Re: [Jmol-users] nucleic acid cartoons bug

[Bob H. <ha...@st...>]

Bob Hanson wrote:

>> There is still the problem of the 5'-terminal portion being colored 
>> red instead of orange when that P atom is missing; likely due to 
>> specific models, not that important.
>>
>>  
>>
> I'll check into that. Is a bit strange.
>
> Bob
>

When the phosphorus is missing, the default is to assign the "lead atom" 
for that group -- the one defining the trace and the color -- to be the 
last atom in the set. In this case it is

ATOM     30  H5T   A     1       6.651   9.928   6.121  1.00  1.43      
143D 112

Being hydrogen, its color is white. So that sets the color for the whole 
group. Using

cartoons 0.01

you can see it better. Probably it's good that it does this -- an 
indication of the 5' end. On models not having hydrogens it is probably 
red and goes through  O5*. If it is not desired, you can just use

select nucleic
color [xff8000]


Bob