[phenixbb] anomalous difference map calculation

Terwilliger, Thomas Charles terwilliger at lanl.gov
Wed Jun 17 10:05:28 PDT 2015

Hi Alexandra,

I'm sorry, I misinterpreted your question. As Pavel and Tim point out there is no need to do anything special in your case to get the anomalous data.

As Pavel mentioned, you can just take your current model and run phenix.refine with that model and your .HKL file and it will produce an anomalous difference map for you.

If you have already refined you model with a different data file, then you should provide the free R flags (test set) from the refinement that you have already carried out. You can transfer these flags to your .HKL file with the reflection file utility in the Phenix GUI if you want.

All the best,
Tom T

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Terwilliger, Thomas Charles [terwilliger at lanl.gov]
Sent: Wednesday, June 17, 2015 7:46 AM
To: Alexandra Marques; phenixbb at phenix-online.org
Subject: Re: [phenixbb] anomalous difference map calculation

Hi Alexandra,

You will have to run the last steps in data processing over and obtain anomalous data in order to calculate that anomalous difference map.  Once you have that data you can also refine the occupancy of your Mo atom, however at 0.97 A the anomalous scattering from Mo is not strong (f" is 1.2 electrons).

All the best,
Tom T

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Alexandra Marques [at.marques at fct.unl.pt]
Sent: Wednesday, June 17, 2015 7:04 AM
To: phenixbb at phenix-online.org
Subject: [phenixbb] anomalous difference map calculation


I am in the last refinement steps of a MR model and I want to calculate an anomalous difference map essentially to confirm the presence of a sulfite molecule and to locate vanadium (present in soaking solution). I read that it is necessary to have a mtz file with anomalous data (i.e. F+,F- or I+,I-). However, my data was collected at “normal” wavelenght (0.97) and it was processed with XDS considering Friedls law= true and my mtz file contain the following columns: H K L FP SIGFP. So, can I still calculate a anomalous difference map based on my data?

Since I also have a Mo atom in the active site can I try to refine its occupancy by using the option “anomalous groups” in the refinement strategy?

Thank you very much,
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