Hi Bob,
here is how I understand it now
compare {22-31} {7-16} SUBSET {*.CA} ATOMS {24-31} {9-16}
this moves {22-31} {7-16} while minimizing the RMSD of the {24-31} {9-16}
Calpha pairs
and then there is the quaternion based approach which minimizes paired group
quaternion orientations
compare {22-31} {7-16} ORIENTATIONS {24-31} {9-16}
here you replace ATOMS with ORIENTATIONS and remove SUBSET {*.CA} (the
quaternion frame that is used must be given outside the compare command with
set quaternionFrame)
The documentation states that "if the SUBSET option is not specified, the
models are matched atom-for-atom based on 'SPINE' atoms..." . I thought that
"compare {22-31} {7-16}" would be the same as "compare {22-31} {7-16} SUBSET
{*.CA or *.C or *.N} ATOMS {22-31} {7-16}". Anyway, they say explicit is better
then implicit.
Best
Alexander
----- Ursprüngliche Mail -----
> Von: "Robert Hanson" <[email protected]>
> An: [email protected]
> Gesendet: Dienstag, 15. Mai 2012 14:18:49
> Betreff: Re: [Jmol-users] 'compare' probably broken in 12.3.10
> Alexander, that sound right to me. You can't compare two totally
> different sets of atoms, with different atom counts. That was an early
> flaw in the design that was fixed. Generally you would, for example,
> pick just the alpha carbons or just the backbone (includes O) or just
> the spine (C, CA, and N). So the correct command would be:
>
> compare {22-31} {7-16} SUBSET {*.CA}
>
> ah, but I think there's a bug there. You have to do it in this order:
>
> load =1crn;compare SUBSET {*.CA} {22-31} {7-16}
>
> That's a bug.
>
>
>
>
> On Tue, May 15, 2012 at 3:47 AM, Alexander Rose <
> [email protected] > wrote:
>
>
> Hi,
>
> I have problems with the compare command and 12.3.10 seems to be the
> first time it occurs.
>
> load =1crn;
> compare {22-31} {7-16} rotate translate;
>
> works in 12.3.9 but just says "RMSD NaN --> NaN Angstroms" in 12.3.10
> and later.
>
> Can someone confirm that.
>
>
> Best
> Alexander
>
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> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
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>
>
> 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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