How to make PyMOL draw bonds between atoms in console / script?
After crawling the PyMol mailinglist, I managed to connect all atoms. e.g. bond (elem pd), (elem pd) draws bonds between all the Pd atoms. Now to the cuttoff radius: bond (elem pd), (elem s) within 2.5 of (elem pd) draws bonds between all Pd atoms and all S atoms within...
R package Bio3D tutorial reproducing
Typically this will work if pymol is in your path for executables (see here: http://tinyurl.com/lzhpz3w for more about where bio3d expects to find pymol and muscle). view.dccm(cij, pdb, launch = FALSE) I don't use windows myself but if you post this question on the bio3d bitbucket issues page https://bitbucket.org/Grantlab/bio3d/issues you...