[phenixbb] anomalous difference map calculation

Alexandra Marques at.marques at fct.unl.pt
Wed Jun 17 10:07:25 PDT 2015

Thank you very much for your replies.

Here is what I did:

1)I rerun xdsconv again with Friedls law=false in order to get the mtz file
with the F(+) and F(-) columns (new.mtz).

2) I used my pdb file from the last refinement together with the new.mtz
file as input for “Calculate maps” in Phenix and selected the option for
anomalous map.

Now I obtained the ANOM PHANOM map. I hope this is correct…

In the anomalous map the largest density is in the Mo and Fe atoms. There
is no density in the S of SO3 or SO4 groups, so, this will not help me to
decide whether there are SO3 groups in the structure (because for the SO4 I
have no doubt).

However, while searching the mailling list I foud this post
worried me. Should I have used from the beginning this “new” mtz file
with F+/F- in order to obtain anomalous differences map at each
refinement step? Do you think that I should go back, transfer the
R-free flags to my new mtz file and repeat all the refinements?

Best regards,


2015-06-17 16:59 GMT+01:00 Pavel Afonine <pafonine at lbl.gov>:

>  Hi Alexandra,
> to get anomalous difference map you do not need to do anything special:
> phenix.refine calculates this map by default as long as your input data are
> Fobs(+) and Fobs(-) or Iobs(+) and Iobs(-).
> Refining occupancy of Mo may not be a bad idea given it is likely to be
> partially occupied.
> Pavel
> On 6/17/15 06:04, Alexandra Marques wrote:
>  Hi,
>  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,
> Alexandra
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