ps -- you could also use
isosurface POCKET cavity 4.0
and remove the need for all that slabbing
Bob
On Tue, Feb 17, 2015 at 6:32 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> 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
>
>
--
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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