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1)
The right mouse button rotates the molecule, or translates it if Shift is
pressed, or rotates the "camera" if Ctrl is pressed.
2) Left-click to select an atom, right-click to deselect all atoms. 3) Use double-clicks and double right-clicks on atoms and bonds to alter their types and captions:
5)
Double
left-click on a bond to alter its type (e.g. to make it dotted), label and
the style of label. 6)
Double
right-click on an atom to alter its style (color, size, etc). 7)
Double
right-click on a bond to alter its style (color, size, etc).
8) You can use the menu item "View/Release all vectors.." for some purposes, in particular if you work with TDDFT computations and want to observe the angle between transition electric dipole moments vectors and transition magnetic dipole moments vectors:
9)
Left-click
on a parameter designation (line, arc) to drag it on the image. 10)
Left-click
on the edge of a parameter designation (line, arc) to alter its size and
orientation:
11)
Right-click
on a parameter designation (line, arc) to alter its style (color, width,
etc). 12)
Pressing
Num5 places the center of molecule rotation into the center of coordinates
of selected atoms or of the whole molecule, if no atom is selected:
13)
Pressing
Space moves the molecule into the center of image. 14)
Pressing
Enter rotates the molecule to be best viewed. 15)
Pressing
Ctrl+D toggles on/off the dragging mode, in which you can drag atoms or
groups of atoms on the molecule's image:
16)
While
an atom is dragged, it can be moved in Z direction (in parallel with the
view axis) via Num2/Num8 keys or buttons at the right panel:
17)
While
a radical fragment is dragged, it can be rotated or moved in Z direction via
Num1-Num6 keys; Num7/Num9 keys alter the length of the bond connecting it
with outer molecule. The right panel duplicate these keys:
19)
To
add/remove a bond, select 2 atoms via left-click and press Ctrl+B. 19)
In
some cases, it is necessary to add or remove bonds in molecule to drag the
required groups of atoms:
20)
To
dock two groups of atoms (two molecules), select 2 hydrogen or dummy atoms
belonging each of the group and choose "Edit/Unite two groups". 21)
If
a radical fragment is copied from one site to another, the atom in it
connected with the outer molecule must be selected firstly:
22)
When
using Chemcraft with Gaussian, typing #P in input files is recommended.
24)
To
examine the value of an angle or a dihedral, select 3 or 4 respective atoms via left-click: the
value will be shown in the textbox at the bottom of the main window.
25)
To
alter a bond length, select 2 respective atoms, enter the new bond length in
the textbox at the bottom and press the "Set" button near it:
26)
To
alter an angle or a dihedral in the molecule, select 3 or 4 respective
atoms, enter the new value in the textbox at the bottom and press the
"Set" button near it. 27)
When
altering a geometrical parameter, you can choose whether the coordinates of
groups of atoms should be modified symmetrically or not:
28)
Menu
items "Edit/Add atom" and "Edit/Add fragment" allow new
molecules to be built from individual atoms or molecular fragments. 29)
Menu
item "Edit/Insert dummy atom into center of selected" places a
dummy atom into the coordinates center of selected atoms. 30)
Menu
item "Edit/Set principal axes" computes the moment of inertia
tensor and sets the axes according to its eigenvectors. 31)
If
Chemcraft incorrectly identifies bonds in your molecule, choose "Tools/Chemcraft
incorrectly…". 32)
In
Coord mode, pressing "Paste" twice automatically switches to Image
mode. 33)
Pressing
Ctrl+R reloads the last opened file.
34)
One of the most useful features of Chemcraft is the utility for setting a
symmetry point group of the molecule:
35)
The option "Tools/Simple utilities/calculate occupancies by energies"
can be used for quick computation of relative energies (e.g. to find the
energy of ionization). 36)
The option "Tools/Scripts/Generate Gaussian batch file" provides a very
convenient way of running multiple jobs. 37)
The option "Tools/Create animation/Build animated…" can be used for
obtaining any animated gif file, not only related to molecules.
38) Chemcraft can quickly compute the energies of reactions for a row of homologues. This utility is evoked via "Tools/Simple utilities/Calculate the energy of a reaction" menu item, then the button "Auto fill form". When using this tool, the user iteratively chooses a series of output files in "open file" dialog box, and Chemcraft automatically extracts the optimized energy from each output file, and then the reaction energies are computed. Note that Chemcraft extracts the energy from the optimization step with minimum energy, and this energy can be slightly lower than the final energy from the last optimization step:
41) With the 2d style, often the fragments in molecule (radicals) should be rotated via the Drag atoms mode / drag fragments to make the molecule planar:
42) One more advice is to simply read the names of all menu items (including submenus) of the Chemcraft main window. These menu items have long and descriptive names, e.g. "Insert dummy atom into center of selected atoms", "Move coordinate center to selected atom", "Release all current captions to supplement the captions with new ones", "Calculate the energy of e reaction", "Modify multiply Gaussian input files", "Build animated gif from a set of bitmap/jpeg files", etc. Besides that, many popup menu items can be evoked from the left panel. They have descriptive names too:
43) For studying enantiomers, it can be important to set correct axes orientations via "Tools/Preferences/View axes orientation": 44) If the molecule is too big and slowly rendered, choose "Display/Quick". Besides that, sometimes problems arise when Chemcraft tries to calculate bonds for a big molecule, in these cases you can switch off bonds calculation via "Tools/Chemcraft incorrectly identifies bonds in this molecule?/Calculate the bonds in your molecules";
45) Chemcraft can open Molden files if they have the .molden
extension. With Turbomole, if you want to render molecular orbitls with
Chemcraft, you should obtain a file in Molden format via tm2molden
46) When you need to compare TD or IR spectra printed in several files, common axes are often required. For this, you can export the band values into Clipboard and paste them into Excel or Origin for each file; the broadened spectrum can be exported as well, but you also need to copy-paste equal interpolation coordinates (corresponding button at left-bottom corner of the spectrum window). In Windows, you can also copy-paste the graph axes ("Set custom frame" button) to make the axes equal for all spectra, and switch between Chemcraft windows via Alt+Tab;
47) To visualize molecular orbitals from Gaussian output files, type "#P GFINPUT POP(FULL)" in .gjf files (or maybe "POP(FULL, NBO)"). To visualize MOs from Orca files, type "!printbasis largeprint". MOs from Gamess-US output files are always visualized since they are printer in the output files by default.
#P GFINPUT POP(FULL
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