Hi there, I am currently attempting to validate SAXS rigid body models by generating theoretical AUC parameters for them and comparing this to experimental AUC values. Although not a crystallographic problem I know some of you will have a solution to this one. Some of the residues in my rigid body SAXS models, which are present in the sequence but not in the rigid bodies I modelled with, are represented as alpha carbons only. To generate theoretical AUC parameters I must convert my SAXS output pdb file into a bead solution model from which the theoretical parameters are derived. The bead models are not simply space fills but take into account surface charge, hydrophobicity etc. which all affect the solvation shell and therefore its AUC characteristics. Therefore to generate the bead models I must first build in the missing residues as alpha carbons are not accepted.
Therefore does anybody know of a quick way to build the remainder of a residue around its alpha carbon, short of manually building in COOT etc. I need to carry out this task on many pdb files so Im looking for as automated a method as possible. I am not concerned about rigorous energy minimisation as the conformation of a couple of localised bond angles will not impact too much on its theoretical AUC. Regards, John John Chipperfield Steve Prince Group Manchester Interdisciplinary Biocenter, 131, Princess Street, Manchester, ENGLAND M1 7DN
