[phenixbb] anomalous difference map calculation

Tim Gruene tg at shelx.uni-ac.gwdg.de
Wed Jun 17 08:16:26 PDT 2015

Dear Alexandra,

I would like to correct the two previous replies: there is no need to
reprocess your data. XDS_ASCII.HKL will contain the anomalous
information. The keyword 'FRIEDEL'S_LAW' affects the scaling, but not
the output format. Actually some people recommend to always process with
FRIEDEL'S_LAW=TRUE whether or not you want to extract the anomalous
signal, because to get higher multiplicity for scaling (There are
caveats if very strong Friedel/Bijvoet  differences are present, but
these are rare, I believe).

You only need to rerun the conversion program and tell it to keep the
Bijvoet pairs separate.

The fastest way to create the anomalous difference map is to use shelxc
for a SAD experiment. shelxc reads the XDS_ASCII.HKL directly and will
also treat it correctly. This creates an _fa.hkl file. When you provide
this and your pdb-file to the program anode (also available from the
SHELX server), it create the anomalous map (ending .pha) that you can
read into Coot.

When you are familiar with shelx c/d/e and anode, it would take you
maybe 1-2 min to create the map. If you are not familiar with the
programs, maybe a few minutes more. Take a look at pages 25-27 in


for a first guide.


On 06/17/2015 03:04 PM, 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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149


-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 173 bytes
Desc: OpenPGP digital signature
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150617/5cc096b0/attachment-0001.sig>

More information about the phenixbb mailing list