[Chimera-users] User Inquiry

[Yen Bui]

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


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