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

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 18 14:08:46 PDT 2011

Hi Wenhe,
As Eric mentioned, in some cases the morph does have the metal ion, but not the metal complex bonds.  I will file that as another bug report.

In the meanwhile, however, if that is the problem you can add the metal complex bonds yourself.  First display the atoms that might be interacting with the metal (example command:  disp ions z<4).  Also, the ribbon hides the backbone atoms, so if you want to see the backbone atom exact positions, hide ribbon too, maybe the whole ribbon (~ribbon) or just the ribbon near the ions (~ribbon ions z<4).  Now that the atoms are shown, there are at least two different ways to add the metal complex bonds.

(A) If you already know exactly which atoms should have lines to the metal, you can just make distance measurements from the metal to each of those, then hide their labels showing the distance values.  This can be controlled in the Distances panel (under Tools... Structure Analysis), set "Labels" to "None."
For how to add distance measurements and change their appearance, see:

- OR -

(B) you can use Metal Geometry (under Tools... Structure Analysis) to identify the possible coordinating atoms and also add the lines.

Example using Metal Geometry:
I opened PDB 2l4i as model 0, and since it is an NMR model there are multiple submodels 0.1-0.10.  I used 0.1 and 0.2 as input to morphing, creating a morph trajectory that is model 1.  

In Metal Geometry,
- I chose #1 MG 500.A MG (model 1, atom name MG, residue 500 in chain A also named MG) from the menu of metal ions.
- clicked on a line in the Coordination Table to choose which atoms are considered coordinated
- clicked the "Create/Update" button to show the metal complex bonds

Then, when you play the morph trajectory those same bonds will be shown throughout regardless of how those atoms move around.

I hope this helps,

On Aug 18, 2011, at 11:51 AM, Eric Pettersen wrote:

> Hi Elaine,
> 	Well if the structures have identical atomic composition, such as the models of NMR entry 2L4I, then the ions are retained in the morph.  That's not to say that the failure to retain the ion between 2gbp and 2fw0 isn't a bug, just that there is some chance that Wenhe's morph retains the ion.  You should definitely Trac the 2gbp/2fw0 thing so we can work on making ion-retention better.  Also, even for 2L4I the metal-complex pseudobonds aren't retained so that could be improved too.
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
> On Aug 18, 2011, at 11:34 AM, Elaine Meng wrote:
>> 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
>> ----------
>> 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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