4bb] Density changes from Positive to negative after ligand addition and refinement

Negative (or positive) density tells you what you that what you've modelled is wrong. If you have 1.15A X-ray data and it's telling you what you think is Ca2+ is not Ca2+, then I would think your X-ray data wins and your previous structures lose (a lot can happen from one structure to the next

[ccp4bb] Elspeth Garman's husband

Dear all Last night, John Barnett, physicist and husband of Elspeth Garman, passed away after a long battle with cancer. Please join me in passing condolences to Elspeth and her family. She mentioned that she may not be particularly responsive in the next while. Frank

Re: [ccp4bb] Extremely long c-axis...reasonable?

Totally reasonable, yes. (But when it's that wrong, you easily get it wrong, too.) It's probably P6122 or P4122. Be careful to mount your crystals so you can rotate around the long axis, otherwise you'll never get non-overlapping data. phx On 03/08/2010 12:45, Christian Strube wrote: Hi

Re: [ccp4bb] Two cells, one crystal

I'd expect anything from crystals, and this would not surprise me either. Especially if it's a big crystal. That said: if the big cell has pseudo-translational symmetry, it will have lots of weak spots (?). So getting the "small cell" may just be an artefact of having very weak diffraction

Re: [ccp4bb] Scaling up from an Intelliplate to Linbro Plate

I assume you're sure you even *need* to scale up? Most of our structures come from crystals from "small" (150-300nl) drops, we consider a 100um crystal already "huge". And if a smaller crystal doesn't diffract far enough on a modern beamline, chances are a large one won't either (quite apart

Re: [ccp4bb] Can CCP4 refine B factors for several residues only?

The requirement sounds extremely suspect: every atom in the structure contributes to every reflection, so refining "only some atoms" makes as little mathematical sense as refining against "only a subset of reflections". Especially not Bfactors, which are after all where errors get pushed int

Re: [ccp4bb] Can CCP4 refine B factors for several residues only?

The requirement sounds extremely suspect: every atom in the structure contributes to every reflection, so refining "only some atoms" makes as little mathematical sense as refining against "only a subset of reflections". I agree with you that the requirement sounds dubious. But the specif

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