Hi Vandra, For changes in a dimer when comparing two crystal forms, in addition to looking at the change in the NCS axis, you may want to consider the following software:
DynDom S. Hayward, A. Kitao, H. J. C. Berendsen, "Model-Free Methods of Analyzing Domain Motions in Proteins from Simulation: A Comparison of Normal Mode Analysis and Molecular Dynamics Simulation of Lysozyme" Proteins, Structure, Function and Genetics, 27:3, 425-437, 1997. http://fizz.cmp.uea.ac.uk/dyndom/ HingeFinder Willy Wriggers and Klaus Schulman, "Protein Domain Movements: Detection of Rigid Domains and Visualization of Effective Rotations in Comparisons of Atomic Coordinates." Proteins: Structure, Function, and Genetics, 29:1, 1-14, 1997. http://biomachina.org/disseminate/hingefind/hingefind.html I’ve personally found the above software to be very helpful. Cheers, Genevieve Dr Genevieve Evans ------------------------ School of Chemistry and Biochemistry The University of Western Australia (M310) 35 Stirling Highway CRAWLEY WA 6009 Australia On 30 Jun 2017, at 8:12 AM, Zhijie Li <[email protected]<mailto:[email protected]>> wrote: Hi Vandna, Assuming you have two copies, chain A and B. In UCSF chimera: 1) open two copies of the pdb (model #0 and #1) 2) in command line, type: match #1:.B@CA #0:.A@CA showMatrix true Besides moving model #1 chain B to model #0 chain A, the match command also outputs the rotation and translation matrices and angles, axes in Favorite-> Reply Log. Note that you might need to specify residue number range for the two chains if the number of CAs in them are not equal - just to make the match working. The match command does not guess the range of residues to align as the MatchMaker does. Alt confs involving CAs also count. You may run: del @CA.B to delete all alt conf B CA atoms before the match command to make it working If you wish to draw the rotation axis in Chimera, you need to make a bild file that draws an arrow from the "Axis point" with direction specified by the Axis vector. Assuming the "Axis" is "Ax Ay Az" and the "Axis point" is "x y z", you need to calculate X1=x+Ax*20, Y1=y+Ay*20, Z1=z+Az*20, then put this in the arrow.bld file: .arrow x y z X1 Y1 Z1 https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html COOT also outputs the matrices in the terminal window. But COOT does not seem to directly show the more human friendly "rotation angle" and "shift along axis". Zhijie On 29/06/2017 3:16 PM, Vands wrote: Hi every one , I am looking for a tool to perfectly determine the NCS axis. I have two forms of crystals where diamer is with NCS but on a comparison of both forms, it looks like NCS axis is little off when i superpose two forms, i would like to measure rotation or translation between axes . -- Vandna Kukshal Senior Scientist Dept. Biochemistry and Molecular Biophysics Washington University School of Medicine 660 S. Euclid, Campus Box 8231 St. Louis, MO 63110
