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

[Schreuder, Herman /DE]

Dear Jessica,

Thank you for this positive news on electron diffraction on small molecules. A 
point which is still not clear to me: is it possible to determine the absolute 
configuration with electron diffraction? Some claim that it cannot be done, 
others claim that it can be done using 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<mailto:owner-ccp...@jiscmail.ac.uk>

Hi Garib, Tim and James,

Thank you for the helpful information. I look forward to testing this out on 
some of our data. Hopefully it helps!

To Garib, I think that electron diffraction/microED of small molecules is 
actually in a pretty good position for this technique to really take off. To 
your concerns:
1. Our group is personally very happy with the data coming from our detector 
(CETA-D). The thicker scintillator really seems to have helped. And there are 
other good detectors out there. I have some data posted in zenodo in case you 
are interested (10.5281/zenodo.3905397 and 10.5281/zenodo.3937740).
2. Crystal handling is thankfully very straightforward for dry, small molecule 
crystals. Just dab a TEM grid on some (crystalline) powder and in most cases 
you should be ready to collect. Protein crystals are unfortunately 
significantly more difficult to work with. We'll see how work in that area 
progresses...
3. As for rotation, I am curious to hear what concerns you have about rotation? 
Are you concerned about completeness? Or the lower data quality in the high 
tilt angle frames? Or the accuracy of the goniometer with regard to position 
and constant speed maintenance? If your concerns are about completeness, I 
would say that we have been able to get fairly decent completeness by combining 
data from multiple crystals. In our hands (18 small molecule ED structures 
solved in house), about half of these reached >95% completeness, another 
quarter were >90% and the rest were in the 81-90% range.

You may also be interested to know that of these 18 small molecule structures, 
three had to be refined in REFMAC5 because the resolution was a little low 
(1.2-1.7A) or the data to parameter ratio was too poor for SHELXL. I understand 
your time is limited, but I do think that electron diffraction for small 
molecules is really gaining momentum. We have collected data from almost fifty 
different samples from our clients all across pharma since installing our new 
camera in September. Many of these probably won't end up in public databases, 
but they have been hugely impactful for these chemists.

Have a wonderful weekend.

Best wishes,
Jessica



On Fri, Jul 17, 2020 at 2:11 AM Garib Murshudov 
mailto:ga...@mrc-lmb.cam.ac.uk>> wrote:
Dear Tim,


I understand the problem. If the problem is the distance only then only one 
parameter is needed for refinement of lattice parameters.

I do think that microED has good potential. However engineering problems need 
to be sorted out (detector, crystal handling, rotation etc).

When the problem becomes urgent then I can coniblue working on this problem. I 
have already implemented using all data (chemistry and crystal data) for 
lattice refinement. They need to be tested properly.
There are several issues that need to be sorted out.

Regards
Garib



On 17 Jul 2020, at 08:29, Tim Gruene 
mailto:tim.gru...@univie.ac.at>> wrote:

Dear Garib,

thank you very much for the details! If everything goes to plan, we are
going to use the Dectris QUADRO in September(ish), ideally also with
some protein crystals. In ED, distance calibration is more difficult
than with X-rays because of instabilities in the lens system (at least
with the older instruments), and because I do not work with a parallel
beam, but focus the beam onto the detector surface. This is not a very
reproducible process. In those cases where I got high resolution data,
the cell is often quite stable, and the distance can vary by about 5%...

Best regards,
Tim

On Thu, 16 Jul 2020 23:21:54 +0100
Garib Murshudov mailto:ga...@mrc-lmb.cam.ac.uk>> wrote:


One correction: Model should after molecular replacement and few
cycles of refinement (perhaps with a little bir relaxed geometry, but
not too much).

There is an option to use a model after molecular replacement but it
is being migrated to another program that will have proper tests.

Regards
Garib



On 16 Jul 2020, at 22:34, Garib Murshudov 
mailto:ga...@mrc-lmb.cam.ac.uk>>
wrote:

Hi Tim,

There is an option to do unit cell parameter refinement (for all
six parameters in general which can only happen in P1). It is
undocumented.

Celrefine/lattice refine all # if you give scale instead of all
then only one parameter is refined.

Cellrefine select .  # use only atomic B value < Bmedian +
alpha * 

Re: [ccp4bb] Quote source inquiry

[Jessica Bruhn]

a hutch
> that was completely empty 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
> installation and alignment, unbelievably we were able to collect
> our data and get a publication from it.
>
> Best,
>
> 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 Buffalo, SUNY
> 700 Ellicott Street, Buffalo, NY 14203-1102
> hwi.buffalo.edu <http://hwi.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-
> 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 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:
>
>
> 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 statistics. Some interesting
> observations:
>
>
> - the geometry had been very tightly restrained so that didn't
> give a clue  about the cell error (WhatCheck only suggested a
> very small change)
>
> - somewhat surprisingly (I thought) the Ramachandran plot did
> not improve in  the correct model (0.3% outliers in the wwPDB
> validation report), and the  sidechain rotamer outliers even got
> worse (from 1.5 to 2.5 %)
>
> - the map looked surprisingly good for the incorrect cell
>
> - however, RSR-Z told clearly that the map was not good enough
> for the claimed  resolution - the model had 24% outliers! (3% in
> the corrected model which  still only put it at the ~50th
> percentile)
>
> - another good indicator was the clashscore (went from 44 to 7)
>
> - the original model did not include an Rfree, but the R-value
> (>0.3 at 1.6Å
> resolution) ought to have provided a clue to the
> crystallographers and  reviewers one would think
>
> It would be interesting to see what would happen if the
> wavelength would
>
> be set 5% too high.
>
>
> --Gerard
>
>
>
> On Thu, 16 Jul 2020, Clemens Vonrhein 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 well to detect cell
> dimension problems.
>
>
> Indeed.
>
> That said, the problem is uncommon now.
>
>
> Not so sure about that: we all rely on an accurate value of the
> energy/wavelength from the instrument/beamline - and if that is
> off (for whatever reasons) it will result in incorrect cell
> dimensions and a systematic deviation from the various
> restraints.
>
> This would even affect the best experiment done on the best
> crystal ... so fairly easy to spot at the refinement stage,
> especially if such an energy/wavelength offset is constant over
> a long period of time on a given instrument. To spot this at
> the data collection stage one would hope that at some point a
> crystal with very pronounced ice-rings will be looked at
> properly (and the fact these are not where we expect them to
> should cause some head-scratching).
>
> Cheers
>
> Clemens
>
> #
> ###
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of
> www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by
> www.jiscmail.ac.uk, terms & conditions are available at
> https://www.jiscmail.ac.uk/policyandsecurity/
>
>
>
> Best wishes,
>
> --Gerard
>
> *

Re: [ccp4bb] Quote source inquiry

[Garib Murshudov]

 values. 
>>>> 
>>>> We are quite slow on the manuscript for its reference, but for the
>>>> time being, please quote the nanoArgovia (www.nanoscience.ch 
>>>> <http://www.nanoscience.ch/>
>>>> <http://www.nanoscience.ch/ <http://www.nanoscience.ch/>>) project A12.01 
>>>> (A3EDPI).
>>>> 
>>>> cellopt is called liked a shelxl job, i.e. like 'cellopt name'
>>>> where name.ins and name.hkl are present in the directory. You can
>>>> add some constraints to the lattice type. 
>>>> 
>>>> Refmac5 can also refine the unit cell parameters (Max Clabbers has
>>>> made use of this feature), but as far as I understand, refmac5
>>>> only scales the unit cell volume isotropically - I am happy to be
>>>> corrected.
>>>> 
>>>> When you resolution is quite high, say 0.7A like what we get for
>>>> zeolites and some organic compounds, you can refine the cell and
>>>> the distance simultaneously, only the BEAM correlates heavily with
>>>> the distance. DIALS can produce plots for the correlation between
>>>> refined parameters, which is very handy for electron diffraction
>>>> data.
>>>> 
>>>> Best wishes,
>>>> Tim
>>>> 
>>>> 
>>>> On Thu, 16 Jul 2020
>>>> 08:20:11 -0700 Jessica Bruhn
>>>> <450e5de75376-dmarc-requ...@jiscmail.ac.uk 
>>>> <mailto:450e5de75376-dmarc-requ...@jiscmail.ac.uk>
>>>> <mailto:450e5de75376-dmarc-requ...@jiscmail.ac.uk 
>>>> <mailto:450e5de75376-dmarc-requ...@jiscmail.ac.uk>>> wrote: 
>>>>> As someone working with continuous rotation electron diffraction,
>>>>> mostly with small molecules, I am often very concerned about the
>>>>> accuracy of my cell dimensions. I have to heavily restrain my
>>>>> experimental geometry, including the detector distance, because
>>>>> they are so unusual compared to X-ray setups. I also suspect that
>>>>> my goniometer is less able to maintain a constant speed,
>>>>> resulting in small errors in the oscillation per frame,
>>>>> especially for early and late images. I have calibrated my
>>>>> microscope's camera length (analogous to detector distance) with
>>>>> powder diffraction and even include an elliptical distortion
>>>>> correction in DIALS, and I validated my setup with some single
>>>>> crystal data.
>>>>> 
>>>>> I am wondering if there is a way to refine my unit cell at the
>>>>> model refinement step? Most of my structures are 0.9-1.1A and are
>>>>> refined in SHELXL. I would think that refining my cell with the
>>>>> goal of bringing my bond lengths closer to ideal lengths would be
>>>>> helpful. Is there a way to do this?
>>>>> 
>>>>> Best,
>>>>> Jessica
>>>>> 
>>>>> On Thu, Jul 16, 2020 at 7:36 AM Edward Snell
>>>>> mailto:esn...@hwi.buffalo.edu> 
>>>>> <mailto:esn...@hwi.buffalo.edu <mailto:esn...@hwi.buffalo.edu>>> wrote:
>>>>> 
>>>>>> Not completely related to the question but at one particular
>>>>>> European synchrotron there were a group of beamline scientists
>>>>>> that also kept honey bees. The wax from each hive gave very
>>>>>> beautiful powder diffraction patterns with the scattering being
>>>>>> similar but distinctive to each hive. I was fortunate to observe
>>>>>> this before my data collection - this was their calibration of
>>>>>> the beam center.
>>>>>> 
>>>>>> In the US, many years before BluIce there was a 'jiffy' software
>>>>>> 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 powder signature and a magnet with part of a
>>>>>> vial glued to it became part of the tool kit when one would still
>>>>>> routinely travel 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
>>&

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

[Harry Powell - CCP4BB]

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 collect a dataset 
in seconds, the time spent on this step falls below their conscious threshold, 
so why not do it?

> It can be so hard for users to grow crystals and we want to make sure the 
> data quality for our users is the best possible. 

Again, “exactly”. I haven’t been on a data collection and processing course in 
the last decade where _every_ data processing developer hasn’t said something 
along the lines of “data collection is the _last_ experimental step (often of a 
long and painful process) - everything after this is computing, and can be 
repeated ad nauseam”. 

> I also remember getting really frustrated in the old days as a user with 
> incorrect beam position and/or detector distance in image headers and didn't 
> want our users to have to deal with that.

This was really brought home to me when I had a dataset given to me by a user 
which had been collected at a well-known source (which shall remain nameless, 
to protect the guilty…) where _every_ useful piece of metadata in the image 
header was incorrect - wavelength, beam centre, crystal-to-detector distance. 
Fortunately, the user had noted which (fixed wavelength) beamline they had 
actually used, and the data were rescued (after trials of different crystal to 
detector distances & beam centre in the data processing).

In the Mosflm coding I had (for many years) a set of “Trusted” detectors where 
the header values were (at the very least) good approximations to “true” - all 
other detector headers were considered unreliable. Of course, XDS (uniquely?) 
has always ignored the header information, but this has its own problems.

Harry

> On 16 Jul 2020, at 22:49, CARADOC-DAVIES, Tom  wrote:
> 
> 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 degree image of Lab6 at minimum 
> detector distance and then up to 500mm in 100mm steps. They we can analyse 
> the data (using automated fit2d scripts) to refine direct beam position on 
> the detector and the detector distance offset from reported distance. The 
> lab6 pin is stored in the robot dewar in a staff puck and mounting and 
> collecting the 6-8 images is quick (maybe 2 minutes?) as we have automated 
> collection and processing that runs via our user setup GUI.
> This process means that values for distance and direct beam in the image 
> headers for each user experiment have been experimentally determined that 
> morning. This accuracy helps the reliability of our auto-processing 
> (especially for dodgy crystals). Energy is calibrated each user run or if the 
> LaB6 data suggests a change in "distance". 
> 
> This is probably overkill but dates from the early days when we were building 
> user confidence in the beamlines. I also remember getting really frustrated 
> in the old days as a user with incorrect beam position and/or detector 
> distance in image headers and didn't want our users to have to deal with 
> that. I also spent many hours trying to refine beamX/Y from ice rings in 
> imosflm from beamlines with a postit-note stuck to the side of the monitor 
> with cryptic beamX/Y values.
> 
> We do get teased by some of our beamline scientist colleagues for our very 
> extensive beamline setup for each user (we could probably go to monthly for 
> some checks and weekly for others) but it takes so little time to calibrate 
> using powder diffraction we have just kept doing it.
> 
> If you think that is not pedantic enough we also collect a full dataset of 
> cubic insulin for every setup and the user setup report shows the data 
> processing statistics (the users also get the raw data and auto-processing 
> files). If we cannot get really nice data (low Rmerge at low resolution and 
> good low res anomalous signal at 13keV on sulfur) on cubic insulin won't 
> release the beamline to users until we can investigate and fix the issue. It 
> is also quick as we have Eigers and collections are so fast now.
> 
> I guess it is just part of our user support philosophy. It can be so hard for 
> users to grow crystals and we want to make sure the data quality for our 
> users is the best possible. Most users don't get the attention to detail that 
> goes on "under the hood" at the beamlines and this is how it should be. It is 
> our job to handle that stuff and success means users just expect good data 
> from good crystals and they get it. If you don't look for problems in the 
> beamlines you don’t find them. I think lot of MX 

Re: [ccp4bb] Quote source inquiry

[Tim Gruene]

parameters, which is very handy for electron diffraction
> >> data.
> >> 
> >> Best wishes,
> >> Tim
> >> 
> >> 
> >> On Thu, 16 Jul 2020
> >> 08:20:11 -0700 Jessica Bruhn
> >> <450e5de75376-dmarc-requ...@jiscmail.ac.uk
> >> <mailto:450e5de75376-dmarc-requ...@jiscmail.ac.uk>> wrote: 
> >>> As someone working with continuous rotation electron diffraction,
> >>> mostly with small molecules, I am often very concerned about the
> >>> accuracy of my cell dimensions. I have to heavily restrain my
> >>> experimental geometry, including the detector distance, because
> >>> they are so unusual compared to X-ray setups. I also suspect that
> >>> my goniometer is less able to maintain a constant speed,
> >>> resulting in small errors in the oscillation per frame,
> >>> especially for early and late images. I have calibrated my
> >>> microscope's camera length (analogous to detector distance) with
> >>> powder diffraction and even include an elliptical distortion
> >>> correction in DIALS, and I validated my setup with some single
> >>> crystal data.
> >>> 
> >>> I am wondering if there is a way to refine my unit cell at the
> >>> model refinement step? Most of my structures are 0.9-1.1A and are
> >>> refined in SHELXL. I would think that refining my cell with the
> >>> goal of bringing my bond lengths closer to ideal lengths would be
> >>> helpful. Is there a way to do this?
> >>> 
> >>> Best,
> >>> Jessica
> >>> 
> >>> On Thu, Jul 16, 2020 at 7:36 AM Edward Snell
> >>> mailto:esn...@hwi.buffalo.edu>> wrote:
> >>>   
> >>>> Not completely related to the question but at one particular
> >>>> European synchrotron there were a group of beamline scientists
> >>>> that also kept honey bees. The wax from each hive gave very
> >>>> beautiful powder diffraction patterns with the scattering being
> >>>> similar but distinctive to each hive. I was fortunate to observe
> >>>> this before my data collection - this was their calibration of
> >>>> the beam center.
> >>>> 
> >>>> In the US, many years before BluIce there was a 'jiffy' software
> >>>> 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 powder signature and a magnet with part of a
> >>>> vial glued to it became part of the tool kit when one would still
> >>>> routinely travel 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 educational
> >>>> opportunity to install and align the diffractometer. The powder
> >>>> data proved very useful in the energy calibration. After
> >>>> installation and alignment, unbelievably we were able to collect
> >>>> our data and get a publication from it.
> >>>> 
> >>>> Best,
> >>>> 
> >>>> 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 Buffalo, SUNY
> >>>> 700 Ellicott Street, Buffalo, NY 14203-1102
> >>>> hwi.buffalo.edu <http://hwi.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-
> >>>> 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
> >>>> 
> >>>>

Re: [ccp4bb] Quote source inquiry

[Garib Murshudov]

ction in DIALS, and I validated
>>> my setup with some single crystal data.
>>> 
>>> I am wondering if there is a way to refine my unit cell at the model
>>> refinement step? Most of my structures are 0.9-1.1A and are refined in
>>> SHELXL. I would think that refining my cell with the goal of bringing
>>> my bond lengths closer to ideal lengths would be helpful. Is there a
>>> way to do this?
>>> 
>>> Best,
>>> Jessica
>>> 
>>> On Thu, Jul 16, 2020 at 7:36 AM Edward Snell >> <mailto:esn...@hwi.buffalo.edu>>
>>> wrote:
>>> 
>>>> Not completely related to the question but at one particular
>>>> European synchrotron there were a group of beamline scientists that
>>>> also kept honey bees. The wax from each hive gave very beautiful
>>>> powder diffraction patterns with the scattering being similar but
>>>> distinctive to each hive. I was fortunate to observe this before my
>>>> data collection - this was their calibration of the beam center.
>>>> 
>>>> In the US, many years before BluIce there was a 'jiffy' software
>>>> 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 powder signature and a magnet with part of a vial
>>>> glued to it became part of the tool kit when one would still
>>>> routinely travel 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 educational
>>>> opportunity to install and align the diffractometer. The powder
>>>> data proved very useful in the energy calibration. After
>>>> installation and alignment, unbelievably we were able to collect
>>>> our data and get a publication from it.
>>>> 
>>>> Best,
>>>> 
>>>> 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 Buffalo, SUNY
>>>> 700 Ellicott Street, Buffalo, NY 14203-1102
>>>> hwi.buffalo.edu <http://hwi.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-
>>>> 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 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:  
>>>>> 
>>>>> 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 statistics. Some interesting
>>>> observations:  
>>>>> 
>>>>> - the geometry had been very tightly restrained so that didn't
>>>>> give a clue  about the cell error (WhatCheck only suggested a
>>>>> very small change)
>>>>> 
>>>>> - somewhat surprisingly (I thought) the Ramachandran plot did not
>>>>> improve in  the correct model (0.3% outliers in the wwPDB
>>>>> validation report), and the  sidechain rotamer outliers even got
>>>>> worse (from 1.5 to 2.5 %)
>>>&g

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

[CARADOC-DAVIES, Tom]

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 degree image of Lab6 at minimum detector 
distance and then up to 500mm in 100mm steps. They we can analyse the data 
(using automated fit2d scripts) to refine direct beam position on the detector 
and the detector distance offset from reported distance. The lab6 pin is stored 
in the robot dewar in a staff puck and mounting and collecting the 6-8 images 
is quick (maybe 2 minutes?) as we have automated collection and processing that 
runs via our user setup GUI.
This process means that values for distance and direct beam in the image 
headers for each user experiment have been experimentally determined that 
morning. This accuracy helps the reliability of our auto-processing (especially 
for dodgy crystals). Energy is calibrated each user run or if the LaB6 data 
suggests a change in "distance". 

This is probably overkill but dates from the early days when we were building 
user confidence in the beamlines. I also remember getting really frustrated in 
the old days as a user with incorrect beam position and/or detector distance in 
image headers and didn't want our users to have to deal with that. I also spent 
many hours trying to refine beamX/Y from ice rings in imosflm from beamlines 
with a postit-note stuck to the side of the monitor with cryptic beamX/Y values.

We do get teased by some of our beamline scientist colleagues for our very 
extensive beamline setup for each user (we could probably go to monthly for 
some checks and weekly for others) but it takes so little time to calibrate 
using powder diffraction we have just kept doing it.

If you think that is not pedantic enough we also collect a full dataset of 
cubic insulin for every setup and the user setup report shows the data 
processing statistics (the users also get the raw data and auto-processing 
files). If we cannot get really nice data (low Rmerge at low resolution and 
good low res anomalous signal at 13keV on sulfur) on cubic insulin won't 
release the beamline to users until we can investigate and fix the issue. It is 
also quick as we have Eigers and collections are so fast now.

I guess it is just part of our user support philosophy. It can be so hard for 
users to grow crystals and we want to make sure the data quality for our users 
is the best possible. Most users don't get the attention to detail that goes on 
"under the hood" at the beamlines and this is how it should be. It is our job 
to handle that stuff and success means users just expect good data from good 
crystals and they get it. If you don't look for problems in the beamlines you 
don’t find them. I think lot of MX experiments are viable when a beamline has a 
problem (fluctuating intensity, beam position vibration, structure in the beam 
etc) but some experiments are more sensitive than others and users may think 
they just have bad crystals despite pretty diffraction.

So yes, there are people these days who collect powder data for wavelength and 
beam position reference.

Cheers,

Tom


On 16/7/20, 9:26 pm, "CCP4 bulletin board on behalf of Harry Powell - CCP4BB" 
 wrote:

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:
> 
> 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 
statistics. Some interesting observations:
> 
> - the geometry had been very tightly restrained so that didn't give a clue
>  about the cell error (WhatCheck only suggested a very small change)
> 
> - somewhat surprisingly (I thought) the Ramachandran plot did not improve 
in
>  the correct model (0.3% outliers in the wwPDB validation report), and the
>  sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)
> 
> - the map looked surprisingly good for the incorrect cell
> 
> - however, RSR-Z told clearly that the map was not good enough for the 
claimed
>  resolution - the model had 24% outliers! (3% in the corrected model which
>  still only put it at the ~50th percentile)
> 
> - another good indicator was the clashscore (went from 44 to 7)
> 
> - the original model did not include an Rfree, but the R-value (>0.3 at 
1.6Å
>  resolution) ought to have provided a clue to the 

Re: [ccp4bb] Quote source inquiry

[Garib Murshudov]

n patterns with the scattering being similar but
>>> distinctive to each hive. I was fortunate to observe this before my
>>> data collection - this was their calibration of the beam center.
>>> 
>>> In the US, many years before BluIce there was a 'jiffy' software
>>> 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 powder signature and a magnet with part of a vial
>>> glued to it became part of the tool kit when one would still
>>> routinely travel 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 educational
>>> opportunity to install and align the diffractometer. The powder
>>> data proved very useful in the energy calibration. After
>>> installation and alignment, unbelievably we were able to collect
>>> our data and get a publication from it.
>>> 
>>> Best,
>>> 
>>> 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 Buffalo, SUNY
>>> 700 Ellicott Street, Buffalo, NY 14203-1102
>>> hwi.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-
>>> 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 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:  
>>>> 
>>>> 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 statistics. Some interesting
>>> observations:  
>>>> 
>>>> - the geometry had been very tightly restrained so that didn't
>>>> give a clue  about the cell error (WhatCheck only suggested a
>>>> very small change)
>>>> 
>>>> - somewhat surprisingly (I thought) the Ramachandran plot did not
>>>> improve in  the correct model (0.3% outliers in the wwPDB
>>>> validation report), and the  sidechain rotamer outliers even got
>>>> worse (from 1.5 to 2.5 %)
>>>> 
>>>> - the map looked surprisingly good for the incorrect cell
>>>> 
>>>> - however, RSR-Z told clearly that the map was not good enough
>>>> for the claimed  resolution - the model had 24% outliers! (3% in
>>>> the corrected model which  still only put it at the ~50th
>>>> percentile)
>>>> 
>>>> - another good indicator was the clashscore (went from 44 to 7)
>>>> 
>>>> - the original model did not include an Rfree, but the R-value
>>>> (>0.3 at 1.6Å
>>>> resolution) ought to have provided a clue to the
>>>> crystallographers and  reviewers one would think
>>>> 
>>>> It would be interesting to see what would happen if the
>>>> wavelength would  
>>> be set 5% too high.  
>>>> 
>>>> --Gerard
>>>> 
>>>> 
>>>> 
>>>> On Thu, 16 Jul 2020, Clemens Vonrhein wrote:
>>>> 
>>>>> Hi Robbie,
>>>>> 
>>>>> On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote:  
>>>>>> At the same time if you have a a mor

Re: [ccp4bb] Quote source inquiry

[Jon Cooper]

John, I'm sure they were bred by Brother Adam!

There is a nice paper on wax diffraction here:

https://fdocuments.net/document/crystallinity-of-plant-epicuticular-waxes-electron-and-x-ray-diffraction-studies.html

There are others by the DLS team ;-

Also, looks like the d-spacing was 3.72 Angstroms (not 2.72, sorry).

Best wishes, Jon Cooper, E-mail: jon.b.coo...@protonmail.com

 Original Message 
On 16 Jul 2020, 16:56, Jon Cooper wrote:

> That's interesting. I remember the days of wax rings, we even used to do 
> several at different X-D distances. I sort-of lost faith with the advent of 
> cryo since I had now idea of how this would affect the wax d-spacing (was it 
> 2.72 Angstroms at rtp?) but ice-rings were always a life-saver to check the 
> beam-centre. It would be interesting to know if 100K affects the wax d-value 
> significantly. Another thing which slightly confused me is that it was 
> popular belief that you could put the biggest piece of wax you could find in 
> the beam. Maybe I missed something, but how is that ever going to give 
> accurate X-D ;-?
>
> With some structures, for the last round of refinement, I used to reprocess 
> the data with XDS just to use the GLOREF option (sorry specialists!) which 
> refined the cell with all the diffraction spots in the dataset, so as to get 
> super-accurate cell dimensions for the last round. However, the last time I 
> tried this, the GLOREF option had disappeared!! Perhaps there is an 
> equivalent approach these days.
>
> Best wishes, Jon Cooper, E-mail: jon.b.coo...@protonmail.com
>
>  Original Message 
> On 16 Jul 2020, 15:35, Edward Snell wrote:
>
>> Not completely related to the question but at one particular European 
>> synchrotron there were a group of beamline scientists that also kept honey 
>> bees. The wax from each hive gave very beautiful powder diffraction patterns 
>> with the scattering being similar but distinctive to each hive. I was 
>> fortunate to observe this before my data collection - this was their 
>> calibration of the beam center.
>>
>> In the US, many years before BluIce there was a 'jiffy' software 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 powder signature 
>> and a magnet with part of a vial glued to it became part of the tool kit 
>> when one would still routinely travel 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 educational opportunity to install and 
>> align the diffractometer. The powder data proved very useful in the energy 
>> calibration. After installation and alignment, unbelievably we were able to 
>> collect our data and get a publication from it.
>>
>> Best,
>>
>> 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 Buffalo, SUNY
>> 700 Ellicott Street, Buffalo, NY 14203-1102
>> hwi.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-
>> 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 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:
>>>
>>> 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 statistics. Some interesting observations:
>>>
>>> - the geometry had been very tightly restrained so that didn't give a
>>> clue about the cell error (WhatCheck only sugges

Re: [ccp4bb] Quote source inquiry

[Tim Gruene]

Hi Jessica,

Jens Luebben wrote cellopt for this purpose. It is available from
github, https://github.com/JLuebben/CellOpt

It is based on the idea available in whatcheck, i.e. to optimise the
unit cell parameters based on geometry restraints DFIX/DANG. Those need
to be three-dimensional: I've had cases where the restraints do not
span all three dimensions. In this case one of the cell parameters can
refine to unrealistic values. 

We are quite slow on the manuscript for its reference, but for the time
being, please quote the nanoArgovia (www.nanoscience.ch) project A12.01
(A3EDPI).

cellopt is called liked a shelxl job, i.e. like 'cellopt name' where
name.ins and name.hkl are present in the directory. You can add some
constraints to the lattice type. 

Refmac5 can also refine the unit cell parameters (Max Clabbers has made
use of this feature), but as far as I understand, refmac5 only scales
the unit cell volume isotropically - I am happy to be corrected.

When you resolution is quite high, say 0.7A like what we get for
zeolites and some organic compounds, you can refine the cell and the
distance simultaneously, only the BEAM correlates heavily with the
distance. DIALS can produce plots for the correlation between refined
parameters, which is very handy for electron diffraction data.

Best wishes,
Tim


On Thu, 16 Jul 2020
08:20:11 -0700 Jessica Bruhn
<450e5de75376-dmarc-requ...@jiscmail.ac.uk> wrote:

> As someone working with continuous rotation electron diffraction,
> mostly with small molecules, I am often very concerned about the
> accuracy of my cell dimensions. I have to heavily restrain my
> experimental geometry, including the detector distance, because they
> are so unusual compared to X-ray setups. I also suspect that my
> goniometer is less able to maintain a constant speed, resulting in
> small errors in the oscillation per frame, especially for early and
> late images. I have calibrated my microscope's camera length
> (analogous to detector distance) with powder diffraction and even
> include an elliptical distortion correction in DIALS, and I validated
> my setup with some single crystal data.
> 
> I am wondering if there is a way to refine my unit cell at the model
> refinement step? Most of my structures are 0.9-1.1A and are refined in
> SHELXL. I would think that refining my cell with the goal of bringing
> my bond lengths closer to ideal lengths would be helpful. Is there a
> way to do this?
> 
> Best,
> Jessica
> 
> On Thu, Jul 16, 2020 at 7:36 AM Edward Snell 
> wrote:
> 
> > Not completely related to the question but at one particular
> > European synchrotron there were a group of beamline scientists that
> > also kept honey bees. The wax from each hive gave very beautiful
> > powder diffraction patterns with the scattering being similar but
> > distinctive to each hive. I was fortunate to observe this before my
> > data collection - this was their calibration of the beam center.
> >
> > In the US, many years before BluIce there was a 'jiffy' software
> > 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 powder signature and a magnet with part of a vial
> > glued to it became part of the tool kit when one would still
> > routinely travel 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 educational
> > opportunity to install and align the diffractometer. The powder
> > data proved very useful in the energy calibration. After
> > installation and alignment, unbelievably we were able to collect
> > our data and get a publication from it.
> >
> > Best,
> >
> > 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 Buffalo, SUNY
> > 700 Ellicott Street, Buffalo, NY 14203-1102
> > hwi.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-
> > 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

Re: [ccp4bb] Quote source inquiry

[Robbie Joosten]

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 inquiry
> 
> Not completely related to the question but at one particular European
> synchrotron there were a group of beamline scientists that also kept honey
> bees. The wax from each hive gave very beautiful powder diffraction
> patterns with the scattering being similar but distinctive to each hive. I was
> fortunate to observe this before my data collection - this was their
> calibration of the beam center.
> 
> In the US, many years before BluIce there was a 'jiffy' software 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 powder signature and a
> magnet with part of a vial glued to it became part of the tool kit when one
> would still routinely travel 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 educational opportunity to install
> and align the diffractometer. The powder data proved very useful in the
> energy calibration. After installation and alignment, unbelievably we were
> able to collect our data and get a publication from it.
> 
> Best,
> 
> 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 Buffalo, SUNY
> 700 Ellicott Street, Buffalo, NY 14203-1102 hwi.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-
> 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 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:
> >
> > 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
> statistics. Some interesting observations:
> >
> > - the geometry had been very tightly restrained so that didn't give a
> > clue  about the cell error (WhatCheck only suggested a very small
> > change)
> >
> > - somewhat surprisingly (I thought) the Ramachandran plot did not
> > improve in  the correct model (0.3% outliers in the wwPDB validation
> > report), and the  sidechain rotamer outliers even got worse (from 1.5
> > to 2.5 %)
> >
> > - the map looked surprisingly good for the incorrect cell
> >
> > - however, RSR-Z told clearly that the map was not good enough for the
> > claimed  resolution - the model had 24% outliers! (3% in the corrected
> > model which  still only put it at the ~50th percentile)
> >
> > - another good indicator was the clashscore (went from 44 to 7)
> >
> > - the original model did not include an Rfree, but the R-value (>0.3
> > at 1.6Å
> >  resolution) ought to have provided a clue to the crystallographers
> > and  reviewers one would think
> >
> > It would be interesting to see what would happen if the wavelength would
> be set 5% too high.
> >
> > --Gerard
> >
> >
> >
> > On Thu, 16 Jul 2020, Clemens Vonrhein 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 well to detect cell dimension problems.
> >>
> >> In

Re: [ccp4bb] Quote source inquiry

[John R Helliwell]

Hi,
Two aspects:-
Frank Herbstein investigated the precision of unit cell parameters in chemical 
crystallography, which I imagine will be of interest:-
https://scripts.iucr.org/cgi-bin/paper?bk0071

Secondly, at the synchrotron, the pure metal foil scan, eg of nickel that I 
purchased from Goodfellow Metals, was my preference. Hence 1.488 Angstrom as 
the set lambda was a common one. Then a direct beam marking as per 
https://doi.org/10.1107/S0021889883011097 . This left the x to d to measure. 
Otherwise if all three of these three were left undetermined, ouch. For silicon 
powder as standard, purchase it from NISTm and you get a calibration of purity 
certificate. 
Now then Eddie, bees wax from personal beehives of the beamline staffwhich 
type of bees? (:-).

Greetings,
John 

Emeritus Professor John R Helliwell DSc




> On 15 Jul 2020, at 17:36, Jeffrey B Bonanno  
> wrote:
> 
> 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 the uncertainty on cell dimensions through to the esd 
> on atomic bond lengths and angles when refining in shelxl. To verify this 
> (what, you believed everything your postdoc advisor told you?), I took a 
> working dataset and increased (only) the error on unit cell dimensions in the 
> instruction file for the final round of full matrix least squares refinement 
> in shelxl. Sure enough, the errors on the bonds and angles shot up. I was 
> more careful in determining the unit cell thereafter. That is, until, I 
> became a macromolecular crystallographer...
> 
> After an inciteful (sp? lol) discussion with Wladek about cell dimensions, I 
> was directed to read this paper:
> 
> Acta Crystallogr D Biol Crystallogr. 2015 Nov 1; 71(Pt 11): 2217–2226.
> 
> Have a look, it is interesting.
> 
> Having never followed up on these studies to see what happened to bonds and 
> angles in proteins and their ligands when varying cell dimensions, I can't 
> say with any confidence. However, I would guess that the quality of the 
> refined ligand coordinates could only be as good as some combination of 
> factors including but not limited to 1) the data (resolution, B factor, etc), 
> 2) the actual occupancy of the ligand, and 3) the restraints employed.
> 
> jbb
> 
> Jeffrey B. Bonanno, Ph.D.
> Department of Biochemistry
> Albert Einstein College of Medicine
> 1300 Morris Park Avenue
> Bronx, NY 10461
> off. 718-430-2452 fax. 718-430-8565
> 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 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 macromolecules [...]" and then goes on to 
> explain why this is the case.
> 
> In the attached 2003 paper (pooling the wisdom of several of the usual 
> suspects, including Eleanor) it says something similar (p 1057):
> 
> "Coordinates of molecules that have been determined in complex with 
> macromolecules previously can of course also be retrieved from the PDB 
> (Bernstein et al., 1977; Berman et al., 2000), HIC-Up (Kleywegt and Jones, 
> 1998), or CHEMPDB (Boutselakis et al., 2003). However, one should keep in 
> mind that these coordinates are the result of refinement against comparatively
> low-resolu- tion data where the small molecule constituted only a minute 
> fraction of the total scattering matter. This makes these coordinates 
> inherently much less accurate than those obtained from the CSD. In addition, 
> the coordi- nates may contain errors due to the use of incorrect restraints.
> Hence, such coordinate sets should only be used as a last resort, and only 
> after verification that they are reliable. The latter can be facilitated by 
> inspection of the electron density for the compound in question, for instance 
> at the Uppsala Electron-Density Server (http:// fsrv1.bmc.uu.se/eds) (G.J.K.
> et al., submitted)."
> 
> Happy to be confused with George though!
> 
> --Gerard (no, the other one)
> 
> 
> 
>> On Tue, 14 Jul 2020, 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 molecul

Re: [ccp4bb] Quote source inquiry

[Jon Cooper]

That's interesting. I remember the days of wax rings, we even used to do 
several at different X-D distances. I sort-of lost faith with the advent of 
cryo since I had now idea of how this would affect the wax d-spacing (was it 
2.72 Angstroms at rtp?) but ice-rings were always a life-saver to check the 
beam-centre. It would be interesting to know if 100K affects the wax d-value 
significantly. Another thing which slightly confused me is that it was popular 
belief that you could put the biggest piece of wax you could find in the beam. 
Maybe I missed something, but how is that ever going to give accurate X-D ;-?

With some structures, for the last round of refinement, I used to reprocess the 
data with XDS just to use the GLOREF option (sorry specialists!) which refined 
the cell with all the diffraction spots in the dataset, so as to get 
super-accurate cell dimensions for the last round. However, the last time I 
tried this, the GLOREF option had disappeared!! Perhaps there is an equivalent 
approach these days.

Best wishes, Jon Cooper, E-mail: jon.b.coo...@protonmail.com

 Original Message 
On 16 Jul 2020, 15:35, Edward Snell wrote:

> Not completely related to the question but at one particular European 
> synchrotron there were a group of beamline scientists that also kept honey 
> bees. The wax from each hive gave very beautiful powder diffraction patterns 
> with the scattering being similar but distinctive to each hive. I was 
> fortunate to observe this before my data collection - this was their 
> calibration of the beam center.
>
> In the US, many years before BluIce there was a 'jiffy' software 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 powder signature and a magnet 
> with part of a vial glued to it became part of the tool kit when one would 
> still routinely travel 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 educational opportunity to install and align 
> the diffractometer. The powder data proved very useful in the energy 
> calibration. After installation and alignment, unbelievably we were able to 
> collect our data and get a publication from it.
>
> Best,
>
> 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 Buffalo, SUNY
> 700 Ellicott Street, Buffalo, NY 14203-1102
> hwi.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-
> 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 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:
>>
>> 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 
>> statistics. Some interesting observations:
>>
>> - the geometry had been very tightly restrained so that didn't give a
>> clue about the cell error (WhatCheck only suggested a very small
>> change)
>>
>> - somewhat surprisingly (I thought) the Ramachandran plot did not
>> improve in the correct model (0.3% outliers in the wwPDB validation
>> report), and the sidechain rotamer outliers even got worse (from 1.5
>> to 2.5 %)
>>
>> - the map looked surprisingly good for the incorrect cell
>>
>> - however, RSR-Z told clearly that the map was not good enough for the
>> claimed resolution - the model had 24% outliers! (3% in the corrected
>> model which still only put it at the ~50th percentile)
>>
>> - another good indicator was the clashscore (went from 44 to 7)
>>
>> - the original model did not include an Rfree, but the R-value (>0.3
>> at 1.6Å
>> resolution) ought

Re: [ccp4bb] Quote source inquiry

[Jessica Bruhn]

As someone working with continuous rotation electron diffraction, mostly
with small molecules, I am often very concerned about the accuracy of my
cell dimensions. I have to heavily restrain my experimental geometry,
including the detector distance, because they are so unusual compared to
X-ray setups. I also suspect that my goniometer is less able to maintain a
constant speed, resulting in small errors in the oscillation per frame,
especially for early and late images. I have calibrated my microscope's
camera length (analogous to detector distance) with powder diffraction and
even include an elliptical distortion correction in DIALS, and I validated
my setup with some single crystal data.

I am wondering if there is a way to refine my unit cell at the model
refinement step? Most of my structures are 0.9-1.1A and are refined in
SHELXL. I would think that refining my cell with the goal of bringing my
bond lengths closer to ideal lengths would be helpful. Is there a way to do
this?

Best,
Jessica

On Thu, Jul 16, 2020 at 7:36 AM Edward Snell  wrote:

> Not completely related to the question but at one particular European
> synchrotron there were a group of beamline scientists that also kept honey
> bees. The wax from each hive gave very beautiful powder diffraction
> patterns with the scattering being similar but distinctive to each hive. I
> was fortunate to observe this before my data collection - this was their
> calibration of the beam center.
>
> In the US, many years before BluIce there was a 'jiffy' software 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 powder
> signature and a magnet with part of a vial glued to it became part of the
> tool kit when one would still routinely travel 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 educational opportunity to install and
> align the diffractometer. The powder data proved very useful in the energy
> calibration. After installation and alignment, unbelievably we were able to
> collect our data and get a publication from it.
>
> Best,
>
> 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 Buffalo, SUNY
> 700 Ellicott Street, Buffalo, NY 14203-1102
> hwi.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-
> 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 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:
> >
> > 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 statistics. Some interesting observations:
> >
> > - the geometry had been very tightly restrained so that didn't give a
> > clue  about the cell error (WhatCheck only suggested a very small
> > change)
> >
> > - somewhat surprisingly (I thought) the Ramachandran plot did not
> > improve in  the correct model (0.3% outliers in the wwPDB validation
> > report), and the  sidechain rotamer outliers even got worse (from 1.5
> > to 2.5 %)
> >
> > - the map looked surprisingly good for the incorrect cell
> >
> > - however, RSR-Z told clearly that the map was not good enough for the
> > claimed  resolution - the model had 24% outliers! (3% in the corrected
> > model which  still only put it at the ~50th percentile)
> >
> > - another good indicator was the clashscore (went from 44 to 7)
> >
> > - the original model did not include an Rfree, but the R-value (>0.3
> > at 1.6Å
> >  resolution) ought to have provided a clue to the crystallographers
> > and  rev

Re: [ccp4bb] Quote source inquiry

[Edward Snell]

Not completely related to the question but at one particular European 
synchrotron there were a group of beamline scientists that also kept honey 
bees. The wax from each hive gave very beautiful powder diffraction patterns 
with the scattering being similar but distinctive to each hive. I was fortunate 
to observe this before my data collection - this was their calibration of the 
beam center.

In the US, many years before BluIce there was a 'jiffy' software 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 powder signature and a magnet 
with part of a vial glued to it became part of the tool kit when one would 
still routinely travel 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 educational opportunity to install and align 
the diffractometer. The powder data proved very useful in the energy 
calibration. After installation and alignment, unbelievably we were able to 
collect our data and get a publication from it.

Best,

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 Buffalo, SUNY
700 Ellicott Street, Buffalo, NY 14203-1102
hwi.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-
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 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:
> 
> 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 
> statistics. Some interesting observations:
> 
> - the geometry had been very tightly restrained so that didn't give a 
> clue  about the cell error (WhatCheck only suggested a very small 
> change)
> 
> - somewhat surprisingly (I thought) the Ramachandran plot did not 
> improve in  the correct model (0.3% outliers in the wwPDB validation 
> report), and the  sidechain rotamer outliers even got worse (from 1.5 
> to 2.5 %)
> 
> - the map looked surprisingly good for the incorrect cell
> 
> - however, RSR-Z told clearly that the map was not good enough for the 
> claimed  resolution - the model had 24% outliers! (3% in the corrected 
> model which  still only put it at the ~50th percentile)
> 
> - another good indicator was the clashscore (went from 44 to 7)
> 
> - the original model did not include an Rfree, but the R-value (>0.3 
> at 1.6Å
>  resolution) ought to have provided a clue to the crystallographers 
> and  reviewers one would think
> 
> It would be interesting to see what would happen if the wavelength would be 
> set 5% too high.
> 
> --Gerard
> 
> 
> 
> On Thu, 16 Jul 2020, Clemens Vonrhein 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 well to detect cell dimension problems.
>> 
>> Indeed.
>> 
>>> That said, the problem is uncommon now.
>> 
>> Not so sure about that: we all rely on an accurate value of the 
>> energy/wavelength from the instrument/beamline - and if that is off 
>> (for whatever reasons) it will result in incorrect cell dimensions 
>> and a systematic deviation from the various restraints.
>> 
>> This would even affect the best experiment done on the best crystal 
>> ... so fairly easy to spot at the refinement stage, especially if 
>> such an energy/wavelength offset is constant over a long period of 
>> time on a given instrument. To spot thi

Re: [ccp4bb] Quote source inquiry

[Harry Powell - CCP4BB]

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:
> 
> 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 calibration would be done
> using an absorption edge. I can remember Richard Kahn using a Cu metal foil
> to lock precisely onto an energy close to the Ytterbium edge he wanted to
> use in a MAD experiment. When the beam energy is precisely established by
> this diffraction-free method, then a Si powder allows a precise calibration
> of detector distance (and location of beam centre). 
> 
> 
> With best wishes,
> 
>  Gerard.
> 
> --
> On Thu, Jul 16, 2020 at 12:25:55PM +0100, Harry Powell - CCP4BB wrote:
>> 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:
>>> 
>>> 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 statistics. Some interesting observations:
>>> 
>>> - the geometry had been very tightly restrained so that didn't give a clue
>>> about the cell error (WhatCheck only suggested a very small change)
>>> 
>>> - somewhat surprisingly (I thought) the Ramachandran plot did not improve in
>>> the correct model (0.3% outliers in the wwPDB validation report), and the
>>> sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)
>>> 
>>> - the map looked surprisingly good for the incorrect cell
>>> 
>>> - however, RSR-Z told clearly that the map was not good enough for the 
>>> claimed
>>> resolution - the model had 24% outliers! (3% in the corrected model which
>>> still only put it at the ~50th percentile)
>>> 
>>> - another good indicator was the clashscore (went from 44 to 7)
>>> 
>>> - the original model did not include an Rfree, but the R-value (>0.3 at 1.6Å
>>> resolution) ought to have provided a clue to the crystallographers and
>>> reviewers one would think
>>> 
>>> It would be interesting to see what would happen if the wavelength would be 
>>> set 5% too high.
>>> 
>>> --Gerard
>>> 
>>> 
>>> 
>>> On Thu, 16 Jul 2020, Clemens Vonrhein 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 well to detect cell dimension problems.
 
 Indeed.
 
> That said, the problem is uncommon now.
 
 Not so sure about that: we all rely on an accurate value of the
 energy/wavelength from the instrument/beamline - and if that is off
 (for whatever reasons) it will result in incorrect cell dimensions and
 a systematic deviation from the various restraints.
 
 This would even affect the best experiment done on the best crystal
 ... so fairly easy to spot at the refinement stage, especially if such
 an energy/wavelength offset is constant over a long period of time on
 a given instrument. To spot this at the data collection stage one
 would hope that at some point a crystal with very pronounced ice-rings
 will be looked at properly (and the fact these are not where we expect
 them to should cause some head-scratching).
 
 Cheers
 
 Clemens
 
 
 
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 https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
 
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 list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
 https://www.jiscmail.ac.uk/policyandsecurity/
 
>>> 
>>> 
>>> Best wishes,
>>> 
>>> --Gerard
>>> 
>>> **
>>>  Gerard J. Kleywegt
>>> 
>>> http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
>>> **
>>>  The opinions in this message are 

Re: [ccp4bb] Quote source inquiry

[Frances C. Bernstein]

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 orthogonal and there would have been no problem.

Instead the depositor used an incorrect matrix to make the
orthogonal data that was sent to us.

The depositor told me that something looked wrong in the
active site graphically and that is how s/he realized that
there was a problem.

I think that this occurred before we did packing analysis
as the letter we sent was short with just the outlier distances
and angles. The depositor would have had to send a new magnetic
tape to us and it was trivial to just do the requisite math
myself.

Frances

=
Bernstein + Sons
*   *   Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
*   * ***
 *Frances C. Bernstein
  *   ***  f...@bernstein-plus-sons.com
 *** *
  *   *** 1-631-286-1339FAX: 1-631-286-1999
=

On Thu, 16 Jul 2020, Gerard DVD Kleywegt wrote:


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 necessary rebuilt 
some residues followed by more refinement.


--Gerard



On Thu, 16 Jul 2020, Frances C. Bernstein wrote:


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 typical of
an entry without 'problems'.  So I sent the proposed entry to the
depositor and got a panicked call that something was wrong based
on the depositor looking at a display of the entry.  By the next
day the depositor had figured out that s/he had decided to convert
to orthogonal for deposition and mistyped one of the cell dimensions
by 1 Angstrom.  That length was about 135 so the error was less than
1% in one direction and I was very impressed that the depositor had
spotted it graphically.

After I did the appropriate linear algebra to correct the coordinates
I took a look at the distance and angle outliers.  Of course they
were different but to my great surprise there were about the same
number of outliers for the 'bad' and the corrected entries.  So based
on the checking at that time we could not tell the bad from the good.

I would be interested to know what would happen now with all the
additional checking that is available.  Perhaps someone should do
that experiment.

Frances

=
Bernstein + Sons
*   *   Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
*   * ***
 *Frances C. Bernstein
 *   ***  f...@bernstein-plus-sons.com
 *** *
 *   *** 1-631-286-1339FAX: 1-631-286-1999
=

On Thu, 16 Jul 2020, Gerard DVD Kleywegt wrote:


 There was a case a few years ago (not too many though) where a 1.6 ?
 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 statistics. Some interesting observations:

 - the geometry had been very tightly restrained so that didn't give a 
clue

  about the cell error (WhatCheck only suggested a very small change)

 - somewhat surprisingly (I thought) the Ramachandran plot did not improve
 in
  the correct model (0.3% outliers in the wwPDB validation report), and 
the

  sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)

 - the map looked surprisingly good for the incorrect cell

 - however, RSR-Z told clearly that the map was not good enough for the
 claimed
  resolution - the model had 24% outliers! (3% in the corrected model 
which

  still only put it at the ~50th percentile)

 - another good indicator was the clashscore (went from 44 to 7)

 - the original model did not include an Rfree, but the R-value (>0.3 at
 1.6?
  resolution) ought to have provided a clue to the crystallographers and
  reviewers one would think

 It would be interesting to see what would happen if the wavelength would
 be set 5% too high.

 --Gerard



 On Thu, 16 Jul 2020, Clemens Vonrhein 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 

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

[David Schuller]

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 collection. This is one reason I am not eager to jump on the 
"RT is superior" bandwagon.


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



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

[Abhik Mukhopadhyay]

I have a related question. Why calculating/reporting standard deviation for
cell constants is not now mandatory in protein crystallography. Is there
any reason for that (e.g. difficult to calculate or error in calculation).
Now mmcif being the official format and there is mmcif category for esd,
space should not be the issue.

Regards,
Abhik

On Thu, Jul 16, 2020 at 1:29 PM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> You can change the cell dimensions without spoiling the map fit too much,
> but obviously you need to convert deposited orthogonal coordinates back to
> fractional using the given SCALEi matrix, than re-orthogonalise with the
> modified cell..
> Eleanor
>
> On Thu, 16 Jul 2020 at 13:01, Schreuder, Herman /DE <
> herman.schreu...@sanofi.com> wrote:
>
>> My guess is that the model no longer superimposed 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
>> 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 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 typical of an entry without
>> 'problems'.  So I sent the proposed entry to the depositor and got a
>> panicked call that something was wrong based on the depositor looking at a
>> display of the entry.  By the next day the depositor had figured out that
>> s/he had decided to convert to orthogonal for deposition and mistyped one
>> of the cell dimensions by 1 Angstrom.  That length was about 135 so the
>> error was less than 1% in one direction and I was very impressed that the
>> depositor had spotted it graphically.
>>
>> After I did the appropriate linear algebra to correct the coordinates I
>> took a look at the distance and angle outliers.  Of course they were
>> different but to my great surprise there were about the same number of
>> outliers for the 'bad' and the corrected entries.  So based on the checking
>> at that time we could not tell the bad from the good.
>>
>> I would be interested to know what would happen now with all the
>> additional checking that is available.  Perhaps someone should do that
>> experiment.
>>
>>   Frances
>>
>> =
>> Bernstein + Sons
>> *   *   Information Systems Consultants
>> 5 Brewster Lane, Bellport, NY 11713-2803
>> *   * ***
>>  *Frances C. Bernstein
>>*   ***  f...@bernstein-plus-sons.com
>>   *** *
>>*   *** 1-631-286-1339FAX: 1-631-286-1999
>> =
>>
>> On Thu, 16 Jul 2020, Gerard DVD Kleywegt wrote:
>>
>> > There was a case a few years ago (not too many though) where a 1.6 ?
>> > 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 statistics. Some interesting observations:
>> >
>> > - the geometry had been very tightly restrained so that didn't give a
>> > clue  about the cell error (WhatCheck only suggested a very small
>> > change)
>> >
>> > - somewhat surprisingly (I thought) the Ramachandran plot did not
>> > improve in  the correct model (0.3% outliers in the wwPDB validation
>> > report), and the  sidechain rotamer outliers even got worse (from 1.5
>> > to 2.5 %)
>> >
>> > - the map looked surprisingly good for the incorrect cell
>> >
>> > - however, RSR-Z told clearly that the map was not good enough for the
>> > claimed  resolution - the model had 24% outliers! (3% in the corrected
>> > model which  still only put it at the ~50th percentile)
>> >
>> > - another good indicator was the clashscore (went from 44 to 7)
>> >
>> > - the original model did not include an Rfree, but the R-value (>0.3 at
>> 1.6?
>> >  resolution) ought to have provided a clue 

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

[Eleanor Dodson]

You can change the cell dimensions without spoiling the map fit too much,
but obviously you need to convert deposited orthogonal coordinates back to
fractional using the given SCALEi matrix, than re-orthogonalise with the
modified cell..
Eleanor

On Thu, 16 Jul 2020 at 13:01, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:

> My guess is that the model no longer superimposed 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
> 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 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 typical of an entry without
> 'problems'.  So I sent the proposed entry to the depositor and got a
> panicked call that something was wrong based on the depositor looking at a
> display of the entry.  By the next day the depositor had figured out that
> s/he had decided to convert to orthogonal for deposition and mistyped one
> of the cell dimensions by 1 Angstrom.  That length was about 135 so the
> error was less than 1% in one direction and I was very impressed that the
> depositor had spotted it graphically.
>
> After I did the appropriate linear algebra to correct the coordinates I
> took a look at the distance and angle outliers.  Of course they were
> different but to my great surprise there were about the same number of
> outliers for the 'bad' and the corrected entries.  So based on the checking
> at that time we could not tell the bad from the good.
>
> I would be interested to know what would happen now with all the
> additional checking that is available.  Perhaps someone should do that
> experiment.
>
>   Frances
>
> =
> Bernstein + Sons
> *   *   Information Systems Consultants
> 5 Brewster Lane, Bellport, NY 11713-2803
> *   * ***
>  *Frances C. Bernstein
>*   ***  f...@bernstein-plus-sons.com
>   *** *
>*   *** 1-631-286-1339FAX: 1-631-286-1999
> =
>
> On Thu, 16 Jul 2020, Gerard DVD Kleywegt wrote:
>
> > There was a case a few years ago (not too many though) where a 1.6 ?
> > 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 statistics. Some interesting observations:
> >
> > - the geometry had been very tightly restrained so that didn't give a
> > clue  about the cell error (WhatCheck only suggested a very small
> > change)
> >
> > - somewhat surprisingly (I thought) the Ramachandran plot did not
> > improve in  the correct model (0.3% outliers in the wwPDB validation
> > report), and the  sidechain rotamer outliers even got worse (from 1.5
> > to 2.5 %)
> >
> > - the map looked surprisingly good for the incorrect cell
> >
> > - however, RSR-Z told clearly that the map was not good enough for the
> > claimed  resolution - the model had 24% outliers! (3% in the corrected
> > model which  still only put it at the ~50th percentile)
> >
> > - another good indicator was the clashscore (went from 44 to 7)
> >
> > - the original model did not include an Rfree, but the R-value (>0.3 at
> 1.6?
> >  resolution) ought to have provided a clue to the crystallographers
> > and  reviewers one would think
> >
> > It would be interesting to see what would happen if the wavelength
> > would be set 5% too high.
> >
> > --Gerard
> >
> >
> >
> > On Thu, 16 Jul 2020, Clemens Vonrhein 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 well to detect cell dimension problems.
> >>
> >> Indeed.
> >>
&g

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

[Schreuder, Herman /DE]

My guess is that the model no longer superimposed 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
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 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 typical of an entry without 'problems'.  
So I sent the proposed entry to the depositor and got a panicked call that 
something was wrong based on the depositor looking at a display of the entry.  
By the next day the depositor had figured out that s/he had decided to convert 
to orthogonal for deposition and mistyped one of the cell dimensions by 1 
Angstrom.  That length was about 135 so the error was less than 1% in one 
direction and I was very impressed that the depositor had spotted it 
graphically.

After I did the appropriate linear algebra to correct the coordinates I took a 
look at the distance and angle outliers.  Of course they were different but to 
my great surprise there were about the same number of outliers for the 'bad' 
and the corrected entries.  So based on the checking at that time we could not 
tell the bad from the good.

I would be interested to know what would happen now with all the additional 
checking that is available.  Perhaps someone should do that experiment.

  Frances

=
Bernstein + Sons
*   *   Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
*   * ***
 *Frances C. Bernstein
   *   ***  f...@bernstein-plus-sons.com
  *** *
   *   *** 1-631-286-1339FAX: 1-631-286-1999
=

On Thu, 16 Jul 2020, Gerard DVD Kleywegt wrote:

> There was a case a few years ago (not too many though) where a 1.6 ? 
> 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 statistics. Some interesting observations:
>
> - the geometry had been very tightly restrained so that didn't give a 
> clue  about the cell error (WhatCheck only suggested a very small 
> change)
>
> - somewhat surprisingly (I thought) the Ramachandran plot did not 
> improve in  the correct model (0.3% outliers in the wwPDB validation 
> report), and the  sidechain rotamer outliers even got worse (from 1.5 
> to 2.5 %)
>
> - the map looked surprisingly good for the incorrect cell
>
> - however, RSR-Z told clearly that the map was not good enough for the 
> claimed  resolution - the model had 24% outliers! (3% in the corrected 
> model which  still only put it at the ~50th percentile)
>
> - another good indicator was the clashscore (went from 44 to 7)
>
> - the original model did not include an Rfree, but the R-value (>0.3 at 1.6?
>  resolution) ought to have provided a clue to the crystallographers 
> and  reviewers one would think
>
> It would be interesting to see what would happen if the wavelength 
> would be set 5% too high.
>
> --Gerard
>
>
>
> On Thu, 16 Jul 2020, Clemens Vonrhein 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 well to detect cell dimension problems.
>> 
>> Indeed.
>> 
>>> That said, the problem is uncommon now.
>> 
>> Not so sure about that: we all rely on an accurate value of the 
>> energy/wavelength from the instrument/beamline - and if that is off 
>> (for whatever reasons) it will result in incorrect cell dimensions 
>> and a systematic deviation from the various restraints.
>> 
>> This would even affect the best experiment done on the best crystal 
>> ... so fairly easy to spot at the refinement stage, especially if 
>> such an energy/wavelength offset is constant over a long period of 
>> time on a given instrument. To spot this at the data collection stage 
>> one would hope that at some point a crystal with very pronounced 
>> ice-rings will be looked at properly (and the 

Re: [ccp4bb] Quote source inquiry

[Gerard DVD Kleywegt]

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 necessary rebuilt some 
residues followed by more refinement.


--Gerard



On Thu, 16 Jul 2020, Frances C. Bernstein wrote:


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 typical of
an entry without 'problems'.  So I sent the proposed entry to the
depositor and got a panicked call that something was wrong based
on the depositor looking at a display of the entry.  By the next
day the depositor had figured out that s/he had decided to convert
to orthogonal for deposition and mistyped one of the cell dimensions
by 1 Angstrom.  That length was about 135 so the error was less than
1% in one direction and I was very impressed that the depositor had
spotted it graphically.

After I did the appropriate linear algebra to correct the coordinates
I took a look at the distance and angle outliers.  Of course they
were different but to my great surprise there were about the same
number of outliers for the 'bad' and the corrected entries.  So based
on the checking at that time we could not tell the bad from the good.

I would be interested to know what would happen now with all the
additional checking that is available.  Perhaps someone should do
that experiment.

Frances

=
Bernstein + Sons
*   *   Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
*   * ***
 *Frances C. Bernstein
 *   ***  f...@bernstein-plus-sons.com
 *** *
 *   *** 1-631-286-1339FAX: 1-631-286-1999
=

On Thu, 16 Jul 2020, Gerard DVD Kleywegt wrote:


 There was a case a few years ago (not too many though) where a 1.6 ?
 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 statistics. Some interesting observations:

 - the geometry had been very tightly restrained so that didn't give a clue
  about the cell error (WhatCheck only suggested a very small change)

 - somewhat surprisingly (I thought) the Ramachandran plot did not improve
 in
  the correct model (0.3% outliers in the wwPDB validation report), and the
  sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)

 - the map looked surprisingly good for the incorrect cell

 - however, RSR-Z told clearly that the map was not good enough for the
 claimed
  resolution - the model had 24% outliers! (3% in the corrected model which
  still only put it at the ~50th percentile)

 - another good indicator was the clashscore (went from 44 to 7)

 - the original model did not include an Rfree, but the R-value (>0.3 at
 1.6?
  resolution) ought to have provided a clue to the crystallographers and
  reviewers one would think

 It would be interesting to see what would happen if the wavelength would
 be set 5% too high.

 --Gerard



 On Thu, 16 Jul 2020, Clemens Vonrhein 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 well to detect cell dimension problems.


 Indeed.


 That said, the problem is uncommon now.


 Not so sure about that: we all rely on an accurate value of the
 energy/wavelength from the instrument/beamline - and if that is off
 (for whatever reasons) it will result in incorrect cell dimensions and
 a systematic deviation from the various restraints.

 This would even affect the best experiment done on the best crystal
 ... so fairly easy to spot at the refinement stage, especially if such
 an energy/wavelength offset is constant over a long period of time on
 a given instrument. To spot this at the data collection stage one
 would hope that at some point a crystal with very pronounced ice-rings
 will be looked at properly (and the fact these are not where we expect
 them to should cause some head-scratching).

 Cheers

 Clemens

 

 To unsubscribe from the CCP4BB list, click the following link:
 https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
 mailing list 

Re: [ccp4bb] Quote source inquiry

[Frances C. Bernstein]

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 typical of
an entry without 'problems'.  So I sent the proposed entry to the
depositor and got a panicked call that something was wrong based
on the depositor looking at a display of the entry.  By the next
day the depositor had figured out that s/he had decided to convert
to orthogonal for deposition and mistyped one of the cell dimensions
by 1 Angstrom.  That length was about 135 so the error was less than
1% in one direction and I was very impressed that the depositor had
spotted it graphically.

After I did the appropriate linear algebra to correct the coordinates
I took a look at the distance and angle outliers.  Of course they
were different but to my great surprise there were about the same
number of outliers for the 'bad' and the corrected entries.  So based
on the checking at that time we could not tell the bad from the good.

I would be interested to know what would happen now with all the
additional checking that is available.  Perhaps someone should do
that experiment.

 Frances

=
Bernstein + Sons
*   *   Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
*   * ***
 *Frances C. Bernstein
  *   ***  f...@bernstein-plus-sons.com
 *** *
  *   *** 1-631-286-1339FAX: 1-631-286-1999
=

On Thu, 16 Jul 2020, Gerard DVD Kleywegt wrote:

There was a case a few years ago (not too many though) where a 1.6 ? 
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 
statistics. Some interesting observations:


- the geometry had been very tightly restrained so that didn't give a clue
 about the cell error (WhatCheck only suggested a very small change)

- somewhat surprisingly (I thought) the Ramachandran plot did not improve in
 the correct model (0.3% outliers in the wwPDB validation report), and the
 sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)

- the map looked surprisingly good for the incorrect cell

- however, RSR-Z told clearly that the map was not good enough for the 
claimed

 resolution - the model had 24% outliers! (3% in the corrected model which
 still only put it at the ~50th percentile)

- another good indicator was the clashscore (went from 44 to 7)

- the original model did not include an Rfree, but the R-value (>0.3 at 1.6?
 resolution) ought to have provided a clue to the crystallographers and
 reviewers one would think

It would be interesting to see what would happen if the wavelength would be 
set 5% too high.


--Gerard



On Thu, 16 Jul 2020, Clemens Vonrhein 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 well to detect cell dimension problems.


Indeed.


That said, the problem is uncommon now.


Not so sure about that: we all rely on an accurate value of the
energy/wavelength from the instrument/beamline - and if that is off
(for whatever reasons) it will result in incorrect cell dimensions and
a systematic deviation from the various restraints.

This would even affect the best experiment done on the best crystal
... so fairly easy to spot at the refinement stage, especially if such
an energy/wavelength offset is constant over a long period of time on
a given instrument. To spot this at the data collection stage one
would hope that at some point a crystal with very pronounced ice-rings
will be looked at properly (and the fact these are not where we expect
them to should cause some head-scratching).

Cheers

Clemens



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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Best wishes,

--Gerard

**
  Gerard J. Kleywegt

 http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
  The opinions in this message are fictional.  Any similarity
  to actual 

Re: [ccp4bb] Quote source inquiry

[Gerard Bricogne]

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 calibration would be done
using an absorption edge. I can remember Richard Kahn using a Cu metal foil
to lock precisely onto an energy close to the Ytterbium edge he wanted to
use in a MAD experiment. When the beam energy is precisely established by
this diffraction-free method, then a Si powder allows a precise calibration
of detector distance (and location of beam centre). 


 With best wishes,

  Gerard.

--
On Thu, Jul 16, 2020 at 12:25:55PM +0100, Harry Powell - CCP4BB wrote:
> 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:
> > 
> > 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 statistics. Some interesting observations:
> > 
> > - the geometry had been very tightly restrained so that didn't give a clue
> >  about the cell error (WhatCheck only suggested a very small change)
> > 
> > - somewhat surprisingly (I thought) the Ramachandran plot did not improve in
> >  the correct model (0.3% outliers in the wwPDB validation report), and the
> >  sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)
> > 
> > - the map looked surprisingly good for the incorrect cell
> > 
> > - however, RSR-Z told clearly that the map was not good enough for the 
> > claimed
> >  resolution - the model had 24% outliers! (3% in the corrected model which
> >  still only put it at the ~50th percentile)
> > 
> > - another good indicator was the clashscore (went from 44 to 7)
> > 
> > - the original model did not include an Rfree, but the R-value (>0.3 at 1.6Å
> >  resolution) ought to have provided a clue to the crystallographers and
> >  reviewers one would think
> > 
> > It would be interesting to see what would happen if the wavelength would be 
> > set 5% too high.
> > 
> > --Gerard
> > 
> > 
> > 
> > On Thu, 16 Jul 2020, Clemens Vonrhein 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 well to detect cell dimension problems.
> >> 
> >> Indeed.
> >> 
> >>> That said, the problem is uncommon now.
> >> 
> >> Not so sure about that: we all rely on an accurate value of the
> >> energy/wavelength from the instrument/beamline - and if that is off
> >> (for whatever reasons) it will result in incorrect cell dimensions and
> >> a systematic deviation from the various restraints.
> >> 
> >> This would even affect the best experiment done on the best crystal
> >> ... so fairly easy to spot at the refinement stage, especially if such
> >> an energy/wavelength offset is constant over a long period of time on
> >> a given instrument. To spot this at the data collection stage one
> >> would hope that at some point a crystal with very pronounced ice-rings
> >> will be looked at properly (and the fact these are not where we expect
> >> them to should cause some head-scratching).
> >> 
> >> Cheers
> >> 
> >> Clemens
> >> 
> >> 
> >> 
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >> 
> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> >> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> >> https://www.jiscmail.ac.uk/policyandsecurity/
> >> 
> > 
> > 
> > Best wishes,
> > 
> > --Gerard
> > 
> > **
> >   Gerard J. Kleywegt
> > 
> >  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
> > **
> >   The opinions in this message are fictional.  Any similarity
> >   to actual opinions, living or dead, is purely coincidental.
> > **
> >   Little known gastromathematical curiosity: let "z" be the
> >   radius and "a" the thickness of a pizza. Then the volume
> >of that pizza is equal 

Re: [ccp4bb] Quote source inquiry

[Mark J van Raaij]

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
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/


> On 16 Jul 2020, at 13:25, Harry Powell - CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> 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:
>> 
>> 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 
>> statistics. Some interesting observations:
>> 
>> - the geometry had been very tightly restrained so that didn't give a clue
>> about the cell error (WhatCheck only suggested a very small change)
>> 
>> - somewhat surprisingly (I thought) the Ramachandran plot did not improve in
>> the correct model (0.3% outliers in the wwPDB validation report), and the
>> sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)
>> 
>> - the map looked surprisingly good for the incorrect cell
>> 
>> - however, RSR-Z told clearly that the map was not good enough for the 
>> claimed
>> resolution - the model had 24% outliers! (3% in the corrected model which
>> still only put it at the ~50th percentile)
>> 
>> - another good indicator was the clashscore (went from 44 to 7)
>> 
>> - the original model did not include an Rfree, but the R-value (>0.3 at 1.6Å
>> resolution) ought to have provided a clue to the crystallographers and
>> reviewers one would think
>> 
>> It would be interesting to see what would happen if the wavelength would be 
>> set 5% too high.
>> 
>> --Gerard
>> 
>> 
>> 
>> On Thu, 16 Jul 2020, Clemens Vonrhein 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 well to detect cell dimension problems.
>>> 
>>> Indeed.
>>> 
 That said, the problem is uncommon now.
>>> 
>>> Not so sure about that: we all rely on an accurate value of the
>>> energy/wavelength from the instrument/beamline - and if that is off
>>> (for whatever reasons) it will result in incorrect cell dimensions and
>>> a systematic deviation from the various restraints.
>>> 
>>> This would even affect the best experiment done on the best crystal
>>> ... so fairly easy to spot at the refinement stage, especially if such
>>> an energy/wavelength offset is constant over a long period of time on
>>> a given instrument. To spot this at the data collection stage one
>>> would hope that at some point a crystal with very pronounced ice-rings
>>> will be looked at properly (and the fact these are not where we expect
>>> them to should cause some head-scratching).
>>> 
>>> Cheers
>>> 
>>> Clemens
>>> 
>>> 
>>> 
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>> 
>>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>>> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
>>> https://www.jiscmail.ac.uk/policyandsecurity/
>>> 
>> 
>> 
>> Best wishes,
>> 
>> --Gerard
>> 
>> **
>>  Gerard J. Kleywegt
>> 
>> http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
>> **
>>  The opinions in this message are fictional.  Any similarity
>>  to actual opinions, living or dead, is purely coincidental.
>> **
>>  Little known gastromathematical curiosity: let "z" be the
>>  radius and "a" the thickness of a pizza. Then the volume
>>   of that pizza is equal to pi*z*z*a !
>> **
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>> list hosted by 

Re: [ccp4bb] Quote source inquiry

[Harry Powell - CCP4BB]

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:
> 
> 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 
> statistics. Some interesting observations:
> 
> - the geometry had been very tightly restrained so that didn't give a clue
>  about the cell error (WhatCheck only suggested a very small change)
> 
> - somewhat surprisingly (I thought) the Ramachandran plot did not improve in
>  the correct model (0.3% outliers in the wwPDB validation report), and the
>  sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)
> 
> - the map looked surprisingly good for the incorrect cell
> 
> - however, RSR-Z told clearly that the map was not good enough for the claimed
>  resolution - the model had 24% outliers! (3% in the corrected model which
>  still only put it at the ~50th percentile)
> 
> - another good indicator was the clashscore (went from 44 to 7)
> 
> - the original model did not include an Rfree, but the R-value (>0.3 at 1.6Å
>  resolution) ought to have provided a clue to the crystallographers and
>  reviewers one would think
> 
> It would be interesting to see what would happen if the wavelength would be 
> set 5% too high.
> 
> --Gerard
> 
> 
> 
> On Thu, 16 Jul 2020, Clemens Vonrhein 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 well to detect cell dimension problems.
>> 
>> Indeed.
>> 
>>> That said, the problem is uncommon now.
>> 
>> Not so sure about that: we all rely on an accurate value of the
>> energy/wavelength from the instrument/beamline - and if that is off
>> (for whatever reasons) it will result in incorrect cell dimensions and
>> a systematic deviation from the various restraints.
>> 
>> This would even affect the best experiment done on the best crystal
>> ... so fairly easy to spot at the refinement stage, especially if such
>> an energy/wavelength offset is constant over a long period of time on
>> a given instrument. To spot this at the data collection stage one
>> would hope that at some point a crystal with very pronounced ice-rings
>> will be looked at properly (and the fact these are not where we expect
>> them to should cause some head-scratching).
>> 
>> Cheers
>> 
>> Clemens
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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>> 
> 
> 
> Best wishes,
> 
> --Gerard
> 
> **
>   Gerard J. Kleywegt
> 
>  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
> **
>   The opinions in this message are fictional.  Any similarity
>   to actual opinions, living or dead, is purely coincidental.
> **
>   Little known gastromathematical curiosity: let "z" be the
>   radius and "a" the thickness of a pizza. Then the volume
>of that pizza is equal to pi*z*z*a !
> **
> 
> 
> 
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Re: [ccp4bb] Quote source inquiry

[Gerard DVD Kleywegt]

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 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
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 wrote:


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 <

vonrh...@globalphasing.com>

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 well to detect cell dimension problems.


Indeed.


That said, the problem is uncommon now.


Not so sure about that: we all rely on an accurate value of the
energy/wavelength from the instrument/beamline - and if that is off
(for whatever reasons) it will result in incorrect cell dimensions and
a systematic deviation from the various restraints.

This would even affect the best experiment done on the best crystal
... so fairly easy to spot at the refinement stage, especially if such
an energy/wavelength offset is constant over a long period of time on
a given instrument. To spot this at the data collection stage one
would hope that at some point a crystal with very pronounced ice-rings
will be looked at properly (and the fact these are not where we expect
them to should cause some head-scratching).

Cheers

Clemens



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Best wishes,

--Gerard

**
Gerard J. Kleywegt

   http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
The opinions in this message are fictional.  Any similarity
to actual opinions, living or dead, is purely coincidental.
**
Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
 of that pizza is equal to pi*z*z*a !
**





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Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



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Re: [ccp4bb] Quote source inquiry

[Gerard DVD Kleywegt]

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 
statistics. Some interesting observations:


- the geometry had been very tightly restrained so that didn't give a clue
  about the cell error (WhatCheck only suggested a very small change)

- somewhat surprisingly (I thought) the Ramachandran plot did not improve in
  the correct model (0.3% outliers in the wwPDB validation report), and the
  sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)

- the map looked surprisingly good for the incorrect cell

- however, RSR-Z told clearly that the map was not good enough for the claimed
  resolution - the model had 24% outliers! (3% in the corrected model which
  still only put it at the ~50th percentile)

- another good indicator was the clashscore (went from 44 to 7)

- the original model did not include an Rfree, but the R-value (>0.3 at 1.6Å
  resolution) ought to have provided a clue to the crystallographers and
  reviewers one would think

It would be interesting to see what would happen if the wavelength would be 
set 5% too high.


--Gerard



On Thu, 16 Jul 2020, Clemens Vonrhein 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 well to detect cell dimension problems.


Indeed.


That said, the problem is uncommon now.


Not so sure about that: we all rely on an accurate value of the
energy/wavelength from the instrument/beamline - and if that is off
(for whatever reasons) it will result in incorrect cell dimensions and
a systematic deviation from the various restraints.

This would even affect the best experiment done on the best crystal
... so fairly easy to spot at the refinement stage, especially if such
an energy/wavelength offset is constant over a long period of time on
a given instrument. To spot this at the data collection stage one
would hope that at some point a crystal with very pronounced ice-rings
will be looked at properly (and the fact these are not where we expect
them to should cause some head-scratching).

Cheers

Clemens



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Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



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Re: [ccp4bb] Quote source inquiry

[Robbie Joosten]

I don't know what the return on investment would be, but after establishing 
that there are cell dimension deviations one should actually try to find the 
source of the problem. If it is the reported geometry of the experiment than it 
is just a matter of changing the cell dimension, but if the wavelength come 
into play as Clemens pointed out (hooray for home sources) one should also 
correct the wavelength in order to get better scattering factors. If you don't 
have ice rings as a reference can you still do that? Perhaps refine f' and f''. 
Has anyone does 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 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
> mailto:vonrh...@globalphasing.com> >
> 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 well to detect cell dimension problems.
> 
>   Indeed.
> 
>   > That said, the problem is uncommon now.
> 
>   Not so sure about that: we all rely on an accurate value of the
>   energy/wavelength from the instrument/beamline - and if that is off
>   (for whatever reasons) it will result in incorrect cell dimensions and
>   a systematic deviation from the various restraints.
> 
>   This would even affect the best experiment done on the best crystal
>   ... so fairly easy to spot at the refinement stage, especially if such
>   an energy/wavelength offset is constant over a long period of time
> on
>   a given instrument. To spot this at the data collection stage one
>   would hope that at some point a crystal with very pronounced ice-
> rings
>   will be looked at properly (and the fact these are not where we
> expect
>   them to should cause some head-scratching).
> 
>   Cheers
> 
>   Clemens
> 
>   
> 
> 
>   To unsubscribe from the CCP4BB list, click the following link:
>   https://www.jiscmail.ac.uk/cgi-bin/WA-
> JISC.exe?SUBED1=CCP4BB=1
> 
>   This message was issued to members of www.jiscmail.ac.uk/CCP4BB
> <http://www.jiscmail.ac.uk/CCP4BB> , a mailing list hosted by
> www.jiscmail.ac.uk <http://www.jiscmail.ac.uk> , terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
> 
> 
> 
> 
> 
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Re: [ccp4bb] Quote source inquiry

[Eleanor Dodson]

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
> 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 wrote:
>
> > 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 <
> vonrh...@globalphasing.com>
> > 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 well to detect cell dimension problems.
> >>
> >> Indeed.
> >>
> >>> That said, the problem is uncommon now.
> >>
> >> Not so sure about that: we all rely on an accurate value of the
> >> energy/wavelength from the instrument/beamline - and if that is off
> >> (for whatever reasons) it will result in incorrect cell dimensions and
> >> a systematic deviation from the various restraints.
> >>
> >> This would even affect the best experiment done on the best crystal
> >> ... so fairly easy to spot at the refinement stage, especially if such
> >> an energy/wavelength offset is constant over a long period of time on
> >> a given instrument. To spot this at the data collection stage one
> >> would hope that at some point a crystal with very pronounced ice-rings
> >> will be looked at properly (and the fact these are not where we expect
> >> them to should cause some head-scratching).
> >>
> >> Cheers
> >>
> >> Clemens
> >>
> >> 
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >>
> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> >> available at https://www.jiscmail.ac.uk/policyandsecurity/
> >>
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
> >
>
>
> Best wishes,
>
> --Gerard
>
> **
> Gerard J. Kleywegt
>
>http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
> **
> The opinions in this message are fictional.  Any similarity
> to actual opinions, living or dead, is purely coincidental.
> **
> Little known gastromathematical curiosity: let "z" be the
> radius and "a" the thickness of a pizza. Then the volume
>  of that pizza is equal to pi*z*z*a !
> **
>



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Re: [ccp4bb] Quote source inquiry

[Gerard DVD Kleywegt]

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 wrote:


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:

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 well to detect cell dimension problems.


Indeed.


That said, the problem is uncommon now.


Not so sure about that: we all rely on an accurate value of the
energy/wavelength from the instrument/beamline - and if that is off
(for whatever reasons) it will result in incorrect cell dimensions and
a systematic deviation from the various restraints.

This would even affect the best experiment done on the best crystal
... so fairly easy to spot at the refinement stage, especially if such
an energy/wavelength offset is constant over a long period of time on
a given instrument. To spot this at the data collection stage one
would hope that at some point a crystal with very pronounced ice-rings
will be looked at properly (and the fact these are not where we expect
them to should cause some head-scratching).

Cheers

Clemens



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Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



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Re: [ccp4bb] Quote source inquiry

[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:
> > 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 well to detect cell dimension problems.
>
> Indeed.
>
> > That said, the problem is uncommon now.
>
> Not so sure about that: we all rely on an accurate value of the
> energy/wavelength from the instrument/beamline - and if that is off
> (for whatever reasons) it will result in incorrect cell dimensions and
> a systematic deviation from the various restraints.
>
> This would even affect the best experiment done on the best crystal
> ... so fairly easy to spot at the refinement stage, especially if such
> an energy/wavelength offset is constant over a long period of time on
> a given instrument. To spot this at the data collection stage one
> would hope that at some point a crystal with very pronounced ice-rings
> will be looked at properly (and the fact these are not where we expect
> them to should cause some head-scratching).
>
> Cheers
>
> Clemens
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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Re: [ccp4bb] Quote source inquiry

[Clemens Vonrhein]

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 well to detect cell dimension problems.

Indeed.

> That said, the problem is uncommon now.

Not so sure about that: we all rely on an accurate value of the
energy/wavelength from the instrument/beamline - and if that is off
(for whatever reasons) it will result in incorrect cell dimensions and
a systematic deviation from the various restraints.

This would even affect the best experiment done on the best crystal
... so fairly easy to spot at the refinement stage, especially if such
an energy/wavelength offset is constant over a long period of time on
a given instrument. To spot this at the data collection stage one
would hope that at some point a crystal with very pronounced ice-rings
will be looked at properly (and the fact these are not where we expect
them to should cause some head-scratching).

Cheers

Clemens



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Re: [ccp4bb] Quote source inquiry

[Ian Tickle]

Hi Robbie

Yes I was (perhaps rashly!) assuming that the data are properly weighted
relative to the restraints.

Thanks for pointing that out.

Cheers

-- Ian


On Wed, 15 Jul 2020 at 20:23, Robbie Joosten 
wrote:

> Hi Ian,
>
> Errors in cell dimensions can have a large effect in MX with certain
> refinement doctrines. The school of "bond length rmsd must be $NUMBER"
> (which is still going strong unfortunately) will suffer from poor R-factors
> because the target cannot be satisfied without harming the fit to the data.
> 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 well to
> detect cell dimension problems. That said, the problem is 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 difference between macromolecular and small molecule
> > refinement: except at ultra-high resolution the bond lengths in the
> former
> > are almost always strongly restrained, whereas those in the latter are
> almost
> > without exception completely unrestrained (except possibly bond lengths
> to
> > H atoms in XRD).  In other words, MX accurately determines the orthogonal
> > atomic co-ordinates, whereas XRD accurately determines their fractional
> co-
> > ordinates (it's no accident that the different programs output
> co-ordinates in
> > those formats).
> >
> > This means that since the cell dimensions are then used to convert
> fractional
> > to orthogonal in XRD, the final bond lengths will be much more sensitive
> to
> > errors in the cell dimensions, so having accurate cell dimensions is more
> > critical if you want accurate bond lengths (e.g. for use as restraints
> in MX!).
> > Obviously there's also a limit to the errors in the cell dimensions that
> can be
> > tolerated in MX: large errors will lead to errors in calculated d*
> values and
> > hence the scattering factors, which is likely to have a significant
> effect, and
> > there may be issues with VdW repulsions if the cell is too small (though
> it's
> > relatively easy for the structure to accommodate that).
> >
> > As Philip pointed out, the bond lengths will be totally insensitive to
> errors in
> > the uncertainties of the cell dimensions, whether artificially
> introduced or
> > poorly estimated from the data.  I don't know of any MX refinement
> > program (other than Shel-X) that takes the uncertainties in the cell
> > dimensions into account, even assuming that you have accurate values for
> > them.
> >
> > Also you should be careful not to confuse uncertainty (imprecision) with
> > error (inaccuracy).  The 'standard uncertainty' (s.u.) is the
> experimental
> > estimate of the 'standard deviation' (in the error)
> > (https://physics.nist.gov/cgi-bin/cuu/Info/Constants/definitions.html),
> and
> > the old term 'estimated standard deviation' (e.s.d.) was deprecated in
> 1993
> > (http://scripts.iucr.org/cgi-bin/paper?S0108767395002340).  You can have
> > an error in an uncertainty (which is what you were introducing in your
> test),
> > but you can't have an uncertainty in an error, since errors are by their
> nature
> > unknown anyway!
> >
> > It goes without saying that it's not a good idea to use bond lengths
> from a
> > restrained refinement as restraints in other refinements!
> >
> > Cheers
> >
> > -- Ian
> >
> >
> > On Wed, 15 Jul 2020 at 17:56, Jeffrey B Bonanno
> >  > <mailto:jeffrey.bona...@einsteinmed.org> > wrote:
> >
> >
> >   Hi Phil,
> >
> >
> >
> >   Being young and impressionable, I only changed ZERR, and you are
> > quiet right the result is the rigorous and expected error propagation of
> > shelxl. Of course the more fun experiment would be in systematically
> > changing various values in UNIT to watch the molecule distort.
> >
> >
> >
> >   Hope all is well,
> >
> >   jbb
> >
> >
> >
> >   Jeffrey B. Bonanno, Ph.D.
> >
> >   Department of Biochemistry
> >
> >   Albert Einstein College of Medicine
> >
> >   1300 Morris Park Avenue
> >
> >   Bronx, NY 10461
> >
> >  

Re: [ccp4bb] Quote source inquiry

[Robbie Joosten]

Hi Ian,

Errors in cell dimensions can have a large effect in MX with certain refinement 
doctrines. The school of "bond length rmsd must be $NUMBER" (which is still 
going strong unfortunately) will suffer from poor R-factors because the target 
cannot be satisfied without harming the fit to the data. 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 well to detect cell dimension problems. That 
said, the problem is 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 difference between macromolecular and small molecule
> refinement: except at ultra-high resolution the bond lengths in the former
> are almost always strongly restrained, whereas those in the latter are almost
> without exception completely unrestrained (except possibly bond lengths to
> H atoms in XRD).  In other words, MX accurately determines the orthogonal
> atomic co-ordinates, whereas XRD accurately determines their fractional co-
> ordinates (it's no accident that the different programs output co-ordinates in
> those formats).
> 
> This means that since the cell dimensions are then used to convert fractional
> to orthogonal in XRD, the final bond lengths will be much more sensitive to
> errors in the cell dimensions, so having accurate cell dimensions is more
> critical if you want accurate bond lengths (e.g. for use as restraints in 
> MX!).
> Obviously there's also a limit to the errors in the cell dimensions that can 
> be
> tolerated in MX: large errors will lead to errors in calculated d* values and
> hence the scattering factors, which is likely to have a significant effect, 
> and
> there may be issues with VdW repulsions if the cell is too small (though it's
> relatively easy for the structure to accommodate that).
> 
> As Philip pointed out, the bond lengths will be totally insensitive to errors 
> in
> the uncertainties of the cell dimensions, whether artificially introduced or
> poorly estimated from the data.  I don't know of any MX refinement
> program (other than Shel-X) that takes the uncertainties in the cell
> dimensions into account, even assuming that you have accurate values for
> them.
> 
> Also you should be careful not to confuse uncertainty (imprecision) with
> error (inaccuracy).  The 'standard uncertainty' (s.u.) is the experimental
> estimate of the 'standard deviation' (in the error)
> (https://physics.nist.gov/cgi-bin/cuu/Info/Constants/definitions.html), and
> the old term 'estimated standard deviation' (e.s.d.) was deprecated in 1993
> (http://scripts.iucr.org/cgi-bin/paper?S0108767395002340).  You can have
> an error in an uncertainty (which is what you were introducing in your test),
> but you can't have an uncertainty in an error, since errors are by their 
> nature
> unknown anyway!
> 
> It goes without saying that it's not a good idea to use bond lengths from a
> restrained refinement as restraints in other refinements!
> 
> Cheers
> 
> -- Ian
> 
> 
> On Wed, 15 Jul 2020 at 17:56, Jeffrey B Bonanno
>  <mailto:jeffrey.bona...@einsteinmed.org> > wrote:
> 
> 
>   Hi Phil,
> 
> 
> 
>   Being young and impressionable, I only changed ZERR, and you are
> quiet right the result is the rigorous and expected error propagation of
> shelxl. Of course the more fun experiment would be in systematically
> changing various values in UNIT to watch the molecule distort.
> 
> 
> 
>   Hope all is well,
> 
>   jbb
> 
> 
> 
>   Jeffrey B. Bonanno, Ph.D.
> 
>   Department of Biochemistry
> 
>   Albert Einstein College of Medicine
> 
>   1300 Morris Park Avenue
> 
>   Bronx, NY 10461
> 
>   off. 718-430-2452 fax. 718-430-8565
> 
>   email jeffrey.bona...@einsteinmed.org
> <mailto:jeffrey.bona...@einsteinmed.org>
> 
> 
> 
>   From: Jeffrey, Philip D. 
>   Sent: Wednesday, July 15, 2020 12:47 PM
>   To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> ;
> Jeffrey B Bonanno  <mailto:jeffrey.bona...@einsteinmed.org> >
>   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 right 
> of
> the Outlook dashboard to repo

Re: [ccp4bb] Quote source inquiry

[Jon Cooper]

Hello,

being a pedant, I guess you mean 'cell':

http://xray.chem.ualberta.ca/xray/shelxl/cell.htm

rather than 'unit':

http://xray.chem.ualberta.ca/xray/shelxl/UNIT.htm

;-?

Best wishes, Jon Cooper

 Original Message 
On 15 Jul 2020, 17:55, Jeffrey B Bonanno wrote:

> Hi Phil,
>
> Being young and impressionable, I only changed ZERR, and you are quiet right 
> the result is the rigorous and expected error propagation of shelxl. Of 
> course the more fun experiment would be in systematically changing various 
> values in UNIT to watch the molecule distort.
>
> Hope all is well,
> jbb
>
> Jeffrey B. Bonanno, Ph.D.
> Department of Biochemistry
> Albert Einstein 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@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 right 
> of the Outlook dashboard to report any suspicious emails.
>
> :: took a working dataset and increased (only) the error on unit cell 
> dimensions in the instruction file for the final round of full matrix :: 
> least squares refinement in shelxl. Sure enough, the errors on the bonds and 
> angles shot up. I was more careful
>
> Question: did you change the unit cell dimensions (UNIT) or the reported 
> standard error in the unit cell dimensions (ZERR) ? If just the latter don't 
> you think that the error propagation is just a factor of SHELXL converting 
> from fractional to orthogonal coordinates to give you bond lengths and bond 
> angles (i.e. the bonds and angles would be numerically the same, but the 
> estimated error associated with them would be higher). Did the e.s.d.'s of 
> the actual coordinates in fractional space change ?
>
> Phil Jeffrey
>
> Princeton
>
> ---
>
> From: CCP4 bulletin board  on behalf of Jeffrey B 
> Bonanno 
> 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 propagation from the uncertainty on cell dimensions through to the esd 
> on atomic bond lengths and angles when refining in shelxl. To verify this 
> (what, you believed everything your postdoc advisor told you?), I took a 
> working dataset and increased (only) the error on unit cell dimensions in the 
> instruction file for the final round of full matrix least squares refinement 
> in shelxl. Sure enough, the errors on the bonds and angles shot up. I was 
> more careful in determining the unit cell thereafter. That is, until, I 
> became a macromolecular crystallographer...
>
> After an inciteful (sp? lol) discussion with Wladek about cell dimensions, I 
> was directed to read this paper:
>
> Acta Crystallogr D Biol Crystallogr. 2015 Nov 1; 71(Pt 11): 2217–2226.
>
> Have a look, it is interesting.
>
> Having never followed up on these studies to see what happened to bonds and 
> angles in proteins and their ligands when varying cell dimensions, I can't 
> say with any confidence. However, I would guess that the quality of the 
> refined ligand coordinates could only be as good as some combination of 
> factors including but not limited to 1) the data (resolution, B factor, etc), 
> 2) the actual occupancy of the ligand, and 3) the restraints employed.
>
> jbb
>
> Jeffrey B. Bonanno, Ph.D.
> Department of Biochemistry
> Albert Einstein College of Medicine
> 1300 Morris Park Avenue
> Bronx, NY 10461
> off. 718-430-2452 fax. 718-430-8565
> 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 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 macromolecules [...]" and then goes on to 
> explain why this is the case.
>
> In the attached 2003 paper (pooling the wisdom of several of the usual 

Re: [ccp4bb] Quote source inquiry

[Ian Tickle]

Hi,

There's one big difference between macromolecular and small molecule
refinement: except at ultra-high resolution the bond lengths in the former
are almost always strongly restrained, whereas those in the latter are
almost without exception completely unrestrained (except possibly bond
lengths to H atoms in XRD).  In other words, MX accurately determines the
orthogonal atomic co-ordinates, whereas XRD accurately determines their
fractional co-ordinates (it's no accident that the different programs
output co-ordinates in those formats).

This means that since the cell dimensions are then used to convert
fractional to orthogonal in XRD, the final bond lengths will be much more
sensitive to errors in the cell dimensions, so having accurate cell
dimensions is more critical if you want accurate bond lengths (e.g. for use
as restraints in MX!).  Obviously there's also a limit to the errors in the
cell dimensions that can be tolerated in MX: large errors will lead to
errors in calculated d* values and hence the scattering factors, which is
likely to have a significant effect, and there may be issues with VdW
repulsions if the cell is too small (though it's relatively easy for the
structure to accommodate that).

As Philip pointed out, the bond lengths will be totally insensitive to
errors in the uncertainties of the cell dimensions, whether artificially
introduced or poorly estimated from the data.  I don't know of any MX
refinement program (other than Shel-X) that takes the uncertainties in the
cell dimensions into account, even assuming that you have accurate values
for them.

Also you should be careful not to confuse uncertainty (imprecision) with
error (inaccuracy).  The 'standard uncertainty' (s.u.) is the experimental
estimate of the 'standard deviation' (in the error) (
https://physics.nist.gov/cgi-bin/cuu/Info/Constants/definitions.html), and
the old term 'estimated standard deviation' (e.s.d.) was deprecated in 1993
(http://scripts.iucr.org/cgi-bin/paper?S0108767395002340).  You can have an
error in an uncertainty (which is what you were introducing in your test),
but you can't have an uncertainty in an error, since errors are by their
nature unknown anyway!

It goes without saying that it's not a good idea to use bond lengths from a
restrained refinement as restraints in other refinements!

Cheers

-- Ian


On Wed, 15 Jul 2020 at 17:56, Jeffrey B Bonanno <
jeffrey.bona...@einsteinmed.org> wrote:

> Hi Phil,
>
>
>
> Being young and impressionable, I only changed ZERR, and you are quiet
> right the result is the rigorous and expected error propagation of shelxl.
> Of course the more fun experiment would be in systematically changing
> various values in UNIT to watch the molecule distort.
>
>
>
> Hope all is well,
>
> jbb
>
>
>
> Jeffrey B. Bonanno, Ph.D.
>
> Department of Biochemistry
>
> Albert Einstein 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@JISCMAIL.AC.UK; Jeffrey B Bonanno <
> jeffrey.bona...@einsteinmed.org>
> *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
> right of the Outlook dashboard to report any suspicious emails.*
>
> :: took a working dataset and increased (only) the error on unit cell
> dimensions in the instruction file for the final round of full matrix ::
> least squares refinement in shelxl. Sure enough, the errors on the bonds
> and angles shot up. I was more careful
>
>
>
> Question: did you change the unit cell dimensions (UNIT) or the reported
> standard error in the unit cell dimensions (ZERR) ?  If just the latter
> don't you think that the error propagation is just a factor of SHELXL
> converting from fractional to orthogonal coordinates to give you bond
> lengths and bond angles (i.e. the bonds and angles would be numerically the
> same, but the estimated error associated with them would be higher).  Did
> the e.s.d.'s of the actual coordinates in fractional space change ?
>
>
>
> Phil Jeffrey
>
> Princeton
> --
>
> *From:* CCP4 bulletin board  on behalf of Jeffrey
> B Bonanno 
> *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 owin

Re: [ccp4bb] Quote source inquiry

[Jeffrey B Bonanno]

Hi Phil,

Being young and impressionable, I only changed ZERR, and you are quiet right 
the result is the rigorous and expected error propagation of shelxl. Of course 
the more fun experiment would be in systematically changing various values in 
UNIT to watch the molecule distort.

Hope all is well,
jbb

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein 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@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 right of the 
Outlook dashboard to report any suspicious emails.
:: took a working dataset and increased (only) the error on unit cell 
dimensions in the instruction file for the final round of full matrix :: least 
squares refinement in shelxl. Sure enough, the errors on the bonds and angles 
shot up. I was more careful

Question: did you change the unit cell dimensions (UNIT) or the reported 
standard error in the unit cell dimensions (ZERR) ?  If just the latter don't 
you think that the error propagation is just a factor of SHELXL converting from 
fractional to orthogonal coordinates to give you bond lengths and bond angles 
(i.e. the bonds and angles would be numerically the same, but the estimated 
error associated with them would be higher).  Did the e.s.d.'s of the actual 
coordinates in fractional space change ?

Phil Jeffrey
Princeton

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Jeffrey B Bonanno 
mailto:jeffrey.bona...@einsteinmed.org>>
Sent: Wednesday, July 15, 2020 12:36 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto: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 the uncertainty on cell dimensions through to the esd on 
atomic bond lengths and angles when refining in shelxl. To verify this (what, 
you believed everything your postdoc advisor told you?), I took a working 
dataset and increased (only) the error on unit cell dimensions in the 
instruction file for the final round of full matrix least squares refinement in 
shelxl. Sure enough, the errors on the bonds and angles shot up. I was more 
careful in determining the unit cell thereafter. That is, until, I became a 
macromolecular crystallographer...

After an inciteful (sp? lol) discussion with Wladek about cell dimensions, I 
was directed to read this paper:

Acta Crystallogr D Biol Crystallogr. 2015 Nov 1; 71(Pt 11): 2217-2226.

Have a look, it is interesting.

Having never followed up on these studies to see what happened to bonds and 
angles in proteins and their ligands when varying cell dimensions, I can't say 
with any confidence. However, I would guess that the quality of the refined 
ligand coordinates could only be as good as some combination of factors 
including but not limited to 1) the data (resolution, B factor, etc), 2) the 
actual occupancy of the ligand, and 3) the restraints employed.

jbb

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
email jeffrey.bona...@einsteinmed.org<mailto:jeffrey.bona...@einsteinmed.org>


-Original Message-
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Gerard DVD Kleywegt
Sent: Wednesday, July 15, 2020 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: 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 macromolecules [...]" and then goes on to 
explain why this is the case.

In the attached 2003 paper (pooling the wisdom of several of the usual 
suspects, including Eleanor) it says something similar (p 1057):

"Coordinates of molecules that have been determined in complex with 
macromolecules previously can of course also be retrieved from the PDB 
(Bernstein et al., 1977; Berman et al., 2000), HIC-Up (Kleywegt and Jones, 
1998), or CHEMPDB (Boutselakis et al., 2003). However, one should keep in mind 
that these coordinates are the result of refinement against comparatively
low-resolu- tion data where the small molecule constituted only a minute 
fraction of the tot

Re: [ccp4bb] Quote source inquiry

[Jeffrey, Philip D.]

:: took a working dataset and increased (only) the error on unit cell 
dimensions in the instruction file for the final round of full matrix :: least 
squares refinement in shelxl. Sure enough, the errors on the bonds and angles 
shot up. I was more careful

Question: did you change the unit cell dimensions (UNIT) or the reported 
standard error in the unit cell dimensions (ZERR) ?  If just the latter don't 
you think that the error propagation is just a factor of SHELXL converting from 
fractional to orthogonal coordinates to give you bond lengths and bond angles 
(i.e. the bonds and angles would be numerically the same, but the estimated 
error associated with them would be higher).  Did the e.s.d.'s of the actual 
coordinates in fractional space change ?

Phil Jeffrey
Princeton

From: CCP4 bulletin board  on behalf of Jeffrey B 
Bonanno 
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 
propagation from the uncertainty on cell dimensions through to the esd on 
atomic bond lengths and angles when refining in shelxl. To verify this (what, 
you believed everything your postdoc advisor told you?), I took a working 
dataset and increased (only) the error on unit cell dimensions in the 
instruction file for the final round of full matrix least squares refinement in 
shelxl. Sure enough, the errors on the bonds and angles shot up. I was more 
careful in determining the unit cell thereafter. That is, until, I became a 
macromolecular crystallographer...

After an inciteful (sp? lol) discussion with Wladek about cell dimensions, I 
was directed to read this paper:

Acta Crystallogr D Biol Crystallogr. 2015 Nov 1; 71(Pt 11): 2217–2226.

Have a look, it is interesting.

Having never followed up on these studies to see what happened to bonds and 
angles in proteins and their ligands when varying cell dimensions, I can't say 
with any confidence. However, I would guess that the quality of the refined 
ligand coordinates could only be as good as some combination of factors 
including but not limited to 1) the data (resolution, B factor, etc), 2) the 
actual occupancy of the ligand, and 3) the restraints employed.

jbb

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
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 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 macromolecules [...]" and then goes on to 
explain why this is the case.

In the attached 2003 paper (pooling the wisdom of several of the usual 
suspects, including Eleanor) it says something similar (p 1057):

"Coordinates of molecules that have been determined in complex with 
macromolecules previously can of course also be retrieved from the PDB 
(Bernstein et al., 1977; Berman et al., 2000), HIC-Up (Kleywegt and Jones, 
1998), or CHEMPDB (Boutselakis et al., 2003). However, one should keep in mind 
that these coordinates are the result of refinement against comparatively
low-resolu- tion data where the small molecule constituted only a minute 
fraction of the total scattering matter. This makes these coordinates 
inherently much less accurate than those obtained from the CSD. In addition, 
the coordi- nates may contain errors due to the use of incorrect restraints.
Hence, such coordinate sets should only be used as a last resort, and only 
after verification that they are reliable. The latter can be facilitated by 
inspection of the electron density for the compound in question, for instance 
at the Uppsala Electron-Density Server (http:// fsrv1.bmc.uu.se/eds) (G.J.K.
et al., submitted)."

Happy to be confused with George though!

--Gerard (no, the other one)



On Tue, 14 Jul 2020, 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 method".
>
>
>
> Any citable source - George Sheldrick might be a suspect.
>
>
>
> Thanks & best regards, BR
>
>
>
> --
>
> Bernhard Rupp
>
> <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.
>

Re: [ccp4bb] Quote source inquiry

[Gerard DVD Kleywegt]

Thanks - very interesting paper, Jeffrey.

I think your analysis is correct, but you forgot: (4) the skill of the 
crystallographer...


Best wishes,

--Gerard


On Wed, 15 Jul 2020, Jeffrey B Bonanno wrote:


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 the uncertainty on cell dimensions through to the esd on 
atomic bond lengths and angles when refining in shelxl. To verify this (what, 
you believed everything your postdoc advisor told you?), I took a working 
dataset and increased (only) the error on unit cell dimensions in the 
instruction file for the final round of full matrix least squares refinement in 
shelxl. Sure enough, the errors on the bonds and angles shot up. I was more 
careful in determining the unit cell thereafter. That is, until, I became a 
macromolecular crystallographer...

After an inciteful (sp? lol) discussion with Wladek about cell dimensions, I 
was directed to read this paper:

Acta Crystallogr D Biol Crystallogr. 2015 Nov 1; 71(Pt 11): 2217–2226.

Have a look, it is interesting.

Having never followed up on these studies to see what happened to bonds and 
angles in proteins and their ligands when varying cell dimensions, I can't 
say with any confidence. However, I would guess that the quality of the 
refined ligand coordinates could only be as good as some combination of 
factors including but not limited to 1) the data (resolution, B factor, 
etc), 2) the actual occupancy of the ligand, and 3) the restraints employed.


jbb

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
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 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 macromolecules [...]" and then goes on to explain why 
this is the case.

In the attached 2003 paper (pooling the wisdom of several of the usual 
suspects, including Eleanor) it says something similar (p 1057):

"Coordinates of molecules that have been determined in complex with 
macromolecules previously can of course also be retrieved from the PDB (Bernstein et 
al., 1977; Berman et al., 2000), HIC-Up (Kleywegt and Jones, 1998), or CHEMPDB 
(Boutselakis et al., 2003). However, one should keep in mind that these coordinates 
are the result of refinement against comparatively
low-resolu- tion data where the small molecule constituted only a minute 
fraction of the total scattering matter. This makes these coordinates 
inherently much less accurate than those obtained from the CSD. In addition, 
the coordi- nates may contain errors due to the use of incorrect restraints.
Hence, such coordinate sets should only be used as a last resort, and only 
after verification that they are reliable. The latter can be facilitated by 
inspection of the electron density for the compound in question, for instance 
at the Uppsala Electron-Density Server (http:// fsrv1.bmc.uu.se/eds) (G.J.K.
et al., submitted)."

Happy to be confused with George though!

--Gerard (no, the other one)



On Tue, 14 Jul 2020, 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 method".



Any citable source - George Sheldrick might be a suspect.



Thanks & best regards, BR



--

Bernhard Rupp

<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.
hofkristallamt.org%2Fdata=02%7C01%7Cjeffrey.bonanno%40einsteinmed
.org%7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e6
2025%7C0%7C0%7C637304250594203532sdata=9FFCpYd9D%2BrHR48DtL%2BglM
W2dbZ%2FmSTw0fF88XRwR7o%3Dreserved=0>
https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.h
ofkristallamt.org%2Fdata=02%7C01%7Cjeffrey.bonanno%40einsteinmed.
org%7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e62
025%7C0%7C0%7C637304250594203532sdata=9FFCpYd9D%2BrHR48DtL%2BglMW
2dbZ%2FmSTw0fF88XRwR7o%3Dreserved=0

<mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish

at the presence of thought

--

Re: [ccp4bb] Quote source inquiry

[Jeffrey B Bonanno]

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 the uncertainty on cell dimensions through to the esd on 
atomic bond lengths and angles when refining in shelxl. To verify this (what, 
you believed everything your postdoc advisor told you?), I took a working 
dataset and increased (only) the error on unit cell dimensions in the 
instruction file for the final round of full matrix least squares refinement in 
shelxl. Sure enough, the errors on the bonds and angles shot up. I was more 
careful in determining the unit cell thereafter. That is, until, I became a 
macromolecular crystallographer...

After an inciteful (sp? lol) discussion with Wladek about cell dimensions, I 
was directed to read this paper:

Acta Crystallogr D Biol Crystallogr. 2015 Nov 1; 71(Pt 11): 2217–2226.

Have a look, it is interesting.

Having never followed up on these studies to see what happened to bonds and 
angles in proteins and their ligands when varying cell dimensions, I can't say 
with any confidence. However, I would guess that the quality of the refined 
ligand coordinates could only be as good as some combination of factors 
including but not limited to 1) the data (resolution, B factor, etc), 2) the 
actual occupancy of the ligand, and 3) the restraints employed.

jbb

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
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 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 macromolecules [...]" and then goes on to 
explain why this is the case.

In the attached 2003 paper (pooling the wisdom of several of the usual 
suspects, including Eleanor) it says something similar (p 1057):

"Coordinates of molecules that have been determined in complex with 
macromolecules previously can of course also be retrieved from the PDB 
(Bernstein et al., 1977; Berman et al., 2000), HIC-Up (Kleywegt and Jones, 
1998), or CHEMPDB (Boutselakis et al., 2003). However, one should keep in mind 
that these coordinates are the result of refinement against comparatively
low-resolu- tion data where the small molecule constituted only a minute 
fraction of the total scattering matter. This makes these coordinates 
inherently much less accurate than those obtained from the CSD. In addition, 
the coordi- nates may contain errors due to the use of incorrect restraints.
Hence, such coordinate sets should only be used as a last resort, and only 
after verification that they are reliable. The latter can be facilitated by 
inspection of the electron density for the compound in question, for instance 
at the Uppsala Electron-Density Server (http:// fsrv1.bmc.uu.se/eds) (G.J.K.
et al., submitted)."

Happy to be confused with George though!

--Gerard (no, the other one)



On Tue, 14 Jul 2020, 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 method".
>
>
>
> Any citable source - George Sheldrick might be a suspect.
>
>
>
> Thanks & best regards, BR
>
>
>
> --
>
> Bernhard Rupp
>
> <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.
> hofkristallamt.org%2Fdata=02%7C01%7Cjeffrey.bonanno%40einsteinmed
> .org%7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e6
> 2025%7C0%7C0%7C637304250594203532sdata=9FFCpYd9D%2BrHR48DtL%2BglM
> W2dbZ%2FmSTw0fF88XRwR7o%3Dreserved=0> 
> https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.h
> ofkristallamt.org%2Fdata=02%7C01%7Cjeffrey.bonanno%40einsteinmed.
> org%7Cf0b1878c0df040bb2e5308d828d6b0ed%7C9c01f0fd65e040c089a82dfd51e62
> 025%7C0%7C0%7C637304250594203532sdata=9FFCpYd9D%2BrHR48DtL%2BglMW
> 2dbZ%2FmSTw0fF88XRwR7o%3Dreserved=0
>
> <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
>
> ###

Re: [ccp4bb] Quote source inquiry

[Bernhard Rupp]

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 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 macromolecules [...]" and then goes on
to explain why this is the case.

In the attached 2003 paper (pooling the wisdom of several of the usual
suspects, including Eleanor) it says something similar (p 1057):

"Coordinates of molecules that have been determined in complex with
macromolecules previously can of course also be retrieved from the PDB
(Bernstein et al., 1977; Berman et al., 2000), HIC-Up (Kleywegt and Jones,
1998), or CHEMPDB (Boutselakis et al., 2003). However, one should keep in
mind that these coordinates are the result of refinement against
comparatively
low-resolu- tion data where the small molecule constituted only a minute
fraction of the total scattering matter. This makes these coordinates
inherently much less accurate than those obtained from the CSD. In addition,
the coordi- nates may contain errors due to the use of incorrect restraints.

Hence, such coordinate sets should only be used as a last resort, and only
after verification that they are reliable. The latter can be facilitated by
inspection of the electron density for the compound in question, for
instance at the Uppsala Electron-Density Server (http://
fsrv1.bmc.uu.se/eds) (G.J.K. 
et al., submitted)."

Happy to be confused with George though!

--Gerard (no, the other one)



On Tue, 14 Jul 2020, 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 method".
>
>
>
> Any citable source - George Sheldrick might be a suspect.
>
>
>
> Thanks & best regards, BR
>
>
>
> --
>
> Bernhard Rupp
>
> <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/
>
> <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
>
> ##
> ##
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a 
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are 
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>


Best wishes,

--Gerard

**
Gerard J. Kleywegt

   http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
The opinions in this message are fictional.  Any similarity
to actual opinions, living or dead, is purely coincidental.
**
Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
 of that pizza is equal to pi*z*z*a !
**



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Re: [ccp4bb] Quote source inquiry

[Eleanor Dodson]

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 method”.
>
>
>
> Any citable source - George Sheldrick might be a suspect…
>
>
>
> Thanks & best regards, BR
>
>
>
> --
>
> Bernhard Rupp
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] Quote source inquiry

[Bernhard Rupp]

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 regards, BR

 

--

Bernhard Rupp

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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