[sharp-discuss] Refining rigid group of heavy atoms

Clemens Vonrhein vonrhein at globalphasing.com
Mon Oct 11 09:35:27 BST 2004


Dear Allister,

at the moment you can't do rigid-body refinement inside SHARP.

However, since I would expect the Fe-S cluster in your protein to have
a very similar geometry to other Fe-S clusters, I would try and find a
Fe-S cluster from the PDB that best fits the residual maps from
SHARP. Then keep the coordinates fixed in SHARP - and just refine
occupancies (and maybe B-factors). Have a look again at the resulting
residual maps: maybe they will allow you to place the cluster even
better?

Also, if you are already able to do some solvent flattening
(especially, if the two hands give significantly different statistics
- so you know that one is correct), you can include the solvent
flattened phases into the next SHARP run. This might stabilize the
refinement - and quite often it improves the residual maps. Important:
don't use these phases in the final phasing step of a SHARP run - this
just introduces bias.

Hope that helps.

Cheers

Clemens

On Sun, Oct 10, 2004 at 04:20:35PM +0100, b229857 wrote:
> Sharp users,
> 
> I am trying to phase Fe-MAD data collected on an FeS cluster at low resolution 
> (~3.5A). I have some poor phases from treating the clusters as single 
> 'super-atoms' (ie a single Fe atom at the centre of the cluster position with 
> large b-factors and occupancies that become greater than 1), from which I can 
> roughly deduce the positions of individual Fe and S atoms by docking an FeS 
> cluster (from an unrelated previously solved structure) into the density. I 
> now want to refine the positions of the cluster to get better phases but when 
> I do so the geometry of the cluster becomes totally ruined! Is it possible to 
> refine the atoms of the FeS cluster as a rigid group in Sharp?
> 
> Allister Crow
> 
> 
> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss at www.globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss
> 

-- 

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* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
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