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There used to be a program called OMIT in CCP4. Seems to be still supported.
I believe I used it years ago but I vaguely remember problems with some space groups (might be wrong though...) 

Regards,
Roberto

On 11 Dec 2008, at 16:20, rajan sreekanth wrote:

 
Hi
What about the SFcheck omit map calculation in 'Map and Mask utilities' module in CCP4?


R.Sreekanth

On Wed, 10 Dec 2008 Kathleen Frey wrote :
>Hi Everyone,
>
>Can anyone tell me a relatively easy way to generate an omit density map for
>a ligand? I know that CNS can do this, but I was wondering if there's a CCP4
>related program to generate omit maps.
>
>Thanks,
>Kathleen




---
Roberto Steiner
Randall Division of Cell and Molecular Biophysics
New Hunt's House
King's College London
Guy's Campus
London, SE1 1UL
Phone +44 (0)20-7848-8216
Fax   +44 (0)20-7848-6435