Lucas Bleicher wrote: > 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.
An excellent suggestion - thanks! I've added it to the Modeller wishlist in the Modeller wiki at: http://salilab.org/modeller/wiki/Wishlist Please feel free to add any similar suggestions to those pages or to this list.
It's difficult to add code to Modeller to fix anything 'automatically', since the PDB is too variable, but we can certainly put in more informative error messages with pointers to where in the PDB the missing residues might be.
Ben Webb, Modeller Caretaker