[Jmol-users] Drawing isosurface cavities after excluding occupying atoms

[Alan H. <he...@il...>]

On 11 February 2010 20:40, Robert Hanson <ha...@st...>  wrote:
>
>  {atomno < 10}.property_abc = 3

OK, as before I select atoms I want to exclude but then instead of hiding
them I assign them a property_abc=3 (not sure why the property value is
limited to a number <10 but it doesn't matter)

{selected}.property_abc = 3

Then I simply do:
selectionHalos OFF;select all and visible;isosurface cavity resolution 2.0
ignore(property_abc = 3) minset 5 cavity 0.4 sasurface 0.15;color
isosurface blue;isosurface fullylit

instead of:
selectionHalos OFF;select all and visible;isosurface cavity resolution 2.0
ignore(hidden) minset 5 cavity 0.4 sasurface 0.15;color isosurface
blue;isosurface fullylit

The latter ignores all the hidden atoms surrounding the cell, which causes
the isosurface to blow out at the cell edges.

BTW I think you added the isosurface qualifiers INTERIOR and POCKET to
satisfy Christian, but finally I dropped the distinction; whether a
surface is closed or open depends anyway on the probe parameters. And I
use a small minset because it is quite interesting to check for cavities
only big enough to accomodate a single ion/atom.

It took me a while, since I am less familiar with the syntax than you
imagine :-) And I posted this to the list because it may be of general
interest.

Thanks again Bob, Alan.

> On Thu, Feb 11, 2010 at 1:35 PM, Alan Hewat <ala...@ne...>
> wrote:
>>
>> > You could create your own property name and assign it to just the atoms
>> > you want, then select those.
>>
>> Yes, I thought to assign them as "solvent" for example - when I work
>> out how to do that...
______________________________________________
Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
<Ala...@Ne...> +33.476.98.41.68
      http://www.NeutronOptics.com/hewat
______________________________________________