Just a quick tip: I came across a PDB file containing a number of NMR structures. Besides the actual protein atoms, the file also contained "pseudo atoms" corresponding to the geometrical average of groups of equivalent hydrogen atoms (or something like that). I found that these extra atoms can be quickly selected with a command like
select dummies,(name QA,QB,QD,QD1,QD2,QE,QE2,QG, \ QG1,QG2,QH1,QH2,QQD,QQG,QR,QZ) The atoms can then be deleted using the "remove atoms" command on the "dummies" selection in the PyMOL menu. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
