Hi Francesco, I will assume this is just a building issue. If Sirius is doing something else such as automatically adjusting the charges where the atoms are being joined, you would have to do that yourself. Why not just use the original structure that already includes the covalently bound residue? Even though you would have to chop it into pieces for the RESP part, if it is just a matter of putting the atoms back together to recreate the original structure, instead just use that structure. If there is no original structure with that group, you can create the group attached to the protein using Build Structure in Chimera, the Modify Atoms section. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...

You can put pre-existing multi-atom pieces together with Chimera, but it is currently rather inconvenient. When you create a bond between fragments in Chimera, it does not automatically reposition either fragment but connects them without changing their positions. So if they weren't already in the correct positions relative to each other, you would have to get them in such a position manually. The next issue is that usually you can't move groups of atoms relative to others unless they are in two different models, but then you can't bond them unless they are in the same model. If they needed to be moved, you would need to open them from separate files (so they would be separate models), reposition relative to each other by activating/ deactivating and using the mouse, <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> then put them in the same model, then add the bond with Build Structure or the command "bond." <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> You could put them in the same model by writing out PDB files and text- editing to create a single file, or by using the new "combine" command or "copy/combine" function in the Model Panel (would need a recent daily build for these to be available). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> Instead of all this, I would probably just build the group onto the protein from scratch using Build Structure, as mentioned above. 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 On Oct 31, 2008, at 12:36 AM, Francesco Pietra wrote:

Subject: Combining fragments for RESP charges

I was reading Ross Walker's tutorial A1, in the suite of tutorials for Amber.

When deriving RESP charges for an unusual molecule covalently bound to a protein, the unusual molecule is first detached from the protein and then further divided into fragments. RESP charges are derived for the fragments, then the fragments are recombined using Sirius visualization program. The recombined fragments are then attached to the protein, again using Sirius.

Can these recombinations be carried out with Chimera? Thanks francesco pietra