[sharp-discuss] Bug in mask files?

[Clemens Vonrhein]

Paul,

it's a 'feature' of SOLOMON to always set the spacegroup of the o/p
mask to P1. Another 'feature' is that the mask will have 0 and 1
swapped:

- a usual solvent envelope/mask has 1 in places of protein and 0 in
  solvent region

- SOLOMON masks have 1 in solvent region and 0 in protein part

So you need to revert this by doing:

  mapmask mapin solomon.msk \
          mskout solomon_new.msk \
          <<end_ip
  ! invert map
  SCAL FACT -1 1.0
  ! convert to mask
  MASK CUT 0.5
  END
  end_ip

Hope that helps.

Cheers

Clemens

On Mon, Mar 04, 2002 at 03:04:46PM -0600, Paul Hubbard wrote:
> Hi,
> 
> I have been having trouble with masks generated during the solvent
> flipping routine in SHARP. I used the last mask generated in the routine
> (t_cycle72.msk), and wanted to extend it round the part of the molecule
> I have already traced using MAPMASK in CCP4i. However, the programme
> says that the mask doesn't cover the A.S.U. I checked the file, and
> noticed the space group is set to 1 (p1). I edited the file so that it
> was set to the correct space group, and the extention worked fine.
> 
> Is this a bug - or have I assumed something incorrectly?
> 
> Thanks
> 
> AGS
> 
> --
> Paul Hubbard
> Dept. of Biochemistry
> Medical College of Wisconsin
> Phone: 414-456 4305
> Fax: 414-456 6510
> URL: iris9.biochem.mcw.edu
> 
> 
> 
> 
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> sharp-discuss mailing list
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