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*