[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Quote source inquiry

multiple diffraction events. What is your experience? Best, Herman Von: CCP4 bulletin board Im Auftrag von Jessica Bruhn Gesendet: Samstag, 18. Juli 2020 02:16 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] Quote source inquiry EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk

Re: [ccp4bb] Quote source inquiry

Snell Ph.D. > > Director of the NSF BioXFEL Science and Technology Center > President and CEO Hauptman-Woodward Medical Research Institute > BioInnovations Chaired Professorship, University at Buffalo, SUNY > 700 Ellicott Street, Buffalo, NY 14203-1102 > hwi.buffalo.edu <http://hwi.

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are >>>>>> routine that would take a powder pattern and accurately calculate >>>>>> the beam center. This saved one of our structures. Wax, silicon >>>>>> powder, and other test samples were used. If I remember correctly >>>>&

Re: [ccp4bb] Quote source inquiry [SEC=UNCLASSIFIED]

Hi Tom Welcome to the old folks club! There are a few points in your post that I think are incredibly relevant here, and worth picking out for the casual reader - > it takes so little time to calibrate using powder diffraction Exactly! For a user collecting on a modern beamline that can coll

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avel to the beamline. > >>>> > >>>> I've been saved once with the powdered silicon. We had a hutch > >>>> that was completely empty when we arrived due to an unanticipated > >>>> emergency. A week of beamtime turned into an amazing ed

Re: [ccp4bb] Quote source inquiry

pty when we arrived due to an unanticipated >>>> emergency. A week of beamtime turned into an amazing educational >>>> opportunity to install and align the diffractometer. The powder >>>> data proved very useful in the energy calibration. After >>>> install

Re: [ccp4bb] Quote source inquiry [SEC=UNCLASSIFIED]

Hi Harry, I laughed when I read your question below "Or is this considered just something that old folk do?". At the Australian Synchrotron MX beamlines (MX1 and MX2) we also go old-school and collect Lanthanum hexaboride powder diffraction data during each user setup. We collect a single 180

Re: [ccp4bb] Quote source inquiry

t;>> >>> Best, >>> >>> Eddie >>> >>> Edward Snell Ph.D. >>> >>> Director of the NSF BioXFEL Science and Technology Center >>> President and CEO Hauptman-Woodward Medical Research Institute >>> BioInnovations Ch

Re: [ccp4bb] Quote source inquiry

Phone: (716) 898 8631 Fax: (716) 898 8660 >> Skype: eddie.snell Email: esn...@hwi.buffalo.edu >> Webpage: https://hwi.buffalo.edu/scientist-directory/snell/ >> >> -Original Message- >> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Harry >

Re: [ccp4bb] Quote source inquiry

wi.buffalo.edu > > Phone: (716) 898 8631 Fax: (716) 898 8660 > > Skype:eddie.snell Email: > > esn...@hwi.buffalo.edu Webpage: > > https://hwi.buffalo.edu/scientist-directory/snell/ > > > > > > -Original Message- &

Re: [ccp4bb] Quote source inquiry

I suppose that this is where the phrase "Mind your own beeswax" comes from 😉 > -Original Message- > From: CCP4 bulletin board On Behalf Of Edward > Snell > Sent: Thursday, July 16, 2020 16:36 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Quote source

Re: [ccp4bb] Quote source inquiry

ona...@einsteinmed.org > > > -Original Message- > From: CCP4 bulletin board On Behalf Of Gerard DVD > Kleywegt > Sent: Wednesday, July 15, 2020 11:49 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Quote source inquiry > > Well, I've had this

Re: [ccp4bb] Quote source inquiry

https://hwi.buffalo.edu/scientist-directory/snell/ > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Harry > Powell - CCP4BB > Sent: Thursday, July 16, 2020 7:26 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Quote s

Re: [ccp4bb] Quote source inquiry

> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Harry Powell - CCP4BB > Sent: Thursday, July 16, 2020 7:26 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Quote source inquiry > > Hi > > Does anyone bother collecting a powder imag

Re: [ccp4bb] Quote source inquiry

[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Harry Powell - CCP4BB Sent: Thursday, July 16, 2020 7:26 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Quote source inquiry Hi Does anyone bother collecting a powder image (e.g. Si powder) these days so they actually have a reference that can be use

Re: [ccp4bb] Quote source inquiry

Hi Gerard Indeed. Calibration used to be part of the experiment, but it’s often forgotten these days (or it’s assumed that someone else has done it to an adequate standard - fortunately, this assumption is usually valid enough). Harry > On 16 Jul 2020, at 12:37, Gerard Bricogne wrote: > > D

Re: [ccp4bb] Quote source inquiry

I think I wasn't totally clear. The structure was refined with the correct cell dimensions and those fractional coordinates then were converted to orthogonal as the last step before sending them to the PDB. Had the depositor simply sent us the fractional data, we would have changed them to ortho

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Quote source inquiry

There are cases where cell dimensions vary in a very real way. I have a system in which the unit cell volume can differ by more than 10%. When I first explored this system in the long ago times, before cryo-crystallography was a thing, the unit cell dimensions would change during data collectio

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Quote source inquiry

imposed well onto the electron >> density map, which should be easy to spot. >> Best, >> Herman >> >> -Ursprüngliche Nachricht- >> Von: CCP4 bulletin board Im Auftrag von Frances >> C. Bernstein >> Gesendet: Donnerstag, 16. Juli 2020 13:44 >>

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Quote source inquiry

s > C. Bernstein > Gesendet: Donnerstag, 16. Juli 2020 13:44 > An: CCP4BB@JISCMAIL.AC.UK > Betreff: [EXTERNAL] Re: [ccp4bb] Quote source inquiry > > EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk > > > > I do not remember the date or the PDB entry but it was during

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Quote source inquiry

Betreff: [EXTERNAL] Re: [ccp4bb] Quote source inquiry EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk I do not remember the date or the PDB entry but it was during the time that the PDB at BNL was including distance and angle outliers in the checking report sent back to the depositor

Re: [ccp4bb] Quote source inquiry

Hi Frances, I'm not surprised. Just correcting (from old orthogonal via fractional to new orthogonal) will "stretch" bonds ever so slightly. I would have done rigid-body followed by some all-atom refinement and maybe checked the map and model fit afterwards (esp. at crystal contacts), and if n

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I do not remember the date or the PDB entry but it was during the time that the PDB at BNL was including distance and angle outliers in the checking report sent back to the depositor. It was a not-too-large protein and there were perhaps half a dozen outliers each on distances and angles which was

Re: [ccp4bb] Quote source inquiry

Dear Harry, I think that sharp ice rings (or, better, a powder pattern from silicon powder) are only part of the solution to the calibration of beam energy, as there is an interaction with the detector distance. If I recall what I saw in my now distant days at LURE, a precise energy calibrati

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I think most of us are such "excellent" cryo-coolers that for every beamline shift we have multiple crystals with ice ring diffraction :-) Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 Sect

Re: [ccp4bb] Quote source inquiry

Hi Does anyone bother collecting a powder image (e.g. Si powder) these days so they actually have a reference that can be used to check both the wavelength and the beam centre? Or is this considered just something that old folk do? Harry > On 16 Jul 2020, at 12:19, Gerard DVD Kleywegt wrote:

Re: [ccp4bb] Quote source inquiry

No, I only wore Dutch clogs :-) Uppsala was an observer I think so Alwyn and I could attend the meetings, but we couldn't hire anyone. --G On Thu, 16 Jul 2020, Eleanor Dodson wrote: Well - it was Hamburg high resolution data - I guess we all had a stake in it.. Good meetings but You were par

Re: [ccp4bb] Quote source inquiry

There was a case a few years ago (not too many though) where a 1.6 Å structure had been solved using an incorrect value for the wavelength (~5% too low, leading to a cell that was slightly too small for its contents to be comfortable). It was later corrected so we could compare their validation

Re: [ccp4bb] Quote source inquiry

that in a systematic way? Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Eleanor > Dodson > Sent: Thursday, July 16, 2020 12:57 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Quote source inquiry > > Hmm - remember Gerard, the EU Valida

Re: [ccp4bb] Quote source inquiry

Well - it was Hamburg high resolution data - I guess we all had a stake in it.. Good meetings but You were part of them? Did you wear a Dutch hat? E On Thu, 16 Jul 2020 at 12:07, Gerard DVD Kleywegt wrote: > Hi Eleanor, > > Yes, I remember those meetings, when the UK was still an EU member and >

Re: [ccp4bb] Quote source inquiry

Hi Eleanor, Yes, I remember those meetings, when the UK was still an EU member and Sweden not yet (so Uppsala couldn't be formally involved) :-) Did Victor look into this too? I remember Gert doing it. And maybe Tom Oldfield? Best wishes, --Gerard On Thu, 16 Jul 2020, Eleanor Dodson wro

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Hmm - remember Gerard, the EU Validation initiative in the 1990s? We analysed these effects, or at least Victor Lamsin did, and we applauded him. Cheers Eleanor On Thu, 16 Jul 2020 at 11:52, Clemens Vonrhein wrote: > Hi Robbie, > > On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote:

Re: [ccp4bb] Quote source inquiry

Hi Robbie, On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote: > At the same time if you have a a more relaxed approach to restraints > than you might find systematic deviations in bond lengths. A test > for that has been in WHAT_CHECK for decades and it actually works > surprisingly w

Re: [ccp4bb] Quote source inquiry

e > > > -Original Message- > > From: CCP4 bulletin board On Behalf Of Ian > > Tickle > > Sent: Wednesday, July 15, 2020 20:25 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] Quote source inquiry > > > > > > Hi, > &g

Re: [ccp4bb] Quote source inquiry

s uncommon now. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Ian > Tickle > Sent: Wednesday, July 15, 2020 20:25 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Quote source inquiry > > > Hi, > > There's one

Re: [ccp4bb] Quote source inquiry

rg > > From: Jeffrey, Philip D. > Sent: Wednesday, July 15, 2020 12:47 PM > To: CCP4BB@JISCMAIL.AC.UK; Jeffrey B Bonanno > Subject: Re: [ccp4bb] Quote source inquiry > > CAUTION: This email comes from an external source; the attachments and/or > links may compromise our sec

Re: [ccp4bb] Quote source inquiry

nstein College of Medicine > > 1300 Morris Park Avenue > > Bronx, NY 10461 > > off. 718-430-2452 fax. 718-430-8565 > > email jeffrey.bona...@einsteinmed.org > > > > *From:* Jeffrey, Philip D. > *Sent:* Wednesday, July 15, 2020 12:47 PM > *To:* CCP4BB@JI

Re: [ccp4bb] Quote source inquiry

@JISCMAIL.AC.UK; Jeffrey B Bonanno Subject: Re: [ccp4bb] Quote source inquiry CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the "Phish Alert" button on the top ri

Re: [ccp4bb] Quote source inquiry

anno Sent: Wednesday, July 15, 2020 12:36 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Quote source inquiry Hi Gerard and Bernhard, As a postdoc in an unnamed small molecule lab, I was instructed by my lab head to get better unit cell estimates prior to data collection owing to error propagatio

Re: [ccp4bb] Quote source inquiry

8-430-8565 email jeffrey.bona...@einsteinmed.org -Original Message- From: CCP4 bulletin board On Behalf Of Gerard DVD Kleywegt Sent: Wednesday, July 15, 2020 11:49 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Quote source inquiry Well, I've had this in my CSHL X-ray Course tal

Re: [ccp4bb] Quote source inquiry

t: Re: [ccp4bb] Quote source inquiry Well, I've had this in my CSHL X-ray Course talk for many years. In the attached 2007 Acta D paper it says (p 95): "Macromolecular X-ray crystallography is a notoriously poor method for determining the structure of small molecules that are bound to

Re: [ccp4bb] Quote source inquiry

Close enough verbatim and dead on in spirit. Many thanks, BR -Original Message- From: Gerard DVD Kleywegt Sent: Wednesday, July 15, 2020 08:49 To: b...@hofkristallamt.org Cc: CCP4 Bulletin Board Subject: Re: [ccp4bb] Quote source inquiry Well, I've had this in my CSHL X-ray C

Re: [ccp4bb] Quote source inquiry

True but who would claim it was On Tue, 14 Jul 2020 at 21:22, Bernhard Rupp wrote: > Hi Fellows, > > > > afaicrimps (as far as I can recall in my progressing senility) someone > once wrote/stated/cursed somewhere that “Macromolecular refinement is not a > small molecule structure determination

[ccp4bb] Quote source inquiry

Hi Fellows, afaicrimps (as far as I can recall in my progressing senility) someone once wrote/stated/cursed somewhere that "Macromolecular refinement is not a small molecule structure determination method". Any citable source - George Sheldrick might be a suspect. Thanks & best regar

Re: [ccp4bb] quote source

Hi Bernard, I googled the phrase 'hydrogen bond for physiology" and got lots of results as many people have cited that paragraph. But the following result should give you what you need. http://books.google.com/books?id=OnSG9cMHqnkC&pg=PA851&lpg=PA851&dq=%22hydrogen+bond+for+physiology%22&sou

Re: [ccp4bb] quote source

Re: [ccp4bb] quote source

9,M1 Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp Sent: Wednesday, July 23, 2008 10:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] quote source Dear All, does someone know the proper reference of this L. Pauling stateme

[ccp4bb] quote source

Dear All, does someone know the proper reference of this L. Pauling statement? "Although the hydrogen bond is not strong it has great significance in determining the properties of substances. Because of its small bond energy and the small activation energy involved in its formation and rupture, t