Re: [Jmol-users] set ssbonds backbone

[Jan R. <jr...@im...>]

Miguel schrieb:

>>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.
>  
>
I agree.

>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.
>  
>
you are right, I had tried this I thought, but I had used ssbond instead 
of ssbonds:-)
this works fine, thank you, Jan

>
>I will look at the code and get back to you.
>
>
>Miguel
>  
>