[phenixbb] Anomalous or not?

Francis Reyes Francis.Reyes at colorado.edu
Thu Jul 10 11:00:37 PDT 2014


You should see something in an anomalous difference fourier  map using the model as a source of phases (make sure your Br is not in the model used to compute it). 

F


On Jul 10, 2014, at 1:48 PM, CPMAS Chen <cpmasmit at gmail.com> wrote:

> 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 contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
> 
> 
> 
> -- 
> 
> ***************************************************
> 
> Charles Chen
> 
> Research Associate
> 
> University of Pittsburgh School of Medicine
> 
> Department of Anesthesiology
> 
> ******************************************************
> 
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb



More information about the phenixbb mailing list