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

[Dr Nicholas Keep <n.keep@mail.cryst.bbk.ac.uk>]

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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'll try all the above and compare
Thank you all for your time.
Nick






-- 
Dr Nicholas H. Keep
School of Crystallography,
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