[Chimera-users] Hide (pseudo-)bond between neighboring residues

Konstantin Richter konstantin.richter at bbz.uni-leipzig.de
Thu Feb 18 03:22:39 PST 2021

Dear Chimera Community,
I currently experience some trouble hiding certain bonds that Chimera  
automatically displays. But first things first:

I want to design a figure of the active site of two very similar  
protein structures (models #0 and #1; let's assume they are mutants of  
the same molecule differing in only a few amino acid residues). I  
therefore display the ribbon as well as certain residues of model #0.  
Additionally, I align #1 on #0 and display the same residues in #1,  
but without the ribbon. So, the side chains of #1 should end in the  
ribbon of #0 (which is basically identical to ribbon #1). Since  
Chimera automatically displays all atoms of the residues when the  
respective ribbon is hidden, I also hide C,O,N of #1 residues. Now  
this looks fine expect for one thing. Chimera creates long  
(pseudo?)bonds between the CA atoms of residues that follow one  
another in sequence, e.g. res 64 and 65. This very long 'bond' messes  
up my figure, and I haven't yet figured out how to delete or hide it.

I already tried the ~bond #1:64-65 at CA command, but this one hides ALL  
bonds in residue 64 (but not the one between 64-Ca and 65-Ca) and  
other variations of the atom specifier. Is something wrong with my  
atom specification, or is this command not suitable for what I want to  
do? I also tried the bonddisplay command without succes, since it  
deletes all bonds in one residue.

In the end, I want the residues of #1 to contain all atoms except for  
C,N,O including bonds between all atoms, but not the elongated  
connection between Ca atoms.

best regards
Konstantin Richter
P. Konstantin Richter - M.Sc. Biochemistry
Department of Structure Analysis of Biopolymers - Institute of  
Bioanalytical Chemistry
Center for Biotechnology and Biomedicine (BBZ) - Leipzig University
Deutscher Platz 5
D-04103 Leipzig

Tel.: +49 341 9731316

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