Jmol/Storymorph: Difference between revisions

This is a draft documentation for [[Image:storymorph.spt]], a suite of Jmol functions to help with superimposing and morphing between two structures representing different conformations of a molecule or molecular assembly. For more general information, see [[Jmol/superposition]] and [[Morphs]]. If you load storymorph.spt into a Jmol session where no structures have loaded, it will run a demonstration superposition and morph based on calmodulin strutures. Most examples in this documentation are from this demo.

 

If the anchor selection is part of another domain, the morph algorithm will ensure that the distance of the domain to the anchor remains constant throughout the morph. In essence, the other domain "drags along" the domain in question. To maintain connectivity between domains linke by a single covalent bond, an appropriate anchor would be the atom or residue the domain is directly attached to. If their are multiple covelent connections between domains, you can choose the anchor to include all the connection points.

  <nowiki>load files "=1prw" "=1cll"</nowiki>

Here, the selection is the first and the second structure loaded. For models in a single-structure file, you would use "1.1" and "1.2" instead. For subunits with different conformation, you would select by chain name, e.g. "chain=A" and "chain=B". More complicated cases are possible (chain B of the second model vs. chain A of the third model) but probably rare.

The superimpose function works the same way as the Jmol compare function, but it first verifies the required atom selections to prevent Jmol from crashing or freezing. The superimpose function takes two or three parameters. The first paramenter always defines the two structures (see above). The second parameter is either a single domain selection (when calling with two parameters), or it is the list of list describing all domains, with the third parameter an integer designating which domain is to be used in the superposition. The superposition leaves the  first structure in its original orientation and moves the second structure to minimize the distances between corresponding atoms (defined by the domain selection). Different from the morph function, the superposition function alters coordinates for the remainder of the session. Because morphs connect initial and final atomic positions with a path, the orientation of the final state with respect to the initial one is crucial, and the choice of superposition defines this orientation. Said in a different way, you get a different morph if you choose to superimpose the two structures in a different way before starting the morph.

== Examples ==

superimpose(structures, domains[1])

  <nowiki>load apo.pdb

morph(20, conformations, domains, timing)</nowiki>

==Live example==

<StructureSection load='' size='350' side='right' caption='' scene=''>

This live example uses the structures of calmodulin [[1prw]] and [[1cll]]. We first load and display the two structures, and then you can click on the buttons below to superimpose and morph. Try different combinations to get a feel for what is possible.

structures = [{1.1}, {2.1}];

domains = [[{78-147},{78-147}, {(78-138)}], [{4-77}, {78}],];

timing = [[0,1,0],[0,1,0]]

Choose a morph

    <script>domains = [[{78-147}], [{4-77}, {78}],]; morph(20, structures, domains, timing);</script>

    <script>morph_skiprigid=1;domains = [[{4-147}],]; morph(10, structures, domains, timing);morph_skiprigid=0;</script>

      <script>timing = [[0,1,0],[0,1,0]] </script>

      <script>timing = [[0,1,1],[0,1,1]]</script>

Parameters that tweak the morph

{{subst:Mid-morph break|morph_pause = 1|morph_pause = 0}}