Re: [ccp4bb] generating omit maps

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: updated XDS binaries available
From: Justin Lecher j {- dot -} lecher {- at -} FZ-JUELICH {- dot -} DE
Date: 2008-12-15

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Subject: Re: updated XDS binaries available
From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2008-12-15

Subject: Re: generating omit maps
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-12-15

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 roberto.steiner@kcl.ac.uk
>>
>>
>>
>>
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: updated XDS binaries available
From: Justin Lecher j {- dot -} lecher {- at -} FZ-JUELICH {- dot -} DE
Date: 2008-12-15

Next message:
Subject: Re: updated XDS binaries available
From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2008-12-15