Take a look at MAMA from Uppsala Software Factory
http://xray.bmc.uu.se/usf/mama_man.html
It can generate the mask from the PDB file. This will, however, leave
internal cavities belonging to "solvent". If you don't want that, the
following MAMA script will fix it giving you the mask of the protein
with its internal cavities
---
read m1 model.mask
not m1
island_erase m1
not m1
write m1 envelope.mask
---
I used this long time ago to correct for internal cavities in bulk
solvent correction(but may be better ways to do this, e.g. fill_voids
command). The output will be a (compressed) mask file. Unless you are
using O, it may need to be converted to map that coot can read (if you
want to visualize it). There is another excellent USF program MAPMAN
that can do this.
Ed.
PS. Apparently, all of the above can also be done in CCP4 - look under
Create/Edit masks in Map & Mask Utilities.
On Wed, 2010-08-11 at 16:37 -0700, Alastair Fyfe wrote:
> Does anyone know of software that will segment a unit cell into volume
> internal/external to a calculated molecular surface ?
> thanks!
> Alastair Fyfe
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
