Hi Amanda, That message is for when you have to enter only one name but are saving multiple files, and you literally have to include “$name” or “$number” in the name that you enter (not just the “$” part). If you chose the option to save both structures to a single file, you would not get that message. However, that is a side issue as the resulting PDB files do not have matrices in them, just coordinates. The “matrixcopy” command applies the matrix from one model to another model. (You could save a matrix to file with “matrixget” and apply from that file to a model with “matrixset” but that’s not necessary when you can do it directly directly with “matrixcopy”.) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html> But let’s step back because I don’t understand why you want to do anything with the matrices. Why don’t you just compare between three different superpositions: (1) superposition of the N-term parts (2) superposition of the C-term parts (3) superposition of the whole thing I am confused by your description “apply the resulting matrix to the superposition” because if you apply the matrix it would change the superposition. In each of those superpositions, you can measure RMSD between any sets of atoms (apo vs. bound) in the current positions with the “rmsd” command. You could use backbone/CA of the entire proteins, or of the N-term subunits, or of the C-term subunits. Also bear in mind that you can open multiple copies of the same thing if it makes the comparisons easier, like 3 different copies of the ligand-bound structure superimposed differently with the apo structure (to calculate RMSDs between different superpositions of the bound structure) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> See also the command “measure rotation” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> For example, I could measure a hinge motion of about 30 degrees when apo structure 2fvy binds glucose (bound structure 2fw0) commands: open 2fvy open 2fw0 open 2fw0 mm #0 #1 mm #0:111-295 #2:111-295 measure rotation #1 #2 That opens two copies of the ligand-bound structure (#1 and #2). The first “mm” matches #0 and #1 using one domain, and then I looked up the residue numbers of the other domain and used that in another “mm” command to match #0 and #2 using the other domain. Then I measured the rotation between the two different copies of the ligand-bound structure (#1 and #2). The Reply Log reports a 30-degree rotation: Position of 2fw0 (#2) relative to 2fw0 (#1) coordinates: Matrix rotation and translation 0.91415915 0.19432894 0.35573770 19.67294933 -0.29970804 0.91491318 0.27038670 12.98184314 -0.27292515 -0.35379392 0.89461820 -10.03917469 Axis -0.61535481 0.61977367 -0.48705138 Axis point -12.25426979 0.00000000 -59.69380347 Rotation angle (degrees) 30.47559559 Shift along axis 0.82955445 I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Oct 23, 2017, at 10:05 AM, Amanda Constantinides <aconstantinides1@student.gsu.edu> wrote:

I have a structure with two subunits. I am trying to show movement of the C-terminal subunit upon ligand binding by superposition with another structure from the same strain in the apo form. I want to superpose the N-terminal subunits (A), note the RMSD, then apply the resulting matrix to the superposition of both subunits of the molecule with both subunits of the other (B),then I want to superpose on the C-terminal subunits (C), and then measure the RMSD between (C) and the C-terminal subunits from (B). How can I do this in Chimera? I know how to superpose molecules and calculate the RMSD in Chimera, but I do not know how to apply the resulting matrix from (A) to (B). I tried to save the aligned structures from (A) as a PDB file to check and see if there was a matrix in the file, but an error message came up saying that I needed to save the file as $name or $number. I tried to save the file with $ in front of the name, but it didn't work.

Thanks in advance,

Amanda Constantinides Graduate Research Assistant Georgia State University