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 <[email protected]>
> *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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