[Chimera-users] question

A G Szabo agszabo at bell.net
Mon Mar 14 19:57:44 PDT 2016

I have included a part of a structure in this Email.

In January Elaine Meng communicated with me about how to color an individual
atom in an amino acid that is shown as a ball and stick.

So you see I have colored an oxygen atom red in a threonine residue that is
part of a peptide that is bound to the protein that is mainly shown as a
ribbon structure.

Note the Glutamic acid residue shown only as a stick and colored lime green.
The peptide backbone of this residue which is in a ribbon representation is
also colored lime green

So question #1, how can I just color the side chain and not the peptide bond
which is in the ribbon. I want to keep the ribbon a continuous blue.

 Note the Aspartic acid residue that is part of pink ribbon and represented
as a ball and stick. So I want to color the side chain the same lime green,
I know how to do that, but again the ribbon part of that Asp will also be
lime green.

Even if all I want is to have one of the oxygen atoms of the side chain
colored red, I can do that as well except that the ribbon portion, the
peptide bond also is colored red.

Question #2: There is a metal ion colored light blue or cyan, How can I get
rid of the four short dashed lines that link it to the aforementioned Glu
and Asp, as well as another Asp residue?


Thank you for your assistance.

Arthur G. Szabo

Professor Emeritus
Wilfrid Laurier University.
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