Hi Bob,
As to your observations on our scripting, our application generates the script
from sliders, checkboxes, and list selections and could be smarter. Thanks for
the suggestions.
--Chuck
----- Original Message -----
From: Robert Hanson
To: [email protected]
Sent: Saturday, June 26, 2010 11:27 AM
Subject: Re: [Jmol-users] Bug or Feature? "display WITHIN(2.0,selected)" does
not hide isosurface
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 <[email protected]> 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
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