I recommend
isosurface cavity 4.0
This will create a cavity based on a solvent-accessible surface with probe
radius 4.0, which is sufficient to get rid of all but the helical core.
Alternatively you could use
isosurface set 1 cavity
and just pick up the largest cavity that way.
Bob
On Mon, Feb 16, 2015 at 7:12 PM, Eric Martz <ema...@microbio.umass.edu>
wrote:
> The (theoretical) model available here
>
> https://www.dropbox.com/sh/ma70sia6zz7oa11/AADXgWY-X4PBv51LR_uF3XV5a?dl=0
>
> is a fiber with a helical channel down its center. The channel is
> roughly 12x17 Angstroms in diameter.
>
> I can visualize the inside channel surface as follows (be patient, 20K
> atoms):
>
> load Pseudomonas-pilus-PubMed15100690.pdb
> rotate x -90
> hide all
> isosurface resolution 1.0 solvent
> slab 51
> depth 0
> slab on
> axes
>
> How would I get just the channel as a surface object, without the
> surface of the rest of the model?
>
> (It happens that the long axis of this model is the Z axis.)
>
> Thanks! Eric
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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