I agree.Now I noticed, that the ssbonds could not be colored independently, e.g.
with 1crn
http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1crn
ssbonds on
set ssbonds backbone
renders two lines, a yellow between the *.SG atoms and a green between
*.CA,
Thanks for giving me feedback on this.
This is about the first feedback I have received on ssbonds ... it probably has some bugs
The reason the ssbonds are green is because your backbone carbon atoms are green.
I do _not_ plan to implement ssbonds in exactly the same way as
RasMol/Chime. I may be mistaken, but I believe that RasMol does *not* show
ssbonds by default. And they are not affected by normal 'wireframe'
commands. This is a mistake. ssbonds are normal covalent bonds and should
be detected and rendered and should behave like any other bond.
you are right, I had tried this I thought, but I had used ssbond instead of ssbonds:-)Now, I understand that we want to have this 'special' behavior of 'set ssbonds backbone' so that we can show these disulfide linkages in backbone/cartoon representations.
I expected ssbonds backbone to toggle between these renderings and
the backbone connection to be yellow, too.
I think that you are right. In this cartoon representation I agree that you want to see yellow bonds between the backbone and that you don't want to see the bond between the actual Sulphur atoms.
My be it would be desirable to have a
set ssbonds backbone [only|and] and a
color ssbond yellow command,
and what about an set ssbonds cartoon only command.
Those are good ideas.
It looks like you can currently say 'color ssbonds yellow'
and that will explicitly fix part of the problem.
this works fine, thank you, Jan
I will look at the code and get back to you.
Miguel
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