[Chimera-users] Morph with Chimera: how to make visible connection/interaction in Morph

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 18 11:34:38 PDT 2011

Hi Wenhe,
If the morph trajectory includes the metal ion, you could just display it and nearby residues with commands something like

sel #2 & ions
disp #2 & sel z<4

(in that example the trajectory is model 2).  

If you already see the metal ion and those atoms but no lines between them, that is a different issue -- if that's the problem, let us know, and I can give more explanation of how to add the lines.

However, I suspect the morph trajectory does not include the ions.  I just tried morphing between two structures that both contain a Ca++ ion, 2gbp and 2fw0, but the resulting morph trajectory only included the protein part, even if I edited the files first so that the Ca++ had the same residue number.

The morph trajectory is supposed to include the atoms that are in both input structures, but for some reason the Ca++ ion is not recognized as being the same.  I don't know how easy this would be to fix (I'm not one of the programmers), but I will report this as a bug and include your email address so that you will receive update messages if anything happens.  Maybe somebody else has an idea of how to work around this problem?

Sorry about that,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 18, 2011, at 9:40 AM, WENHE ZHONG wrote:

> Dear all,
> I would like to show the visible metal-residue interaction during the Morph movie. Anyone knows how to do that in Chimera? Thank you.
> King regards,
> Wenhe 

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