Dear all,

I'm willing to model a protein containing zinc atoms, something I've done successfully before using earlier versions of modeller. The template has protein and two zinc ions in chain A, and so I added two dots in the end of my alignment sequences, but I get the "Number of residues in the alignment and pdb files are different" message (the difference is actually the two additional residues). The FAQ (question #17) suggests running a simple script to see what Modeller is reading from the PDB and, running it on PDB 1HRA, I get this:

>P1;1hra structureX:1hra: 1 :A:+80 :A:MOL_ID 1; MOLECULE RETINOIC ACID RECEPTOR; CHAIN A; ENGINEERED YES:MOL_ID 1; ORGANISM_SCIENTIFIC HOMO SAPIENS; ORGANISM_COMMON HUMAN; ORGANISM_TAXID 9606:-1.00: -1.00 MPRVYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMIYTCHRDKNCVINKVTRNRCQYCRLQKCFEVGMSK ESVRN*

I.e., for some reason modeller only reads the amino acids and not the two zinc ions, and the last two dots are missing. What should I do to read the heteroatoms?

Lucas