Why the atom connectivities in some P2N files generated by Ante_R.E.D. are not correct and how to correct them?
Ante_R.E.D. 2.0 can determine the molecular topology of an input molecule (for more information about this feature click here). However in some cases the procedure might generate local errors and additional atom connectivities might be generated or some connectivities might be missing. This is likeley due to a bad set of Cartesian coordinates provided in the PDB input file. This problem can be easily corrected by using Jmol and following these steps: (i) open the Java applet correcponding to the PDB output file from the Jmol graphical interface generated by R.E.D. Server, (ii) remove/add the additional/missing atom connectivities using the Jmol Model kit (right-click and select “Computation/Model kit”), (iii) optimize the geometry of the structure using the Jmol optimization tool (right-click and select “Optimize structure”), (iv) open the Jmol console (right-click and select “Console”) and (v) save the optimized set of Cartesian coordinates in the PDB file format (write in the console
