Mark J. van Raaij wrote: > as it appears to bear near the guanidine group of an arginine, I would > suggest it is a partially occupied and disordered sulphate and/or > phosphate. > whether this is practically modellable is another matter, a sulphate at > occ. 0.5 is an option, or putting a water with a remark in the pdb that > this water is really modelling partially occupied and disordered > sulphate and/or phosphate.
I've found that remarks in PDB files are quite useless. If you label an atom as a water molecule, every program that reads that file will make the assumption that you believed a water molecule was there. Even most humans will fail to dig into the header of the PDB file to see if you had some specific comment about that particular atom. Since the PDB file is your interpretation of the electron density, and the electron density will be available to anyone who wants it, I don't see the point of marking a spot with a dummy atom when you don't have an interpretation. As for developing an interpretation: I've had good success in cleaning up such maps using Buster. You don't need to add dummy waters in the refinement to remove "vacuum bias", just leave it alone while you fix everything you can figure out. Dale Tronrud > Mark > > Quoting Katja Schleider <katjaschlei...@yahoo.de>: > >> Dear all, >> >> I found some fairly substantial density in the active site of my >> protein structure. But I don´t know what it should be. My >> crystallisation condition consists of lithium sulfate, >> citrate-phosphate and peg1000. The whole lot doesn't make a dashed >> bit of sense! Any suggestions to fill this density with something? >> Picture is attached. >> >> Thanks a lot, >> >> Katja >> >> >> __________________________________________________ >> Do You Yahoo!? >> Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden >> Schutz gegen Massenmails. >> http://mail.yahoo.com
