Carlier Group Gaussian User Manual - Virginia Tech

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$X-ray, Neutron and Electron Diffraction of Crystals Scope and Use of ...$

52 Carlier Group Gaussian User Manual B. Reorient selected structures, if necessary Sometimes the coordinate system appears to have changed and the molecules don't overlay correctly. You can then select the first structure and the second structure. Go to Wizard/Pair Fitting and then use CNTRL-Middle Click to select atom pairs--in each case select the one you want to move, and then the one you want to move it to. Select three pairs in all, and then click the 'Fit 3 pairs' button. If it looks good, click done. Then turn off the first structure, turn on the third, and fit the third to the second. Be sure to use the same anchor atoms in each case. When you are done, 'Save Session' C. Select your display options You will want to make all the carbons the same color and set your other display options. Type in at the command line: show sticks, all set stick_radius, 0.1 set stick_ball, 1 set stick_ball_ratio, 3 color carbon, symbol c If you have a bond-breaking TS, at the TS the non-bonded atom may appear as a cross. To fix this problem with non-bonded atoms show nb_spheres D. Decide on resolution (normally 1024x768) Polo recommends the following viewport 1024,768 set orthoscopic (this command makes the display and ray tracing programs adopt the same perspective) E. Decide on which views you want to start with and move to For example v1 is far away, v2 is rotated far away and v3 is close up As you get each desired view, type view v1, store (then continue for v2, v3, as needed).
Carlier Group Gaussian User Manual 53 F. Then use scripts to generate an animation and change viewing options. This is best done in a text editor. The basic command is mvCmd, followed by a frame number, a command, and a filename. Here is the script for my LiNH2 cyclopropyl nitrile deprotonation movie: mvCmd 1, disable h0007a13 mvCmd 1, enable h0007r22 mvSinViewTravel 1-30, v1, v2 mvSinViewTravel 31-60, v2, v3 mvCmd 61, disable h0007r22 mvCmd 61, enable h0007r21 mvCmd 62, disable h0007r21 mvCmd 62, enable h0007r20 mvCmd 63, disable h0007r20 mvCmd 63, enable h0007r19 mvCmd 64, disable h0007r19 mvCmd 64, enable h0007r18 mvCmd 65, disable h0007r18 mvCmd 65, enable h0007r17 mvCmd 66, disable h0007r17 mvCmd 66, enable h0007r16 mvCmd 67, disable h0007r16 mvCmd 67, enable h0007r15 mvCmd 68, disable h0007r15 mvCmd 68, enable h0007r14 mvCmd 69, disable h0007r14 mvCmd 69, enable h0007r13 mvCmd 70, disable h0007r13 mvCmd 70, enable h0007r12 mvCmd 71, disable h0007r12 mvCmd 71, enable h0007r11 mvCmd 72, disable h0007r11 mvCmd 72, enable h0007r10 mvCmd 73, disable h0007r10 mvCmd 73, enable h0007r9 mvCmd 74, disable h0007r9 mvCmd 74, enable h0007r8 mvCmd 75, disable h0007r8 mvCmd 75, enable h0007r7 mvCmd 76, disable h0007r7 mvCmd 76, enable h0007r6 mvCmd 77, disable h0007r6 mvCmd 77, enable h0007r5 mvCmd 78, disable h0007r5 mvCmd 78, enable h0007r4 mvCmd 79, disable h0007r4 mvCmd 79, enable h0007r3 mvCmd 80, disable h0007r3 mvCmd 80, enable h0007r2 mvCmd 81, disable h0007r2 mvCmd 81, enable h0007r1 mvCmd 82, disable h0007r1 mvCmd 82, enable h0006a mvCmd 83, disable h0006a mvCmd 83, enable h0007a1 mvCmd 84, disable h0007a1
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Carlier Group Gaussian User Manual - Virginia Tech

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