David, you can do this using some sort of user-defined functions within
a script. You would, for example, select a group, scale it (I presume
you mean move it as a group, not scale the bond distances), and move on.
Your service would have to define the vectors, but Jmol could run though
all the groups and correlate the vector with the group. This could be
directed by JavaScript or run using Jmol script functions.
You might also think about ways you could do this visually, without the
translations.
I suggest quaternions. A quaternion relative difference map ("quaternion
r difference"command) will precisely describe the orientations of groups
*relative to each other* rather than the translational aspects. The two
would not have to be oriented in any way the same in space, because
quaternion r difference (and "quaternion r difference2" -- the second
derivative) are independent of that. Sounds like a perfect fit to me.
You should add the following setting
set PdbSequential TRUE
This will to Jmol that your listed atoms in PDB format should be
considered connected between groups even if their bonding does not
suggest it.
Bob
[EMAIL PROTECTED] wrote:
> Certain empirical cases published at “StrucClues” (
> http://strucclue.ornl.gov <http://strucclue.ornl.gov/>) identify pairs
> of tertiary substructures A and B, where it is intuitively obvious
> that A is a more “compact” version of B.
>
> Not a “smaller” version of B, in the sense that A lacks a helix or
> strand that is present in B.
>
> But rather, a more “compact” version of B, in the sense that A has
> less residues per helix, and/or less residues per strand, and/or less
> residues per turn.
>
> Since such pairs of tertiary substructures were identified using a
> novel methodology (SCILD) that does not depend on any degree of
> primary structure sequence homology between substructures A and B, it
> is impossible to do a principled structural alignment of A and B using
> gap insertions because there is no principled reason for putting the
> gaps one place rather than another. (See StrucClues site for
> explication of the SCILD methodology.)
>
> So … under the assumption that StrucClues cases of this type actually
> do reflect some “real” or “valid” aspect of tertiary structure, it
> would seem that the only way to “align” substructure A with
>
> substructure B would be by “scaling up” A or “scaling down” B. By
> “scaling up”, I mean artificially
>
> increasing the distiance between any two residues r(i) and r(i+1) of
> A, without changing the orientation of r(i) with respect to r(i+1).
> (And vice-versa, for “scaling down”.)
>
> How easy would it be to add such a “scaling” capability to JMol displays?
>
> Assuming again, of course, that it is empirically defensible to do
> such scaling (based on the kinds of cases accumulating at StrucClues)?
>
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--
Robert M. Hanson
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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