[sharp-discuss] Re: Heavy Atom Negative Density

[Frank Vondelft]

Hi Paul

Any chance that you lost the iron-sulfur during the soaking?  I don't =
know enough about the thing's biology, but what you see is what might =
happen if the derivatives do not have the cluster.  You could try =
defining the cluster only for the "native" (Fe MAD), not for the =
derivatives.  I assume you have set the right scattering factors for the =
Fe in the derivative datasets?=20

(I've not been following this thread, sorry if this has been suggested =
before.)

phx.



> -----Original Message-----
> From: Paul Hubbard [mailto:phubbard@post.its.mcw.edu]
> Sent: Monday, February 04, 2002 8:26 AM
> To: Clemens Vonrhein; sharp; ccp4
> Subject: Re: [sharp-discuss] Re: Heavy Atom Negative Density
>=20
>=20
> Hello,
>=20
> In followup to my previous e-mail, I have run both Fe MAD=20
> data alone, and in
> combination with the Os and Hg derivatives in SHARP. The MAD=20
> data alone gives
> nice positive denisty at the FeS cluster, but I still get=20
> negative density when
> I add the 2 derivatives (including the FeS atoms).
>=20
> NOTE: I know the Os and Hg derivatives are useable since SAS=20
> phaing using native
> in-house data with PHASES, and then doing X-Fouriers shows=20
> really nice peaks in
> the Fo-Fc maps, and this is confirmed using  Fe-MAD phases, and in the
> isomorphous difference Patterson. I also triple checked using=20
> SOLVE - so I'm
> pretty sure its right.
>=20
> However, when I run the data through RESOLVE I get, what=20
> looks like on first
> impressions (though I could be very wrong), a traceable map -=20
> but no FeS cluster.
> Does anyone have any idea what might be wrong? Since the MAD=20
> alone phased map
> looks fine I think there is nothing wrong with scaling or=20
> having bijvoet pairs
> flipped.
>=20
> By the way, I view the RESOLVE map in XTALVIEW by calculating=20
> a PHS file from the
> RESOLVE output with the following script, and viewing the=20
> Fo*f.o.m. map (is this
> wrong?):
>=20
> mtz2various HKLIN resolve.mtz HKLOUT resolve.phs << eof
> OUTPUT USER  -
> '(i3,2i4,4f8.2)'
> labin  FP=3DFP FOM=3DFOMM PHIB=3DPHIM
> end
>=20
> I have a seminar on Friday, and wanted to have the structure=20
> properly phased by
> then. Thanks!
>=20
> AGS
>=20
>=20
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>=20