Dear S, I forgot to mention before that the label will not automatically change when the charge value is changed. You have to re-label to see the new charge. Just thought I would mention that first, in case that is the problem! Otherwise, you only want to change the charge of one atom? Seems like it would be easier to just edit the charge value in the Mol2 file than to use Define Attribute. Also, for one atom you could just use the "setattr" command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html For example, in 1a6m the iron is :hem@fe, so if you wanted charge=1.5, the command would be: setattr a charge 1.5 :hem@fe However, in case you mean FE is just an example and you might want to change the charges of multiple atoms, I attach an example file to use with Define Attribute to define the charges of all the atoms in HEM. This plain text file assumes your structure is open as #0 and has the same HEM atom names you would get by adding hydrogens to 1a6m. You could edit the charge values and atom names as needed, then choose "Tools... Structure Analysis... Define Attribute" and then open this text file, which will set the charge values as specified (FE is 1.75, etc.). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html P.S. If you use only the FE charge from your amber data but not the rest of the values for the HEM residue, it might not add up to the correct net charge. I'm guessing those charges were generated by considering FE and the rest of HEM together as one residue. Just something to consider, and perhaps it is not that important for your purposes. P.P.S. Some details you probably don't care about but maybe others in the list would be interested: I made this attribute definition file using the "Attribute Calculator" tool with the "Formula" set to atom.charge (i.e. I didn't calculate anything, just used the tool to write out an existing attribute), naming the attribute "charge" and specifying "Save calculation results to file." To make sure it worked, I text-edited the FE charge to 1.75 and reassigned the values with this file and "Define Attribute" as described above.