Wishlist/Missing residues

Lucas Bleicher writes:

I use Modeller for about two years and I can rarely set up a .PIR file and run the program with no errors for the first time (and have seen many times questions on alignment errors here). This is not really Modeller's manual fault - I think that what causes most of those errors is that the sequence listed on a PDB entry does not always correspond to what is really on the PDB file. Some entries include, for example, His-tags which are never visible and also residues which could not be seen on electron density maps and therefore were not modeled. Setting up the .PIR file sometimes means to search for missing or modified residues (e.g. Se-Met or modified Cysteines) on a PDB and then fix the alignment file, something that can be really boring in some cases. I have developed a "semi automatic" approach to do that, but perhaps it would be interesting to include on newer versions of modeller a routine to parse the PDB, compare it with the sequence on the alignment file (which may include these missing residues) and fix the file.

Update from Ben Webb:

Modeller 8v2 does not 'automatically' fix the alignment (that would be rather hard) but it does give more informative error messages in this instance.