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
oXFEL 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.buffalo.edu/>
> Phone: (716) 898
gt; 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
>>>>>> cryo-vials had a powde
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
;>>>
> >>>> 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 educational
> >>>> opp
icipated
>>>> 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
>>>> installation and alignment, unbelievably w
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
>>
>>> Eddie
>>>
>>> Edward 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
x: (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
>> Powell - CCP4BB
>
(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 boa
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
.@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
.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 source inquiry
>
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 image (e.g. Si powder) t
@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 used to check both
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:
>
>
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
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
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
>>
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 dur
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
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
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
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
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
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:
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
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
?
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 Validation initiative in
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
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
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:
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
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
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 big
effrey, 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 secure environment. Do
> 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@JISCMAIL.AC.UK; Jeffrey B Bonanno <
> jeffrey.bona...@ei
@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
: 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
propagation from
-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 talk for many
: [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 macromole
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 Course
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
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
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