These types of questions should be posted to jmol-users, not jmol-developers.
> But I have a problem with Jmol defined atoms color (type of atom) for
> some atoms.
> Looks as in the example below:
> If my script: the first part - 3 lines from 3DFR.pdb
> the second part - the same 3 lines without first later
> in atom name ( and greate X coordinate)
> HETATM 1300 AP NDP A 1 9.248 28.142 19.825
> HETATM 1307 AC3* NDP A 1 14.498 17.874 20.291
> HETATM 1331 NO3* NDP A 1 3.901 31.042 14.119
> HETATM 1300 P NDP A 1 14.248 28.142 19.825
> HETATM 1307 C3* NDP A 1 19.498 17.874 20.291
> HETATM 1331 O3* NDP A 1 8.901 31.042 14.119
The problem is that I am not recognizing the element type correctly.
Your file does not have the element identified in columns 77 & 78
(1-based). Therefore, Jmol tries to figure out what the the atom type is
by looking at columns 13 & 14 (1-based).
In this case, it is trying to find the element 'AP'
Q: What do the letters 'A' and 'N' mean in this case?
I am in the process of doing some work in this area of the code.
However, this is *not* going to fix your problem. You also have 'AC'. This
is a valid element symbol. Therefore, I recommend that your files follow
the PDB spec and have the element symbol in columns 77 & 78.
Q: Also, you can make recommendations for algorithms to figure out what
the element type should be based upon columns 13-16 (1-based).
> Rasmol and Jmol have different atoms color (type of atom).
If you prefer the RasMol colors, then you can say
set color rasmol