[ccp4bb] SO4 or PO4

[张士军]

Dear all

I have got a crystal grown at the condition both have ion of SO4 and PO4, and 
the diffraction resolution is very well, but the problem is coming: how to tell 
which is which just from electron density? I think they are exactly same. 
Thanks a lot !!!

Beat Regards

Shijun



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Re: [ccp4bb] SO4 or PO4

[jlliu20022002 liu]

How about collect data at sulfur peak. You might see anomalous peak for
sulfur.

Jinyu

On Sat, Feb 16, 2019 at 4:07 AM 张士军 <21620150150...@stu.xmu.edu.cn> wrote:

> Dear all
>
> I have got a crystal grown at the condition both have ion of SO4 and PO4,
> and the diffraction resolution is very well, but the problem is coming: how
> to tell which is which just from electron density? I think they are exactly
> same. Thanks a lot !!!
>
> Beat Regards
>
> Shijun
>
> --
>
> 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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Re: [ccp4bb] SO4 or PO4

[Roger Rowlett]

Two things to look at that could provide a clue:

Examine the anomalous map for some density over the central atom. Sulfur
will often, but not always have significant anomalous density depending on
the wavelength and quality of data set.

Phosphate is normally HPO4= or H2PO4-. Look for phosphate donor to acceptor
hydrogen bonding contacts. Sulfate rarely has donor to acceptor hydrogen
bonding contacts, as it is SO4= at any reasonable pH.

Roger Rowlett

On Sat, Feb 16, 2019, 4:06 AM 张士军 <21620150150...@stu.xmu.edu.cn wrote:

> Dear all
>
> I have got a crystal grown at the condition both have ion of SO4 and PO4,
> and the diffraction resolution is very well, but the problem is coming: how
> to tell which is which just from electron density? I think they are exactly
> same. Thanks a lot !!!
>
> Beat Regards
>
> Shijun
>
> --
>
> 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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[ccp4bb] Warning - ccp4 update 7.0.069 breaks ccp4i2 on MacBook running Mojave (v 10.14.2)

[david lawson (JIC)]

Hi All,

I installed the latest ccp4 update on my MacBook through the CCP4i2 update 
manager. After doing so, refmac appeared to be broken. I tried to restart the 
I2 GUI but it refused to even after a reboot.
Eventually I got running again by uninstalling this update through the CCP4i 
update manager (i.e. the old GUI). After cloning my failed refmac job in 
CCP4i2, it ran without a hitch.

Dave

---

Dr. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: david.law...@jic.ac.uk




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[ccp4bb] Fwd: [ccp4bb] SO4 or PO4

[Patrick Loll]

S has about 0.56 anomalous electrons at 8 keV, whereas P has about 0.44. This 
is a small difference between two weak signals—unlikely to give a clear result. 
If you could get to the sulfur & phosphorus edges, then you could (in 
principle) answer this, but that’s a very hard experiment to accomplish.


> Begin forwarded message:
> 
> From: jlliu20022002 liu 
> Subject: Re: [ccp4bb] SO4 or PO4
> Date: February 16, 2019 at 11:14:07 AM EST
> To: CCP4BB@JISCMAIL.AC.UK
> Reply-To: jlliu20022002 liu 
> 
> How about collect data at sulfur peak. You might see anomalous peak for 
> sulfur.
> 
> Jinyu
> 
> On Sat, Feb 16, 2019 at 4:07 AM 张士军 <21620150150...@stu.xmu.edu.cn 
> > wrote:
> Dear all
> 
> I have got a crystal grown at the condition both have ion of SO4 and PO4, and 
> the diffraction resolution is very well, but the problem is coming: how to 
> tell which is which just from electron density? I think they are exactly 
> same. Thanks a lot !!!
> 
> Beat Regards
> 
> Shijun
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 
> 
---
Patrick J. Loll, Ph. D.  
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu




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Re: [ccp4bb] SO4 or PO4

[mesters]

Anomalous is the way to go but it helps to think about the final 
concentrations used. With 50 mM PO4 (buffer) and 2 M  SO4 (ammonium 
sulfate) most "bindin sites in quesiton" will be occupied by SO4...


My 2 cents

Jeroen

On Sat, Feb 16, 2019 at 4:07 AM 张士军 <21620150150...@stu.xmu.edu.cn 
> wrote:


Dear all

I have got a crystal grown at the condition both have ion of SO4
and PO4, and the diffraction resolution is very well, but the
problem is coming: how to tell which is which just from electron
density? I think they are exactly same. Thanks a lot !!!

Beat Regards

Shijun




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--
*Dr.math. et dis. nat.Jeroen R. Mesters*
Deputy, Lecturer, Program Coordinator /Infection Biology
/ 
Visiting 
Professorship (South Bohemian University) in Biophysics

Logo Uni Lübeck
*University of Lübeck*
Center for Structural and Cell Biology in Medicine
*Institute of Biochemistry*

Tel +49 451 3101 3105 (secretariate 3101)
Fax +49 451 3101 3104
jeroen.mest...@uni-luebeck.de 
www.biochem.uni-luebeck.de 

*Ratzeburger Allee 160
23538 Lübeck, Schleswig-Holstein
Germany*




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Re: [ccp4bb] Fwd: [ccp4bb] SO4 or PO4

[Jan Stransky]

This can be done at Diamond I23 beamline.

https://doi.org/10.1016/j.nimb.2016.12.005

Best regards,

Jan

Dne 16.02.2019 v 18:49 Patrick Loll napsal(a):
> S has about 0.56 anomalous electrons at 8 keV, whereas P has about
> 0.44. This is a small difference between two weak signals—unlikely to
> give a clear result. If you could get to the sulfur & phosphorus
> edges, then you could (in principle) answer this, but that’s a very
> hard experiment to accomplish.
>
>
>> Begin forwarded message:
>>
>> *From: *jlliu20022002 liu > >
>> *Subject: **Re: [ccp4bb] SO4 or PO4*
>> *Date: *February 16, 2019 at 11:14:07 AM EST
>> *To: *CCP4BB@JISCMAIL.AC.UK 
>> *Reply-To: *jlliu20022002 liu > >
>>
>> How about collect data at sulfur peak. You might see anomalous peak
>> for sulfur.
>>
>> Jinyu
>>
>> On Sat, Feb 16, 2019 at 4:07 AM 张士军 <21620150150...@stu.xmu.edu.cn
>> > wrote:
>>
>> Dear all
>>
>> I have got a crystal grown at the condition both have ion of SO4
>> and PO4, and the diffraction resolution is very well, but the
>> problem is coming: how to tell which is which just from electron
>> density? I think they are exactly same. Thanks a lot !!!
>>
>> Beat Regards
>>
>> Shijun
>>
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>
>
> ---
>
> Patrick J. Loll, Ph. D.  
>
> Professor of Biochemistry & Molecular Biology
>
> Drexel University College of Medicine
>
> Room 10-102 New College Building
>
> 245 N. 15th St., Mailstop 497
>
> Philadelphia, PA  19102-1192  USA
>
>
> (215) 762-7706
>
> pjl...@gmail.com 
>
> pj...@drexel.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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