I am new to MODELLER and would like to know if there is an easy way to accomplish this task. I have a raw sequence that I want to align with my 3D structural alignment that contains nine sequences. First, it seems like my raw sequence should be formatted so that MODELLER can read it. Since this is just a sequence with no corresponding structure shouldn't the second line of the sequence file just be:
It seems strange to me that in the manual all the examples of sequences have a corresponding PDB code when the point of homology modelling is to create the model hence no PDB code. Or for this do I just make one up?
If the sequence file for the target is then correct can I do the following:
READ_ALIGNMENT FILE = 'structures3d.ali', ALIGN_CODES = 'all' # my 3D # structural alignment for nine structures
SET ADD_SEQUENCE = on, ALIGN_BLOCK = NUMB_OF_SEQUENCES
READ_ALIGNMENT FILE = 'sequence.ali', ALIGN_CODES = 'all' # my target # sequence
SET OVERHANG = 0 ALIGN2D GAP_PENALTIES_1D= -400 -150, GAP_PENALTIES_2D = 0.5 0.5 0.5 0.5 0.5 6
Any advice would be much appreciated. General strategies that accomplish the same basic task but don't address my specific problem are also welcome.
Troy Wymore Biomedical Initiatives Group Pittsburgh Supercomputing Center