[Chimera-users] Morph conformation - conformation collapsing

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 18 11:12:37 PDT 2014


Hello Helge,
Your idea of using intermediates to make the morphing go in the desired direction sounds reasonable. I'd probably try the same thing.

I don't know why the resulting morph would collapse.  In general, different numbers of atoms in the start and end structures are not a problem; the tool was meant to handle that by simply omitting unpaired atoms from the morph trajectory.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#pairing>

However, when you make an initial morph trajectory and then save some frames as PDB, those resulting files may be somewhat abnormal because of the missing atoms (those that weren't paired between the original structures), which might in turn confuse the morph calculation when they are used as input.  That's only a guess, without seeing your exact files.  Just now I tried a similar process except with morphing between different proteins (so that several atoms were missing from the intermediates), and I did see one part of  the molecule that looked strange in the resulting secondary morph when intermediates from the first morph were used in combination with the original structures as inputs.  

Without spending a lot of time to figure out exactly what happened or which atoms seemed messed up, I was able to work around this by also saving the first and last frames from the first morph and then using them as inputs to the second morph calculation INSTEAD of the original PDB files.  Although this really shouldn't be necessary, I recommend that you try a similar workaround.  If that still doesn't work, you could try using Help… Report a Bug and attach a session (if you don't  mind sharing your files) and description of how to reproduce the problem.

Other ideas are to make sure the intermediates are correctly superimposed on the start and end,  and maybe try a different interpolation method, although usually the default corkscrew method works best for me).  I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 18, 2014, at 3:06 AM, "Helge.Paternoga at bzh.uni-heidelberg.de" <Helge.Paternoga at bzh.uni-heidelberg.de> wrote:

> 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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