I broke the COMPARE command in 12.2.25 and 12.3.25. Darn. Can't believe I
didn't test that. Definitely working too fast....
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
On Mon, May 21, 2012 at 12:37 AM, Eric Martz <[email protected]>wrote:
> Dear Bob,
>
> The following is in a fresh start of 12.0.31:
>
> $ load 1a4f.pdb
> $ cartoon only
> $ color chain
> $ compare {:a} {:b} subset {*.ca} rotate translate
> RMSD 8.78 --> 2.32 Angstroms
>
> $ zap
>
> $ load 1a4f.pdb
> $ load append 1a4f.pdb
> 2 models
>
> $ cartoon only
> $ color chain
> $ compare {2.1} {1.1} subset {*.ca} rotate translate
> RMSD 0.0 --> 0.0 Angstroms
> $
>
> The following is in 12.2.25:
>
> FIRST TRY:
>
> $ load 1a4f.pdb
> OXYGEN TRANSPORT 29-JAN-98 1A4F
> BAR-HEADED GOOSE HEMOGLOBIN (OXY FORM)
>
> $ cartoon only
> $ color chain
> $ compare {:a} {:b} subset {*.ca} rotate translate
> script ERROR: invalid argument
> ----
> compare { *:a } { *:b } << subset { *.ca } rotate translate
> $
>
> SECOND TRY (after closing and re-starting Jmol):
>
> $ load 1a4f.pdb
> OXYGEN TRANSPORT 29-JAN-98 1A4F
> BAR-HEADED GOOSE HEMOGLOBIN (OXY FORM)
>
> $ load append 1a4f.pdb
> 2 models
>
> $ frame all
> $ cartoon only
> $ color chain
> $ compare {2.1} {1.1} subset {*.ca} rotate translate
> script ERROR: invalid argument
> ----
> compare { 2.1 } { 1.1 } << subset { *.ca } rotate translate
> $
>
> -Eric
>
>
> At 5/20/12, Robert Hanson wrote:
> >what in the world happened to your version, Eric?
> >
> >Try that same thing at
> ><http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm>
> http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm
> >and see if there's the same problem. You can drag/drop PDB or JMOL
> >files into that if you want.
> >
> >On Sun, May 20, 2012 at 8:48 PM, Eric Martz
> ><<mailto:[email protected]>[email protected]> wrote:
> >Dear Bob,
> >
> >I cannot get compare to work in 12.3.25 or 12.2.25.
> >Compare works in 12.0.31, but then I cannot write out the aligned PDB
> result!
> >
> >
> >script ERROR: invalid argument
> >----line 19 command 20 of something.spt:
> > compare { 2.1 } { 1.1 } << subset { *.ca } rotate translate
> >----
> >
> >Thanks, -Eric
> >
> >
>
> >------------------------------------------------------------------------------
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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>
> 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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>
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> threat landscape has changed and how IT managers can respond. Discussions
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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
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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