Carlier Group Gaussian User Manual - Virginia Tech

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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).