Yes, that's probably the most straightforward way. No { } or spaces
necessary around @n:
compare {1.1} {2.1} SUBSET {*} ATOMS @1@2 @2@3 @3@4 @4@1 rotate translate
2
"@2" represents "atomno=2" in both models, but the {1.1} and {2.1} do the
appropriate filtering so that it will be 1.1&@1 2.1 & @2 1.1 & @2
2.1&@3 etc.
I don't think you need the SUBSET {*} part. The idea for that is that you
might have proteins and just want to correlate the CA atoms --- SUBSET
{*.CA}, for example.
compare {1.1} {2.1} ATOMS @1@2 @2@3 @3@4 @4@1 rotate translate 2
The alternative is to just use the description of the first set and an
array for the second:
compare {1.1} {2.1} ATOMS {atomno < 5} [@2 @3 @4 @1] rotate translate 2
Another possibility would be to use a SMARTS string, if the structures are
similar. An example of that is the "Flexible Fit" example at
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm. That example uses this
compare statement:
sm = "c1ccccc1CCN"
compare {1.1} {2.1} SMARTS @sm rotate translate
The SMARTS matching orders the atoms in appropriate pairs.
Also, if it makes life easier the COMPARE command ignores commas:
compare {1.1} {2.1} ATOMS @1@2, @2@3, @3@4, @4@1 rotate translate 2
One of those should work!
Bob
On Fri, Feb 28, 2014 at 8:02 AM, Angel Herráez <angel.herr...@uah.es> wrote:
> Hello Jiayi
>
> I have used this before, but do not remember the details.
> To me, paired list meand one atom from each model. The xample in the
> documentation also looks like that.
> Also, the simple numbers are not good for atom numbers; they mean
> residue numbers in proteins or nucleic acids (see "atom expressions"
> in the doc).
>
> I suggest trying
>
> compare {1.1} {2.1} SUBSET {*} ATOMS {atomno=1} {atomno=2} {atomno=2}
> {atomno=3} {atomno=3} {atomno=4} {atomno=4} {atomno=1} rotate
> translate 2
>
> You may possibly use the shorthand notation for atom numbers:
>
> compare {1.1} {2.1} SUBSET {*} ATOMS {@1} {@2} {@2} {@3} {@3} {@4}
> {@4} {@1} rotate translate 2
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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