Dear All I would like to ask if the PyMOL function to add hydrogens to an entire protein also has options, meaning is it possible to set the protonation state of individual residues specifically? Like in a list or something? h_add, His202:+1 or so? And, it can be relevant at what atom a residue gets protonated: His can be protonated at Nd, or Ne or both. Is there a way to control this?
On a more general note: what other smart hydrogen adding tools are there out there anyway? Does anyone know a really smart tool for this? I know OpenBabel has a pH parameter. But on the other hand OpenBabel just appends the hydrogens to the PDB file, whereas PyMOL really writes them within the block of atoms corresponding to one residue. Also, AutoDock can add hydrogens and it even has an option for the protonation state of histidine, but it doesn't seem to work in my case. Thanks for your answers and input. martin ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
