To whom this may concern, I’m an undergraduate student doing some research at KSTATE this summer and I’ve been assigned to work on a project that utilizes Chimera. My professor is unavailable a lot of the time and I’ve been struggling a bit with a problem. I’ve been successful at opening up the following PDB files: 1DHK 1DPX 1HYL 2CAU 3BLG 1OA6 1JBC 1OA5 I’m able to open up the .pdb files, proceed to use the commands “del solvent” and “del @ .b” in the command line. I’m also able to go to ToolsàHigher Order Structure à Crystal Contacts before changing the contact distance from 1.0 to 4.0 and check mark the create copies of contacting molecules. However when I attempt to do the following actions for the rest of the proteins I run into a variety of issues: For example 2CAU: When I attempt to “measure buried area #0 # 2-7,” I get the following response in my reply log: #0, chain A: JACK BEAN vicilin 6 pairs of NCS asymmetric units of 2CAU contact at distance 1.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 1 0 4 0 0 0 0 1 1 0 5 0 0 0 0 1 1 0 6 -1 0 -1 0 1 1 0 8 0 0 0 0 1 1 0 9 0 0 -1 0 1 1 0 11 0 0 -1 0 1 C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags [End of Reply Log] So I’m not able to get back the calculations I want. Also, when I attempt to use the Surface Analysis à Attributes Calculator to run the following function : sum(atom.buriedSASArea) and check the “Restrict formula domain to current selection, if any” and “Save calculation results to file,” after selecting the “C” atoms I get the reply: Formula evaluation error: expecting vector argument in function Is there something I need to do before I attempt these actions? Also, I have very little experience with programs in general (I’m a chemistry major/upcoming experimental chemist working with theortical physicist…a little out of my element). Thanks in advance, -Yen Bui