Hi Everyone, I am new to this list so please forgive me if I miss something. Over the past few weeks, I have been attempting to match the positions provided by the PDB to the canonical protein structure. For instance, if a pdb file puts a CA Leucine residue at position 5, that does not mean that position 5 in the canonical protein structure (as shown by uniprot or other databases) is a Leucine. That is because the PDB numbering is different. Using CIF files from the PDB database I am more or less able to reconstruct the canonical numbering for about 70% of all files. However, I would like to also align the residues I pull from the CIF file with the canonical structure for the structures that my algorithm fails to process. To do this, I am using the pairwiseAlignment function in the Biostrings package. This function seems to work very well, however, I am new to alignment and am thus wondering what are the best parameters to use for my problem? Suppose I have the canonical protein sequence in "canonical.protein" and the cif sequnce that I pull from the PDB database in "protein.extracted". I then run "pairwiseAlignment(pattern = canonical.protein, subject=protein.extracted)", and use the default settings for the other parameters. If someone has done something similar, can they point me if there parameters that are optimal? Especially for things like gapOpening, gapExtension, etc... Thank you for your help, Greg