Re: refmac for partial p-ala trace / refinements

[Johan Turkenburg <jpt@ysbl.york.ac.uk>]

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Alexandre Urzhumtsev/Ourjoumtsev wrote:
> 
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> Hi,
> 

........cut to save bandwidth

> Including of all data is good when your have a high-resolution data set
> (which rather mean that your crystal is good, your density is good, and
> your model is supposed to be quite good and complete originally - without
> or with some dummy-atoms as it in ARP).
> 
> Best regards,
> 
> Sasha


Hi,


It seems that in practice REFMAC/ARP procedures work much better than
this theory may predict. In a recent case I had a molecular replacement
model that was only about 50% of the structure I was trying to solve.
I had data to 1.9A, but the stats on the data (I/sig(I) and Rsym) would
indicate that the data beyond 2.3A was barely significant.

The model was incomplete in various ways: side chains, loops and a
whole domain.

An initial map was reasonable for the atoms in the mol rep model, but 
showed very little density for the missing 50%. Even missing side chains 
in the model did not come up convincingly. 

Many cycles (something like 100) of refmac/arp later the map was 
gorgeous, and a model was build in under two hours!

Repeating this at 2.3A did not work anywhere near as well, and the 
model could not have been build without further intermittent
refinement.

I'll certainly not try to theoretise on why that was the case. But
next time you have a case like this, give it a go. And your
high res data should of course always be brilliant, but when it is not, 
don't throw it away straight away -:)

Johan



-- 
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Dr. Johan P. Turkenburg			X-ray facilities manager
York Structural Biology Laboratory	
Chemistry Department			Phone (+) 44 1904 432596
University of York			Fax   (+) 44 1904 410519
York YO10 5DD   UK			Email: jpt@yorvic.york.ac.uk
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