Hi Snoze, For bulk calculations of charge, you are going to have to use a Python script. In particular you will need to use the estimateFormalCharge method from the AddCharge module. Here's an example script that works if the only molecule open in Chimera is the one you want to estimate the charge for: ---- from chimera import openModels, Molecule from AddCharge import estimateFormalCharge mol = openModels.list(modelTypes=[Molecule])[0] print estimateFormalCharge(mol.atoms) ---- You would run such a script (if you called the script charge.py) with: chimera --nogui --nostatus molecule.pdb charge.py The charge would be printed on standard output. I would recommend you use at least Chimera 1.2470, and the latest daily build if possible if that works for you. You might want to avoid the overhead of starting Chimera for each molecule by opening them all in one instance of Chimera, in which case the script would be something like: ---- from chimera import openModels, Molecule from AddCharge import estimateFormalCharge for mol in openModels.list(modelTypes=[Molecule]): print mol.name, estimateFormalCharge(mol.atoms) ---- The charge estimation in Chimera works reasonably well, most usually failing when the molecular geometry is poor --causing atom types to be mistyped (e.g. a deprotonated alcohol mistaken for a carbonyl due to the bond length being very short). Therefore you might want to sanity check the charge estimation by adding up the atomic numbers of the atoms and ensuring that when you add the estimated charge you get an even number. Something like: fc = estimateFormalCharge(mol.atoms) atomicSum = 0 for a in mol.atoms: atomicSum += a.element.number if (atomicSum + fc) % 2 == 0: print mol.name, fc else: print "BAD CHARGE ESTIMATE:", mol.name, fc --Eric Eric Pettersen UCSF Computer Graphics Lab On Dec 22, 2007, at 12:16 PM, snoze pa wrote:

Dear Chimera Users,

Is it possible to calculate the net charge or formal charge of unknown residues using chimera. I have a large set of molecules for which i am trying to calculate the net charge on each molecule.

Thanks in advance s

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users