Re: [ccp4bb] maprot question

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

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Subject: resolution shells for each bin in scala?
From: Francis E Reyes Francis {- dot -} Reyes {- at -} COLORADO {- dot -} EDU
Date: 2009-08-03

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Subject: Re: maprot question
From: Peter Grey petgxray {- at -} GMAIL {- dot -} COM
Date: 2009-08-03

Thank you Eleanor and Kevin,

Eleanor suggested separating the two tasks. Eventually, I changed the cell
with maprot and then used MAPMAN to zero the map below the cut-off level.

Kevin described how maprot works and suggested down-scaling the map to have
more reasonable values for densities.

These two suggestions give slightly different results. When the mask is
applied in maprot the distribution of densities close to the cut-off level
is smoothened.

Peter.

On Mon, Aug 3, 2009 at 10:26 AM, Eleanor Dodson wrote:

> I CANT BE SURE of what has happened BUT maprot is a very complicated
> procedure and your script is trying to do 2 things at once - change the cell
> and apply the mask.
> I would try changing the cell first, then generating the mask, then
> applying it
>
> or else: generate mask, apply mask, then change cell.
>
> But at every stage look at the result! ( mapslicer or coot or whatever) to
> make sure you have really achieved what you are aiming for!
>
> Eleanor
>
>
>
> Peter Grey wrote:
>
>> Hi all,
>>
>> I am trying to cut density from EM map (in a small P1 cell) into big P1
>> cell
>> for MR.
>>
>> The mask is defined by a certain cut-off level in mapmask :
>>
>> mapmask
>> mapin em.map
>> mskout em.msk << eof
>> MASK CUT 353
>> MODE mapin
>> eof
>>
>> I use maprot to cut the density to the big P1 (that has the same grid
>> spacing as the original small P1).
>>
>> maprot wrkin em.map mskin em.msk mapout cut.map << eof
>> MODE TO
>> CELL XTAL 1098. 1098. 1098. 90. 90. 90.
>> GRID XTAL 375 375 375
>> SYMM P1
>> AVER 1
>> ROTA EULER 0.0 0.0 0.0
>> TRANS 0.0 0.0 0.0
>> END
>> eof
>>
>> When cut.map is read by mapmask the program reports that the minimum of
>> the
>> map is -310.
>>
>> How come the minimum is not the cut-off level used to define the mask ?
>> What
>> am I missing/Doing wrong ?
>>
>> Many thanks in advance for all suggestions and comments,
>>
>> Peter.
>>
>>
>>
>
>

CCP4bb navigation

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

Previous message:
Subject: resolution shells for each bin in scala?
From: Francis E Reyes Francis {- dot -} Reyes {- at -} COLORADO {- dot -} EDU
Date: 2009-08-03

Next message:
Subject: About sel-met oxidation
From: tat cheung cheng theifire {- at -} YAHOO {- dot -} COM {- dot -} HK
Date: 2009-08-03