Dear all, Two things. First, I just written a small plugin that uses the program "reduce" to add hydrogens to a molecule or to a trajectory loaded in Pymol.(since each frame of the trajectory is hydrogenated by reduce, I think that protonation states could vary between frames) This allow us to have a reliable protonation method in PyMOL, without having to save the structure as PDB and hydrogenate with another app, and using an open-source (as far as I know) and easy to install application.
Since I don't have any website right now, I will try to make it available from the Pymol Wiki. If you want the plugin right now, just e-mail me. The other thing is a doubt in using the APBS Tools. When I use it to calculate electrostatics potentialsof a trajectory (but the PQR is made by PDB2PQR from a PDB made with PyMOL, i.e, only from the first snapshot) I get a .dx map that I think has the potentials only for the first frame. When I display the potential surface in the trajectory, the potentials seems to change between frames, which I wouldn't expect since I think that the calculation was performed only for the first frame. My doubt is: Are these changes alleatory due to a change of the structure's position changes on the grid, or they have some significance?, if the latter, what significance? (maybe the changes are produced by the motion of polar groups?) Thanks in advance, Raul __________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ¡gratis! Regístrate ya - http://correo.espanol.yahoo.com/
