[phenixbb] anomalous difference map
shyabiswas at gmail.com
Sun Mar 27 07:29:27 PDT 2011
I had a similar case before:
1) Synchrotron Fluorescence scan indicates the heavy atom definitely
presents in my protein (my control is a second protein with the same ligand
showed no absorbance spectrum)
just because the wavelength scan shows that the metal is there that does not
mean it is there.
have you tried using autosol? there is a step by step instruction for how to
run autosol in the phenix website all you need is the f' and f'' values for
your heavy atom and your sca file. The output files that you get has the
difference map that you need.
You can also run phenix.xtriage just to check whether you have any anomolous
hope this helps,
On Sat, Mar 26, 2011 at 12:20 AM, Jason <phenix.upitt at gmail.com> wrote:
> Hello Everyone,
> I have an old question about how to create anomalous difference map.
> 1) Synchrotron Fluorescence scan indicates the heavy atom definitely
> presents in my protein (my control is a second protein with the same ligand
> showed no absorbance spectrum)
> 2) xds processed mtz file
> 3) Data resolution ~ 3 angstron
> 3) molecular replacement solved apo structure protein.pdb using
> 4) phenix.maps to generate anomalous map (phenix.refine will also generate
> it, but let's leave it aside for the moment)
> When I load the mtz file to phenix.maps GUI, the mtz label pulldown menu
> indicates 4 possible choices for the column to use:(1) IMEAN, SIGIMEAN
> (2) I(+), sigI(+), I(-), sigI(-) merged (3) F(+), sigF(+), F(-), sigF(-)
> merged (4) F, sigF, Dano SigDano. I have tried the choices of (2) (3) and
> (4). However, there is barely any anomalous signal at 4sigma, which makes me
> wondering if something is not right. The first thing coming to my mind is
> the mtz labels: I(+), sigI(+), I(-), sigI(-) merged. What does merged
> mean? Could this be the reason? Other issues that could causing the trouble?
> Thank you all.
> Structural Biology Department
> University of Pittsburgh
> phenixbb mailing list
> phenixbb at phenix-online.org
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