Re: [Jmol-users] Insertion code specification syntax

[timothy d. <mol...@ma...>]

at 2.18p EDT on 2003 December 15 Monday Jan Reichert said:

> Miguel Howard wrote:
> >
> >If there was another package or scripting language that supported
> >insertion codes then we should look to it as an example.
> >  
> >
> insightII appends it to the residue number but if you want to implement 
> 271e as 271:e, which I suggest not to do, this would case problems.
> I think you only need to implement the explicit syntax, 271:e
> and I change my vote and will now vote for
> [HIS]84D:A.CA;B/1
> (and this should be implemented in the next RasMol, too:-)
> 
if Jmol does not support the chain syntax without colon, you will introduce a
serious compatibility problem with rasmol and chime.  especially if the
syntax switches to indicate insertion code instead!  while I understand the
argument for simplification, existing scripts that refer to chains are much
more abundant than scripts that refer to insertion codes (sorry, Jan).



> as it is so close to the sequence number, I suggest not to use a single 
> character, but may be this should be discussed together with the RasMol 
> list, because I hope that insertion code would be implemented in RasMol, 
> too.
> 
> >If we use a single character ...
> >
> >  I would prefer one of:
> >    1~A 1@A 1$A 1%A 1^A 1_A 1=A
> >  

I have no strong preference for any specific char, but if pressed, I would
vote for

   1^A

the ^ is (or was) a common way to indicate an insertion when editing a
document on paper.


my two cents,

:tim

-- 
timothy driscoll
molvisions - molecular graphics & visualization
<http://www.molvisions.com/>
usa:north carolina:wake forest