[sharp-discuss] no electron density around Se

[Clemens Vonrhein]

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Hi,

as someone else already pointed out: make sure the hand is
correct. In the SIN file editor there is a tool to switch to the
enantiomere. So you can run SHARP twice. However, you should then do
solvent flattening in both hands and compare these two maps.

You can do that easyl by actually using autoSHARP (instead of
SHARP). Just put the SOLVE sites as fractional coordinates into a
*.hatom file (into your sharpfiles/datafiles directory) and fire up
autoSHARP (lot's of documentation on how to fill out the few
fields). The difference in correlation between both hands (printed in
the main logfile of an autoSHARP run) will tell you if you're on the
right track.

I would also suggest looking at solvent flattened maps directly (much
easier on your eyes) - just use the SOLOMON-based tools on the
Phase-improvement panel. Or - if you're lazy - use autoSHARP which
will do everything for you.

Cheers

Clemens


On Thu, Jan 08, 2004 at 06:27:28PM -0500, gte977x@mail.gatech.edu wrote:
> Dear SHARPusers:
>=20
> I am using SHARP version 3.0.15 to refine 30 Se sites that came out of so=
lve in
> space group P212121. MAD data at 3 wavelengths was scaled in scaleit (ccp=
4) to
> 2.5 A and was input in SHARP for refining sites. The run converged and ga=
ve the
> phasing stats but the eden_flattened (including average HA contribution) =
map
> don't show seleniums in electron density. The map shows lots of connectiv=
ites
> but not very clear secondary structures. Along with these maps I am also =
loading
> the heavy atom sites from the "include PDB files" option in output file. =
All the
> selenium sites were in density after the solve run was completed.=20
>=20
> I am not sure what to look for in order to correct this porblem.=20
> Any suggestions will be greatly appreciated.
>=20
> Thanks,
> Akanksha
>=20
>=20
>=20
>=20
>=20
> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss@globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss

--=20

***************************************************************
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park=20
*  Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group      (http://www.globalphasing.com)
***************************************************************

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