Re: [Jmol-users] Bug or Feature? "display WITHIN(2.0, selected)" does not hide isosurface

[Robert H. <ha...@st...>]

Chuck,

feature, not bug.

Isosurfaces are not included in the "display" command. Display, hide, select
-- these are all just atom selections, not objects. But you can create the
isosurface within the specified range first, then display it...



# Select 6 amino acids, hide everything that isn't selected, then display
anything within 100.0 VDW radii of the amino acids' atoms
subset; select {{PROTEIN and {[THR]1:A or [THR]2:A or [CYS]3:A or [CYS]4:A
or [PRO]5:A or [SER]6:A}}};
hide not selected;

#>BH> [why this?] display WITHIN(100.0, selected);

display WITHIN(2.0, selected);

# Show the isosurface for Chain A

#>BH>parallel isn't gaining you anything here because you are only
specifying one process.

subset; parallel makeIsos{process{


#>BH>now do the WITHIN option for isosurface; also modified your ignore
parameter just for looks: select  ...x... ignore ... not x....

subset; select {A and PROTEIN};
isoSurface surfaceA within 2.0 {selected} select(within(chain,*:A)) ignore
(not within(chain,*:A)) VDW 90 % color TRANSLUCENT 230.4 [192,208,255]
NOFILL molecular;

}}; set multiProcessor true; show mulitProcessor; makeIsos;

Bob


On Fri, Jun 25, 2010 at 11:38 AM, Charles Shubert <csh...@mi...> wrote:

> Bug or Feature? "display WITHIN(2.0, selected)" does not hide isosurface.
>  Script below.
>
> Thanks,
>
> --Chuck
>
> # Test script
> load http://pdb.rcsb.org/pdb/files/1CRN.pdb;
>
> # Show the helices
> subset; select {[ILE]7:A or [VAL]8:A or [ALA]9:A or [ARG]10:A or [SER]11:A
> or [ASN]12:A or [PHE]13:A or [ASN]14:A or [VAL]15:A or [CYS]16:A or
> [ARG]17:A or [LEU]18:A or [PRO]19:A or [GLU]23:A or [ALA]24:A or [ILE]25:A
> or [CYS]26:A or [ALA]27:A or [THR]28:A or [TYR]29:A or [THR]30:A};
> structure HELIX {{[ILE]7:A or [VAL]8:A or [ALA]9:A or [ARG]10:A or
> [SER]11:A or [ASN]12:A or [PHE]13:A or [ASN]14:A or [VAL]15:A or [CYS]16:A
> or [ARG]17:A or [LEU]18:A or [PRO]19:A or [GLU]23:A or [ALA]24:A or
> [ILE]25:A or [CYS]26:A or [ALA]27:A or [THR]28:A or [TYR]29:A or
> [THR]30:A}}; color ribbons structure; ribbons 1.66;
>
> # Show the sheet
> subset; select {[THR]1:A or [THR]2:A or [CYS]3:A or [CYS]4:A or [CYS]32:A
> or [ILE]33:A or [ILE]34:A or [ILE]35:A};
> structure SHEET {{[THR]1:A or [THR]2:A or [CYS]3:A or [CYS]4:A or [CYS]32:A
> or [ILE]33:A or [ILE]34:A or [ILE]35:A}}; color ribbons structure; ribbons
> 1.66;
>
> # Show the turns
> subset; select {[PRO]5:A or [SER]6:A or [GLY]20:A or [THR]21:A or [PRO]22:A
> or [GLY]31:A or [PRO]36:A or [GLY]37:A or [ALA]38:A or [THR]39:A or
> [CYS]40:A or [PRO]41:A or [GLY]42:A or [ASP]43:A or [TYR]44:A or [ALA]45:A
> or [ASN]46:A};
> structure TURN {{[PRO]5:A or [SER]6:A or [GLY]20:A or [THR]21:A or
> [PRO]22:A or [GLY]31:A or [PRO]36:A or [GLY]37:A or [ALA]38:A or [THR]39:A
> or [CYS]40:A or [PRO]41:A or [GLY]42:A or [ASP]43:A or [TYR]44:A or
> [ALA]45:A or [ASN]46:A}}; color ribbons structure; ribbons 1.66;
>
> # Show the isosurface for Chain A
> subset; parallel makeIsos{process{ subset; select {A and PROTEIN};
> isoSurface surfaceA select(within(chain,*:A)) ignore (within(chain,not *:A))
> VDW 90 % color TRANSLUCENT 230.4 [192,208,255] NOFILL molecular;}}; set
> multiProcessor true; show mulitProcessor; makeIsos;
>
> # Select 6 amino acids, hide everything that isn't selected, then display
> anything within 100.0 VDW radii of the amino acids' atoms
> subset; select {{PROTEIN and {[THR]1:A or [THR]2:A or [CYS]3:A or [CYS]4:A
> or [PRO]5:A or [SER]6:A}}};
> hide not selected;
> display WITHIN(100.0, selected);
>
> # now display within 2 VDW radiis the selection
> # NOTE: the isosurface doesn't behave like the structures. The entire
> isosurface continues to be displayed.
> # QUESTION: Is this a bug or a feature?
> display WITHIN(2.0, selected);
>
>
>
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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