[phenixbb] Anomalous or not?

[CPMAS Chen]

Yeah. Ideally. But when you have multiple blobs in Fo-Fc map, it is hard to
decide. of course, it need to be fitted. That is what I am working with. No
matter what, the data is there at about 3A for a membrane protein , I
should be able to see something.

Thanks for all the suggestions!

Best,

Charles at Pitt


On Thu, Jul 10, 2014 at 1:29 PM, Oganesyan, Vaheh <OganesyanV at medimmune.com>
wrote:

>  Shouldn’t phases from MR be a better way to look for bromated ligand in
> Fo-Fc maps in such a case?
>
>
>
>
>
>
>
> *Regards,*
>
>
>
> *Vaheh*
>
> *8-5851*
>
>
>
> *From:* phenixbb-bounces at phenix-online.org [mailto:
> phenixbb-bounces at phenix-online.org] *On Behalf Of *CPMAS Chen
> *Sent:* Thursday, July 10, 2014 12:53 PM
> *To:* Ryan Spencer
>
> *Cc:* phenixbb at phenix-online.org
> *Subject:* Re: [phenixbb] Anomalous or not?
>
>
>
> Well, let me make this clear.
>
>
>
> 1. I am using Br anomalous signal to identify the potentially bound ligand.
>
> 2. I do shoot the crystals at 0.92A.
>
> 3. the different crystals have different resolution, but anomalous signal
> was weak as reported by autoxds.
>
>
>
> Charles
>
>
>
> On Thu, Jul 10, 2014 at 12:25 PM, Ryan Spencer <rspencer at uci.edu> wrote:
>
> So I assume you were not able to shoot the crystal at ~0.92 A at SSRL or
> are the crystals sensitive? If you were limited to the single wavelength
> beam which is around 1A you’re dealing with a really low f” of 0.5322.
> There have been crystals solved with Sulfur using an in-house Cu sources
> (takes a lot of merged sets and anomalous is stronger at certain crystal
> angles) which gives about the same anomalous scattering as Br. Is the
> bromine covalent or is it soaked ion?
>
>
>
> Alternatives – soak with potassium iodide and get a dataset from an
> in-house source (iodine f” 6.6 at 1.54), or at least the anomalous
> locations. You may get a partial model to use for replacement at that point.
>
>
>
> Did each processed dataset have the same level of anomalous signal when
> processed individually?
>
>
>
> Ryan
>
>
>
>
>
> *From:* phenixbb-bounces at phenix-online.org [mailto:
> phenixbb-bounces at phenix-online.org] *On Behalf Of *CPMAS Chen
> *Sent:* Thursday, July 10, 2014 8:55 AM
> *To:* Francis Reyes
> *Cc:* phenixbb at phenix-online.org
> *Subject:* Re: [phenixbb] Anomalous or not?
>
>
>
> Francis,
>
>
>
> My anomalous plot for Br is more like your Cobalt 1 site less redundancy.
>
>
>
> Ryan,
>
>
>
> As my Br anomalous signals are weak, I merged signals from multiple
> crystals.
>
>
>
> Meanwhile I am looking into the detail about the autoxds processing as
> suggested by Tim.
>
>
>
> Thanks,
>
>
>
> On Thu, Jul 10, 2014 at 10:02 AM, Francis Reyes <
> Francis.Reyes at colorado.edu> wrote:
>
> In addition to Tim's comments above, using loggraph to see the anomalous
> CC plot from scala is a good qualitative indicator of whether you have
> anomalous signal..
>
>
> Some data points for what reasonable plots  (and their corresponding XDS
> SigANO's) look like:
> https://dl.dropboxusercontent.com/u/19558536/AnomalousCC.pdf
>
>
> F
>
>
> On Jul 10, 2014, at 9:03 AM, CPMAS Chen <cpmasmit at gmail.com> wrote:
>
> >
> > Which result should I trust? By the way, how can I view/display the
> ***.anamplot file, which is apparently xmgr format file, but I can not
> display in CCP4i.
> >
>
>
>
>
>
> --
>
> ***************************************************
>
> Charles Chen
>
> Research Associate
>
> University of Pittsburgh School of Medicine
>
> Department of Anesthesiology
>
> ******************************************************
>
>
>
>
>
> --
>
> ***************************************************
>
> Charles Chen
>
> Research Associate
>
> University of Pittsburgh School of Medicine
>
> Department of Anesthesiology
>
> ******************************************************
>  To the extent this electronic communication or any of its attachments
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-- 

***************************************************

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

******************************************************
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