Command-Line Options

Olex2’s powerful command line

As previously mentioned, Olex2 offers the opportunity to use a command-line approach if preferred. Although this manual focuses predominantly on the use of the GUI panel and graphics screen, it is worth remembering that the command-line offers a number of additional options and functionality. There are some command-line commands that are extremely useful for routine work, especially when you consider that the UP/DOWN arrow keys browse through your command-line history. Frequently used command-line options

Command Description
refine Refines the structure. The number of cycles and peaks can be set e.g. >>refine 4 5 will ask for 4 cycles and return five peaks.
name Change the atom types of the selected atoms
compaq This will assemble a fragmented structure. Also >>compaq -a
fuse Show the asymmetric unit only
grow Generate all missing symmetry equivalent atoms
reap Open a new structure
lines # Change the number of lines of text shown in the main graphics window to # where # is a number.
lines -1 will show all lines.

The command-line is an enormously powerful tool in Olex2. There are only a few commands that are frequently used, but they are used again and again and it is well worth your time to get to know these. Many – if not most – SHELX and/or XP commands can be used directly in Olex2. If you want the bond distances to be the same, simply select the two distances and type >>SADI. If you want them to be the same with a very high weight, type >>SADI 0.001. The same goes for almost all other SHELX commands. If you type such a command, and the atoms become deselected, then you know that it has worked. If you want to convince yourself that it has worked, click on one of the atoms you have modified and then type >>editatom. You will find your instructions in the window that will pop up.

You can also use the command-line to enter any general instructions. For example, if you want to add a remark to the instructions, you can type >>addins REM Atoms sel() are dodgy. The code sel() bit will be expanded to the currently selected atom names. A shortcut for this is >>/ MyInstruction - i.e. a forward-slash followed by a space and then your instruction.