On Tue, May 15, 2012 at 8:31 AM, Alexander Rose <[email protected]
> wrote:
> 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.
>
>
I've adjusted it a bit, and I think now it is as you imagined.
I was wrong about putting SUBSET first -- that was allowed but not
relevant. I've got SUBSET first now (12.3.25) throwing an error.
>
> 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
> > 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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--
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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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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