Hi Bob,
The isosurfaces that we create are for protein chains and are thrown away and
recreated every time the user changes the set of selected protein chains (with
a list control) or the radius of the isosurface (with a slider). We also have a
slider for the transparency of the isosurface. That is why we were interested
in the isosurface generation performance. We really appreciate the work you
did with Ivan on that.
Many thanks,
--Chuck
----- Original Message -----
From: Robert Hanson
To: Charles Shubert ; [email protected]
Sent: Saturday, June 26, 2010 1:16 PM
Subject: Re: [Jmol-users] Bug or Feature? "display WITHIN(2.0, selected)"
does not hide isosurface
Sure. Just make sure if the selections involved are to change the display of
the isosurface, you have to create the isosurface again. Not out of the
question, though, that we could set it up so that
isosurface within 2.0 {whatever}
would act on an existing isosurface....
Bob
On Sat, Jun 26, 2010 at 11:31 AM, Charles Shubert <[email protected]> wrote:
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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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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