> 1. Alignment and Translations/Rotations (Joshua L. Adelman) > rotation of the protein). Ideally what I want to do is do a single > alignment of the last frame of the first sequence with the first frame > of the second sequence (they should be nearly identical structures) > and > then get the translation and rotation matrices that were used and then > apply them to all of the .pdb files that compose the frames of the the > second group of structures.
Probably you already considered to use the programme named LSQKAB from the CCP4 suite, didn't you? If not, so it's worth to try. It runs under a lot of operation systems. This programm can align the given two structures just only by specific residues or the hole protein. It provides you with the rotations/translations matrix which you can apply in another round to overlay the the different frames sets. Best regards, Bartholomeus
