In addition to contouring differences, your mapmask script asks for
a border of only 2 A around the pdb file. If you're looking for
waters, unbuilt loops, or things on the edge of your pdb file, this
will need to be larger. When I used O and created the maps over the
pdb file of interest I used a border at least 5 A.
>
>
> On Feb 14, 2007, at 9:58 AM, mac minista wrote:
>
>> Hi,
>>
>> thank you for your suggestions, the difference I am
>> seeing in the maps is mainly with the Fo-Fc maps i.e.
>> what appears in coot does not always appear in
>> O/Pymol. Here are the scripts for FFT and MAPMASK:
>>
>> FFT
>>
>> #!/bin/sh
>>
>> set -e
>>
>> fft hklin model.mtz mapout fofc_f.map <<eof
>> title fofc map
>> labin F1=FOFCWT PHI=PHFOFCWT
>> end
>> eof
>>
>> #
>> fft hklin model.mtz mapout 2fofc_f.map <<eof
>> title 2fofc map
>> labin F1=2FOFCWT PHI=PH2FOFCWT
>> end
>> eof
>>
>> MAPMASK
>>
>> #!/bin/sh
>>
>> set -e
>>
>> # Run mapmask after fft to extend the map
>> mapmask mapin fofc_f.map mapout fofc_fext.map \
>> xyzin model.pdb <<eof
>> border 2.0
>> eof
>> #
>> mapmask mapin 2fofc_f.map mapout 2fofc_fext.map \
>> xyzin model.pdb <<eof
>> border 2.0
>> eof
>>
>> I will try and get some figures.
>>
>>
>> Regards
>> Mac
>>
>>
>>
>> _____________________________________________________________________
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Sue Roberts
Biochemistry & Biopphysics
University of Arizona
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