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

Eric Pettersen pett at cgl.ucsf.edu
Thu Aug 18 11:51:06 PDT 2011

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 Pettersen
                         UCSF Computer Graphics Lab

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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> Chimera-users at cgl.ucsf.edu
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