Re: Summary [ccp4bb]: What is the CCP4 (refmac5) equivalent of an omit map

[Anastassis Perrakis <perrakis@nki.nl>]

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Dr Nicholas Keep wrote:

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> 
> Thanks for the loads of replies I have had already.
> Answers fall into three camps
> 1)  Shake up the coordinates a bit (with pdbset or moleman2), omit the ligand and run refmac for a few cycles.
> 2)  Use OMIT (CCP4 programme)
> 3) Display some early unbiased map.  Ideally refine the protein as far as you can without building in any ligand.
> 
> Oh and a suggestion to see if Arp/Warp puts atoms there (No guesses as to where that came from).

I guess Nicholas refers to the email I sent to him earlier, but :

	that was NOT AT ALL what I suggested.

I was referring to aan idea/approach (which indeed uses arp/warp) and is 
described for example nicely in :

'Questions about the structure of the botulinum neurotoxin B light chain 
in complex with a target peptide'

by Bernhard Rupp, Brent Segelke

in Nature Structural Biology 8, 663 - 664 (01 Aug 2001)

Seeing if Arp/Warp puts atoms in density is in general terms a bad idea 
and I would not recommend it anybody that has the same problem as Nicholas.


		A.

PS I also suggested nr.1 which is most likely the best idea.