Hi Guy,

  I am a PhD student in the department of Biochemistry of the Tel-Aviv University and often use your great application, CHIMERA.   Is it possible to view on chimera the selected part only? Regarding this, is it possible to split a model to its units (so each chain/ligand) will be considered as a model?

Thanks for your kind note! Yes, you can show just the selected part; for just atoms and bonds, the command show sel or ~disp; disp sel would do it. If you also wanted to show ribbon and/or surface for just the selection, the easiest way would be to undisplay everything and then display the ribbon and/or surface for just the selected part. In commands, that would be ~ribbon; ~surf ribbon sel; surf sel You could do the same thing with the menus, but in that case you would Hide the ribbon and surface before making the selection, then make the selection, then use the menus to Show ribbon/surface (which would automatically affect just the selected part). Currently you cannot split the model into multiple models. However, there are few ways you could end up with the parts in different models. (1) edit the file into multiple files before opening in Chimera (this is only good if you are comfortable with text editing) (2) select a part you want to make a separate model, write that out (Actions... Write PDB with "Save selected atoms only" turned on), read it back in (3) open the file multiple times and then delete from each model all the parts you don't want in that model (can be tedious if you have many chains). For example (commands below; you could also do it with selecting the part you want and then Select... Invert (selected models) and then Actions... Atoms/Bonds... delete): open myfile.pdb open myfile.pdb sel #0:.a sel invert sel delete sel sel #1:.b sel invert sel delete sel This would give model 0 containing only chain A and model 1 containing only chain B. I hope one of these options will be useful for you! 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

Hi Guy, I added a Chimera command called "split" that makes separate molecules out of the chains of a molecule you have opened in Chimera. It is available on the Experimental Chimera Features web page (linked from Chimera download page): http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Tom

Hi Charlie, There is not a standard molecule deep copy routine in Chimera. The "split" command python code (in __init__.py) contains about 80 lines of code to copy atoms of a chain as a separate molecule, preserving most of the display style (ribbon, sphere, coloring, ...). It does not preserve everything, for example, if you change atom radii or bond linewidth, I didn't copy these attributes. Why not? Laziness. Two other Chimera tools, Unit Cell and Multiscale Models, also copy molecules and they use other code (written by me): share/PDBmatrices/copymolecule.py This is even a more basic copying (36 lines of code) that copies only the data (atom names, connectivity, residue numbers) but not the display attributes like colors, ribbon display, atom style (sphere, ball and stick, ...). We probably should have a copy routine that copies everything but it hasn't been a pressing need so far. Tom