[Chimera-users] morph problem

Tom Goddard goddard at sonic.net
Wed Mar 2 11:48:40 PST 2011

Hi Andres,

   The Chimera morph tool does nothing to avoid clashes -- parts of the 
structure can move right through other parts.  If that happens a 
solution is to make a new intermediate state that avoids the clash.  
Instead of morphing from 1 to 2, morph from 1 to 1b to 2.  How would you 
make this 1b state?  Here's an idea.  First make the morph from 1 to 2.  
Go to a point in the morph where the clash happens.  Then modify that 
structure, for example move the helix that is crashing into the RNA to 
some sensible position where it might go to get around the RNA.  How do 
you move the helix?  This where it gets ugly.  I would use the Chimera 
movement mouse mode (menu Tools / Movement) maybe in "move helix, 
strand, turn" mode and use the mouse and drag the helix where I want it 
to go.  Of course that will completely distort the connections at the 
ends of the helix making extremely long bonds.  So I would move the 
adjoining secondary structures, or maybe just several selected residues 
at each end to tidy this up.   It is still going to be energetically 
very bad.  Save the result to a separate PDB file as state 1b and try 
making a new morph from 1 to 1b to 2.  You could try energy minimization 
to clean up the mangled connections to the alpha helix, but the Chimera 
energy minimization tool has seen little development and is unlikely to 
work.  So do your best job placing
the structures by hand.

   This is of course a total hack.  But these morph animations are not 
intended to show how an actual transition occurs, just a graphic to show 
how 2 states differ from each other.  If you keep that in mind, maybe 
this hand-guided morph is acceptable.

   I haven' tried this and their may be unforeseen glitches.


>    Dear Chimera Users,
> I am trying to morph the complex1 and complex2 from the same system
> (protein-RNA) to make a video monitoring the conformational changes.
> As complex 1 is missing one domain and a helix (not visible in the
> crystal structure), I need to remove these parts in complex 2 to have an
> equal number of atoms in both complex and could morph it.
> The resulting video is not so nice because shows the gaps corresponding
> to the missing part. So, to avoid that, I have modelled the missing part
> in the complex 1 to have the same atoms, and afer morph it again to make
> the video, but this is not working.
> In the transition between complex 1 and complex 2, the RNA encounter one
> helix on the way that needs to move out to let the RNA  to get the
> position observed in complex 2. If I take out this helix, the video can
> perfectly be done, but still is not perfect because show gaps.
> Anybody could give an idea in how to solve the problem? We need the
> video to include in a publication,.
> Thanks in advance,
> Andrés Palencia

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