I wish I knew more about OMIT maps, but after testing Kevins procedure
(which omits overlapping sphers with perturbation) and SFCHECK (method
unknown) I got quite biased results. It is years since I have run the
full CNS/Phenix procedure which attempts to remove bias by simulated
annealing.. maybe that is sufficiently drastic to cure the bias.
we all could show beautiful maps revealing parts of the structure such
as ligandsa which have never been included in the phasing, so omit map
can obviously work, so I am not sure at which point the bias appears..
Eleanor
Kevin Cowtan wrote:
I hacked up a little program to do composite omit maps a couple of
years back. The purpose of the program was to try out an idea I had -
an ML-omit map based on real space restraints on the rest of the
density, using the same mathematics as is used for statistical density
modification. This turned out to have no benefit that I could identify.
However the code also implements simple and sigmaa omit maps for
comparison. Using the new version of clipper (either 2.0.9 in CCP4
6.1, or 2.1) it could also be easily updated to produce MLHL composite
omit maps to incorporate experimental phase information.
If anyone wants to pick it up and develop it further, please feel
free. I'd be particularly interested if anyone can find a case where
the 'pirate' omit map gives any significant benefit.
http://www.ysbl.york.ac.uk/~cowtan/ftp/brigantine-src.tgz
Kevin
Roberto Steiner wrote:
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
e-mail [email protected] <mailto:[email protected]>
