Re: [ccp4bb] FW: [ccp4bb] Sulphate or phosphate?

2018-08-02 Thread Charles Ballard - UKRI STFC 
[cid:a3a4faea-08e2-46af-88de-3bde456d9124@fed.cclrc.ac.uk]


Sorry for spamming you all on this, but these images keep on getting stripped 
for Armin and myself.

On 2 Aug 2018, at 16:51, Charles Ballard - UKRI STFC wrote:

> Begin forwarded message (on behalf of Armin Wagner)
> From: ahw78 mailto:armin.wag...@diamond.ac.uk>>
> Date: 2 August 2018 at 09:17:48 BST
> To: Eleanor Dodson 
> mailto:eleanor.dod...@york.ac.uk>>
> Cc: ccp4bb mailto:ccp4bb@jiscmail.ac.uk>>
> Subject: Re: [ccp4bb] Sulphate or phosphate?
> Dear Eleanor,
>
> We can tune the wavelength over a large range (lambda = 1.2 – 6 A). This 
> allows collecting data above and below the absorption edges of Ca, K, Cl, S 
> and even P. Crystal, solvent and loop absorption are of course a problem for 
> the longest wavelengths, but so far we have done quite a fair amount of 
> studies around these absorption edges with strong signal above the edge and 
> obviously no signal below. Resolution in our setup is limited to around 3.2 A 
> at 5 A wavelength, but for anomalous difference fourier maps this is 
> sufficient. I have attached an example for a disulphide bridge which should 
> illustrate it better.
>
> Best regards,
>
>Armin
>
>
>
> [cid:image001.png@01D42A41.AE0B8B60]
>
> From: Eleanor Dodson 
> mailto:eleanor.dod...@york.ac.uk>>
> Date: Wednesday, 1 August 2018 at 19:09
> To: Armin Wagner 
> mailto:armin.wag...@diamond.ac.uk>>
> Cc: "ccp4bb@jiscmail.ac.uk" 
> mailto:ccp4bb@jiscmail.ac.uk>>
> Subject: Re: [ccp4bb] Sulphate or phosphate?
>
> I am not sure if you gave your wave length but it is always worth doing an 
> anomalous map, and looking at relativr peak heights for your known S 
> positions and the putative sulphate or phosphate.
> There are small differences in the expected f" at most wavelengths.
>
> Chemical arguments are doubtless better of Course!
> Eleanor
>
> On 1 August 2018 at 16:54, 
> armin.wag...@diamond.ac.uk 
> mailto:armin.wag...@diamond.ac.uk>> wrote:
> Dear David,
>
> The long-wavelength beamline I23 at Diamond 
> (http://www.diamond.ac.uk/Instruments/Mx/I23.html) can go all way down to the 
> phosphorous edge. While data quality will be obviously compromised by 
> absorption effects (we are working on this), for a reasonably well 
> diffracting crystal like yours we should be able to get anomalous difference 
> fourier maps from data collected above and below the sulphur edge (lambda ~5 
> A) to answer your question.
>
> We’ve published some test crystal work around the sulphur edge a while ago, 
> you might want to have a look here:
> https://doi.org/10.1016/j.nimb.2016.12.005
>
> The beamline is currently in an advanced commissioning phase accepting a 
> limited number of projects. So, please get into touch if you are interested. 
> We are currently sorting out a few more hardware and software aspects before 
> we can run the beamline as a standard user facility, but we have made a lot 
> of progress over the past months. There will be more details here on the 
> bulletin board ahead of the next call for proposals in autumn.
>
> Best regards,
>
>Armin
>
>
> Postdoc position for long-wavelength crystallography:
> https://vacancies.diamond.ac.uk/vacancy/post-doctoral-research-associate-355285.html
>
>
>
>
> On 31/07/2018, 14:38, "CCP4 bulletin board on behalf of David Schuller" 
> mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of 
> schul...@cornell.edu> wrote:
>
>How can one distinguish between a sulphate or phosphate in an electron
>density map? Both are present in the mother liquor, and resolution is in
>the range of 1.75 - 2.25 A
>
>
>--
>===
>All Things Serve the Beam
>===
>David J. Schuller
>modern man in a post-modern world
>MacCHESS, Cornell University
>
> schul...@cornell.edu
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
>
>
> --
> This e-mail and any attachments may contain confidential, copyright and or 
> privileged material, and are for the use of the intended addressee only. If 
> you are not the intended addressee or an authorised recipient of the 
> addressee please notify us of receipt by returning the e-mail and do not use, 
> copy, retain, distribute or disclose the information in or attached to the 
> e-mail.
> Any opinions expressed within this e-mail are those of the individual and not 
> necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any 
> atta

[ccp4bb] FW: [ccp4bb] Sulphate or phosphate?

2018-08-02 Thread Charles Ballard - UKRI STFC 
Begin forwarded message (on behalf of Armin Wagner)
From: ahw78 mailto:armin.wag...@diamond.ac.uk>>
Date: 2 August 2018 at 09:17:48 BST
To: Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>>
Cc: ccp4bb mailto:ccp4bb@jiscmail.ac.uk>>
Subject: Re: [ccp4bb] Sulphate or phosphate?
Dear Eleanor,

We can tune the wavelength over a large range (lambda = 1.2 – 6 A). This allows 
collecting data above and below the absorption edges of Ca, K, Cl, S and even 
P. Crystal, solvent and loop absorption are of course a problem for the longest 
wavelengths, but so far we have done quite a fair amount of studies around 
these absorption edges with strong signal above the edge and obviously no 
signal below. Resolution in our setup is limited to around 3.2 A at 5 A 
wavelength, but for anomalous difference fourier maps this is sufficient. I 
have attached an example for a disulphide bridge which should illustrate it 
better.

Best regards,

Armin



[cid:image001.png@01D42A41.AE0B8B60]

From: Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>>
Date: Wednesday, 1 August 2018 at 19:09
To: Armin Wagner mailto:armin.wag...@diamond.ac.uk>>
Cc: "ccp4bb@jiscmail.ac.uk" 
mailto:ccp4bb@jiscmail.ac.uk>>
Subject: Re: [ccp4bb] Sulphate or phosphate?

I am not sure if you gave your wave length but it is always worth doing an 
anomalous map, and looking at relativr peak heights for your known S positions 
and the putative sulphate or phosphate.
There are small differences in the expected f" at most wavelengths.

Chemical arguments are doubtless better of Course!
Eleanor

On 1 August 2018 at 16:54, 
armin.wag...@diamond.ac.uk 
mailto:armin.wag...@diamond.ac.uk>> wrote:
Dear David,

The long-wavelength beamline I23 at Diamond 
(http://www.diamond.ac.uk/Instruments/Mx/I23.html) can go all way down to the 
phosphorous edge. While data quality will be obviously compromised by 
absorption effects (we are working on this), for a reasonably well diffracting 
crystal like yours we should be able to get anomalous difference fourier maps 
from data collected above and below the sulphur edge (lambda ~5 A) to answer 
your question.

We’ve published some test crystal work around the sulphur edge a while ago, you 
might want to have a look here:
https://doi.org/10.1016/j.nimb.2016.12.005

The beamline is currently in an advanced commissioning phase accepting a 
limited number of projects. So, please get into touch if you are interested. We 
are currently sorting out a few more hardware and software aspects before we 
can run the beamline as a standard user facility, but we have made a lot of 
progress over the past months. There will be more details here on the bulletin 
board ahead of the next call for proposals in autumn.

Best regards,

Armin


Postdoc position for long-wavelength crystallography:
https://vacancies.diamond.ac.uk/vacancy/post-doctoral-research-associate-355285.html




On 31/07/2018, 14:38, "CCP4 bulletin board on behalf of David Schuller" 
mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of 
schul...@cornell.edu> wrote:

How can one distinguish between a sulphate or phosphate in an electron
density map? Both are present in the mother liquor, and resolution is in
the range of 1.75 - 2.25 A


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

schul...@cornell.edu



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



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are free from viruses and we cannot accept liability for any damage which you 
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###

[ccp4bb] FW: [ccp4bb] Sulphate or phosphate?

2018-08-02 Thread armin.wag...@diamond.ac.uk 

Dear all,

Sorry, now with the attachment of an anomalous difference fourier above and 
below the sulphur edge. 

Best regards,

   Armin


On 02/08/2018, 09:17, "CCP4 bulletin board on behalf of 
armin.wag...@diamond.ac.uk"  wrote:

Dear Eleanor,

We can tune the wavelength over a large range (lambda = 1.2 – 6 A). This 
allows collecting data above and below the absorption edges of Ca, K, Cl, S and 
even P. Crystal, solvent and loop absorption are of course a problem for the 
longest wavelengths, but so far we have done quite a fair amount of studies 
around these absorption edges with strong signal above the edge and obviously 
no signal below. Resolution in our setup is limited to around 3.2 A at 5 A 
wavelength, but for anomalous difference fourier maps this is sufficient. I 
have attached an example for a disulphide bridge which should illustrate it 
better.

Best regards,

Armin



[cid:image001.png@01D42A41.AE0B8B60]

From: Eleanor Dodson 
Date: Wednesday, 1 August 2018 at 19:09
To: Armin Wagner 
Cc: "ccp4bb@jiscmail.ac.uk" 
Subject: Re: [ccp4bb] Sulphate or phosphate?

I am not sure if you gave your wave length but it is always worth doing an 
anomalous map, and looking at relativr peak heights for your known S positions 
and the putative sulphate or phosphate.
There are small differences in the expected f" at most wavelengths.

Chemical arguments are doubtless better of Course!
Eleanor

On 1 August 2018 at 16:54, 
armin.wag...@diamond.ac.uk 
mailto:armin.wag...@diamond.ac.uk>> wrote:
Dear David,

The long-wavelength beamline I23 at Diamond 
(http://www.diamond.ac.uk/Instruments/Mx/I23.html) can go all way down to the 
phosphorous edge. While data quality will be obviously compromised by 
absorption effects (we are working on this), for a reasonably well diffracting 
crystal like yours we should be able to get anomalous difference fourier maps 
from data collected above and below the sulphur edge (lambda ~5 A) to answer 
your question.

We’ve published some test crystal work around the sulphur edge a while ago, 
you might want to have a look here:
https://doi.org/10.1016/j.nimb.2016.12.005

The beamline is currently in an advanced commissioning phase accepting a 
limited number of projects. So, please get into touch if you are interested. We 
are currently sorting out a few more hardware and software aspects before we 
can run the beamline as a standard user facility, but we have made a lot of 
progress over the past months. There will be more details here on the bulletin 
board ahead of the next call for proposals in autumn.

Best regards,

Armin


Postdoc position for long-wavelength crystallography:

https://vacancies.diamond.ac.uk/vacancy/post-doctoral-research-associate-355285.html




On 31/07/2018, 14:38, "CCP4 bulletin board on behalf of David Schuller" 
mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of 
schul...@cornell.edu> wrote:

How can one distinguish between a sulphate or phosphate in an electron
density map? Both are present in the mother liquor, and resolution is in
the range of 1.75 - 2.25 A


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

schul...@cornell.edu



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


--
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and 
not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any 
attachments are free from viruses and we cannot accept liability for any damage 
which you may sustain as a result of software viruses which may be transmitted 
in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England 
and Wales with its registered office at Dia