[Chimera-users] Morph conformation - conformation collapsing

Helge.Paternoga at bzh.uni-heidelberg.de Helge.Paternoga at bzh.uni-heidelberg.de
Tue Mar 18 03:06:26 PDT 2014


Hello,

I'm trying to morph two structures which have two chains each. The 
problem is that if I just add the two confirmations one chain will turn 
the wrong way, because it is taking the shortest distance to the final 
position.

What i did now is I used this initial morphing to extract 4 frames of 
the movement of the other chain and inserted the movement of the smaller 
chain in each of these structures by hand (so the movement is in the 
right direction and happening at the same time as the other chain).

But when I now add these 4 structures in my morph confirmation list like 
this:

Start confirmation
frame 1
frame 2
frame 3
frame 4
End confirmation

It nicely starts moving in the right way but then at a transition to a 
new frame the whole structre collapses, bonds get distorted, it somehow 
shrinks and  then extends again later to end up at the final 
confirmation...

I think this is independent of which frame i use (I tried to simplify it 
by using only 2 intermediates)

Do you have any idea what is causing this collapse? The initial 
confirmation has the same number of chains as the end confirmation (with 
the same names) but they have a different number of atoms (which i don't 
quite understand because they are the same macromolecules...) Could this 
be part of the problem?

best regards,

Helge


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