Hi Francesco, As usual in Chimera, there are several possible ways to do this, and what is "best" depends not only on what you plan to do with the result, but also your personal preferences and working style. I would probably start by using either zones or Find Clashes/Contacts with a conservative cutoff to select all the residues you want to keep, which would probably also include several extra residues. If you used Find Clashes/Contacts, one option selects the contacting atoms, and you would press the keyboard up arrow to promote the selection to whole residues. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash...

Next, invert the selection (for example with Select... Invert (all models)) to include the residues you do NOT want, then undisplay them (for example with Actions... Atoms/Bonds... hide). Then you can manually get rid of the few extra residues here and there: Ctrl-click to select one atom or bond in an unwanted residue, press keyboard up arrow to promote to whole residue, undisplay as before. Repeat as needed. I don't know if you meant you wanted to just undisplay atoms or actually delete them. If you wanted to delete them: you could save PDB(s) and choose the option to include only the atoms that are displayed. Alternatively, you could use the approach described above except instead of undisplaying atoms, deleting atoms (for example with Actions... Atoms/ Bonds... Delete) and then save PDB(s). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Oct 12, 2008, at 10:05 AM, Francesco Pietra wrote:

I would like to remove several parts from a complex protein, just leaving the portion where a complex has been created with amberscore. Which is the besr way in Chimera, while observing the pruning on the screen? Thanks francesco pietra