[PyMOL] Tip: removing dummy atoms in NMR PDB files

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 b

[PyMOL] RE: Orient molecule

Steve, This is something PyMOL can do with a little help from Python... # PyMOL script: view2coord.pml # get the current camera matrix v=cmd.get_view() # translate atoms to the current origin of rotation alter_state 1, all, \ (x,y,z) = (x-v[12],y-v[13],z-v[14]) # apply the rotation (matrix m

[PyMOL] cartoon and alternates

hi there, I get broken cartoons with alternate conformations. Is there a quick way to solve this problem? thanks, robert --- Robert Schwarzenbacher, PhD The Joint Center for Structural Genomics phone: 858 822 3637