Gerzon, 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 Miguel ------------------------------------------------------- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
