I think it is a version bug of some sort - when I ran the same mask
creation run in CCP4i on my MacBook laptop (which has the most recent
CCP4) it displays fine and also worked perfectly in dm averaging,
turning a tangled mess into interpretable density.
The mask generated by NCSMASK on my desktop Mac displayed weirdly in
COOT on that machine, and crashed COOT on the laptop as soon as I treid
to display it.
Anyway the job is done - thanks for the advice.
Laurence
Daniel Anderson wrote:
Could it be that NCSMASK folded the mask back into an asymmetric unit?
My NCSMASK input file contains explicit xyzlim boundaries and "notrim"
keyword.
On Tue, 18 Mar 2008, Laurence Pearl wrote:
I'm trying to generate a mask around a molecule using NCSMASK under
the CCP4i interface, for ultimate use in NCS averaging and density
modification in dm. Being a little old-fashioned I wanted to check
that it covered the required molecule. However when displayed in
COOT, there seem to be arbitary flat slabs running through the mask,
with some sort of inversion or other transformation on the other side
of the slab. The mask has a similar appearance in the CCP4mg. The
flattenings are parallel to cell edges, and sometimes, but not always
adjacent to cell faces.
Is this a known problem ? is it NCSMASK ? or is it COOT and CCP4mg ?
--
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Laurence H. Pearl PhD FMedSci
Professor of Protein Crystallography and Section Chairman
Section of Structural Biology, Institute of Cancer Research
Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB
Phone +44-(0)20 7153 5422 : Secretary 5443 : FAX 5457
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