OK, I can confirm the problem. The issue is that mama can make ccp4 maps
which, while they technically obey the CCP4 map format, contain content
which is ambiguous.
In this case, your map extends from -29 to 53 on x, and yet the X-axis
is only 44 grid points long - similar for y and z. So each grid point
appears several times in the map, with possibly inconsistent values.
Clipper (and therefore coot) use magic symmetry and cell repeat to allow
you to visualise the unique contents of the structure anywhere in space,
but as a result, they produce unpredictable results when the map header
disagrees with the map contents.
It is possible to fix the file by the following step:
mapmask mapin my.msk mapout new.map << eof
extend overlap
xyzlim asu
pad 0
eof
It would potentially be possible to include this step when reading a map
in coot. (Clipper would read the map as a non-crystallographic map, and
then convert it to a crystallographic map for coot). The problem is that
sometimes this is *not* what you want to do. I'm not sure what the best
way forward on this is - maybe a 'read mask' option which does exactly this.
Kevin
ohannes Romir wrote:
> Here the mask and a screenshoot of the result: Hope it is not too big.
>
> Johannes
>
>
> 2007/6/29, Kevin Cowtan <[log in to unmask]>:
>> If you send me the mask, I'll have a look and see if I can see the
>> problem.
>>
>> As a work around, you could try using ncsmask in CCP4 to make your mask
>> in the first place.
>>
>> Kevin
>>
>>
>> Johannes Romir wrote:
>> > Dear Cooters
>> >
>> > I am using coot 0.3.1 for OS X, and it seems coot has problems while
>> > displaying maps of masks, created with mama of USF. I converted the
>> > maps to ccp4-format and the map is displayed, but parts are missing.
>> > It looks like the map was sawed of two times in a 90 degree angle. The
>> > map itself works fine on O or pymol. Has anyone else encoutered this
>> > problem? Any suggestions?
>> >
>> > (I will gladly supply pictures and the maps)
>> >
>> >
>>
>
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