How to add missing hydrogens to a PDB file using R.E.D. Server?
Ante_R.E.D. 2.0 cannot yet add missing hydrogens to a structure. However, one can use the Jmol based graphical interface generated by R.E.D. Server to perform this task by the following approach: (i) submit the PDB input file (without hydrogens) to R.E.D. Server/Ante_R.E.D. 2.0., (ii) open the Java applet correcponding to the PDB output file from the graphical interface, (iii) open the Jmol console (right-click and select “Console”), (iv) add the missing hydrogens [write in the console: “calculate hydrogens”; for more information about this command click here; in the case of a bad topology remove/add the additional/missing hydrogens/connectivities using the Jmol Model kit (right-click and select “Computation/Model kit”)], and (v) save the new set of Cartesian coordinates in the PDB file format (write in the console: “write coord PDB”; for more information about this command click here). This new PDB file can now be used as input to generate a P2N file with hydrogens.
