Tim, I understand that you are working on this. So don't answer the questions below. Just keep them in mind as you research a solution.
Miguel > true - about 85% of the structures in the PDB are crystals, and I assume > most of them lack hydrogens. but we can infer the existence of a > hydrogen - rasmol does this very thing when calculating the default > sphere radii to use. (C, N, and O atoms that *should* have a hydrogen > are given modified vdw radii to account for the missing proton.) But RasMol is only looking at specific protein/DNA N & O atoms that they know are good candidates for Hbonding ... > in addition, based on the covalent bonding and group properties, we can > calculate the existence of likely lone pairs (for example, an O in a > carbonyl group will have two lone iars; an O in a hydroxyl will have one > LP and an assumed hydrogen). But, how do we tell whether a C bonded to an O is a C=O or C-O-H (given that there are no H atoms)? ------------------------------------------------------- This SF.net email is sponsored by: IBM Linux Tutorials. Become an expert in LINUX or just sharpen your skills. Sign up for IBM's Free Linux Tutorials. Learn everything from the bash shell to sys admin. Click now! http://ads.osdn.com/?ad_id=1278&alloc_id=3371&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
