[phenixbb] anomalous difference map calculation

Terwilliger, Thomas Charles terwilliger at lanl.gov
Wed Jun 17 10:21:08 PDT 2015

Hi Alexandra,

I think your refinements without the anomalous differences are going to be very similar to those with the anomalous differences, so probably no it is not worth it to go back. However it is worth making sure that you are using the same test set (R_free_flags) throughout.

If you want to get the very best anomalous map possible, then you could use instead Phaser to calculate an LLG map for the anomalous differences.  You provide your refined model (without the anomalously-scattering atoms) and your anomalous data and it can calculate this map for you.

To get the LLG map, in the Phenix GUI go to Experimental Phasing and select Phaser-EP.  Then select the Phaser mode "MR-SAD phasing".  Then put in your model and anomalous data.  Then under "Other Settings" scroll down and check "Output LLG maps".  Then run and that should do it!  Airlie or Randy might have further comments on this!

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 11:07 AM
Cc: phenixbb at phenix-online.org
Subject: Re: [phenixbb] anomalous difference map calculation

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 http://www.phenix-online.org/pipermail/phenixbb/2009-September/013799.html which
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<mailto: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.


On 6/17/15 06:04, Alexandra Marques wrote:

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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