I am even more cautious - if I want to check the anomalous map for a strong
scatterer I set the putative anomalous scatterer occupancy to 0.0 .
Theoretically it shouldn't be necessary - the atom map uses Phic+90 (or
maybe Phic -90??) but if the site is excluded you feel more secure in
drawing con
That just looks like bulk solvent to me. Might be extra dense to the
the barium, but disordered bulk nonetheless.
If, as you say, the anomalous peak only shows up after you model in a
strong anomalous scatterrer and not when you don't model in anomalous
signal, then I suspect all you are seei
;
>> Good luck!
>>
>> Herman
>>
>>
>>
>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
>> von *Betty Chu
>> *Gesendet:* Montag, 21. August 2017 17:19
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* [ccp4bb] Unknown posi
; *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Betty Chu
> *Gesendet:* Montag, 21. August 2017 17:19
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [ccp4bb] Unknown positive electron density
>
>
>
> Dear ccp4bb,
>
> I am refining a 1.40 Angs
anomalous peak is
phosphorus.
Good luck!
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Betty Chu
Gesendet: Montag, 21. August 2017 17:19
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Unknown positive electron density
Dear ccp4bb,
I am refining a 1.40 Angstrom data set for
* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Unknown positive electron density
>
>
>
> Betty,
>
>
>
> I think that f’’ for Ba at this wavelength is around 3.5 electrons, and
> f'' for As is expected to be about 3 electrons. Is there a nearby
> crystallog
Fourier truncation ripples?
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of CRAIG A
BINGMAN
Sent: Monday, August 21, 2017 6:20 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Unknown positive electron density
Betty,
I think that f’’ for Ba at this wavelength is
Betty,
I think that f’’ for Ba at this wavelength is around 3.5 electrons, and f'' for
As is expected to be about 3 electrons. Is there a nearby crystallographic
symmetry axis?
Craig
On Aug 21, 2017, at 5:05 PM, Betty Chu
mailto:chube...@umd.edu>> wrote:
Hi Craig,
The data collection wavele
Hi Craig,
The data collection wavelength was 0.92 Angstroms. Since we observe
anomalous signal for Ba at this wavelength, we would expect greater
anomalous signal if As were present. There is a possibility for weak
anomalous signal in this positive density, but the weak anomalous signal
only shows
What is the data collection wavelength/energy? Would you expect significant
anomalous diffraction from As at this wavelength?
On Aug 21, 2017, at 11:37 AM, Betty Chu
mailto:chube...@umd.edu>> wrote:
Hi Shailesh,
When I modelled in the Barium ion with octahedrally coordinated waters and ran
th
Hi Shailesh,
When I modelled in the Barium ion with octahedrally coordinated waters and
ran the refinement, the distances from the barium to some of the waters
ended up being too close (<2.2 Angstroms). Also, the positive electron
density is connected. If the density indicated barium with coordina
Looks like Ba2+. Since it exist with coordination number 6 or above check
what geometry water is following there (trigonal bipiramidal or so on).
Water might also be shared by symmetry related Ba cation.
Shailesh Kumar Tripathi,
Phone: 9686289668
On Mon, Aug 21, 2017 at 9:17 PM, Betty Chu wro
Yes, I have. The cacodylate ion does not fit well into the density.
On Mon, Aug 21, 2017 at 11:44 AM, Pradeep Pallan
wrote:
> Did you try modelling in a cacodylate ion (CH3)2AsO2-?
>
> On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu wrote:
>
>> Dear ccp4bb,
>>
>> I am refining a 1.40 Angstrom data
Did you try modelling in a cacodylate ion (CH3)2AsO2-?
On Mon, Aug 21, 2017 at 10:19 AM, Betty Chu wrote:
> Dear ccp4bb,
>
> I am refining a 1.40 Angstrom data set for a DNA oligonucleotide. While
> the model for the DNA fits very well into the density, there is a patch of
> positive electron de
Dear ccp4bb,
I am refining a 1.40 Angstrom data set for a DNA oligonucleotide. While the
model for the DNA fits very well into the density, there is a patch of
positive electron density in the solvent space that we are having trouble
with.
The screenshot can be viewed through this link:
https://c
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