|
This example uses the raw hkl data used to determine the crystal
structure of Cs2TiSi6O15
as published in I.E. Grey, R.S. Roth, M.L. Balmer,
Journal of Solid State Chemistry, 131, 38-42 (1997).
Cameron (L. J. Pearce and D. J. Watkin) is a very powerful structure manipulation program from the Oxford University Chemical Crystallography Laboratory [CCP14 Mirror] that is normally distributed as part of the Crystals single crystal suite. Providing you can be bothered reading the manual, it has some quite amazing attributes. Most of this is accessed via building command line requests. Following is just a small set of commands. Refering to the Postscript manual (viewable in the Ghostview software) gives a list of all the commands. One preliminary hint. After editing and removing atoms using the various commands, type END to finish the session. WinGX will then warn if there are still any Q peaks that have not been assigned. The resulting (updated) file is accessible via the REFINE, EDITED menu option has the resulting atom list. Also, if you don't like clicking on the View button each time after you type a command. Just type view [RETURN] to get the screen to update. |
|
At this point we have already obtained a trial structure using
one of the Direct Methods/Patterson programs. To view and
manipulate this in Cameron, select from the top menu, Graphics,
CAMERON which will then prompt whether you want to use
the Shelx INS or RES file. In this case, select the INS file.
This will bring up the following graphics screen and a subset of Cameron commands; mainly the simple ones.
To add atom labels, select the label all menu option
To see how this fits into the unitcell, select the include cell menu option
Or to see how all the atoms pack in a UNIT CELL, select the Pack Complete and Include Cell menu options
|
|
You can rotate or align the atoms using the
XROT, YROT, ZROT, AXIS and PLANE menu options.
The following screen images is using the AXIS C
option.
|
|
To get a distance between 2 atoms, type distance (or DIST) then click on the two atoms with the mouse and press [ENTER]. (or just type in the atom names and press enter)
|
|
To get a bond angle between 3 atoms, type angle then click on the three atoms with the mouse and press enter. (or just type in the atom names)
|
|
To rename an atom (bit of a trick here), type rename name1 name2 then press enter; then do a graphics command to be able to get a screen redraw. In the following case, Q2 is renamed to O7. (click on VIEW once to get the redraw)
|
Deleting an AtomYou can use the exclude, include commands if you want to temporily remove an atom from the screen and then view it again(e.g. exclude q1 [enter] - then press the VIEW button to enable this) (e.g. include q1 [enter] - then press the VIEW button to enable this) If you want to delete an atom, just exclude it - that's all it is. When you type END to finish the session. WinGX will then warn if there are still any Q peaks that have not been assigned. The resulting (updated) file is accessible via the REFINE, EDITED menu option has the resulting atom list. |
|
To align the structure along a particular HKL, this can be done
using the command align h k l
(e.g. align 1 0 0 [enter] - then press the VIEW button to enable this) To view a face on a particular HKL, this can be done using the command face h k l (e.g. face 1 0 0 [enter] - then press the VIEW button to enable this)
To view along a particular bond, this can be done
using the command along atom1 atom2
(e.g. along q1 si3 [enter] - then press the VIEW button to enable this)
Join creates bonds.
(e.g. join full q1 o7 [enter] - then press the VIEW button to enable this) |
|
The connect command can be used to connect atoms, H-bonds/hbonds,
dotted lines, etc. (disconnect is the opposite of this). This seems to
be a more powerful version of join/remove. An example of this would be to add bonds to all Oxygen and Cesiums having a bond distance between 3 and 4 angstrom. (e.g. connect o cs 3 4 [enter] - then press the VIEW button to enable this)
Trick here is that DISCONNECT does not work in exactly the same fashion. disconnect o cs 3 4 WILL NOT WORK as it will only delete bonds outside this distance. Thus to delete these Cs O bonds, type disconnect o cs 1 2 [enter] - then press the VIEW button
To look for O-H-O hydrogen bonds try the following command (H-bonds
will be dotted) - The Connect taper and connect thickness commands can also be used to setup default bond attributes on the screen. |
Printing Postscript Files from CameronCameron can give quite nice Postscript output. This is done in two stages. (3 if you include sending the file to the printer)
Type copy filename.ps [ENTER] (or what ever file extension is appropriate) Either view the file in Ghostscript or send the file to a Postscript printer. (Ghostscript can print Postscript files to non-postscript printers) There a possibly better ways of doing this - but does get the job done. |
|
You can change the radii of atoms displayed on the screen.
using the command ball radii atomname size-in-angstrom (e.g. ball radii o 0.25 [enter] - then press the VIEW button to enable this - all Oxygens are now made 0.5 Angstrom radius) (e.g. ball radii Cs1 0.7 [enter] - then press the VIEW button to enable this - the Cs1 has a 1 Angstrom radius) |
|
The Pack command can be used to fill areas of the cell . (unpack gets
things back to normal after doing a pack or enclosure command)
pack windows 0 1 0 1 0 1 [enter] - then press the VIEW button to enable
the complete unit cell to be filled) (0 to 2 would give two unit cells in each direction)
|
|
To examine co-ordination environments, the enclosure command
can be used.
To examine the co-ordination around the Cs1 atom, type enclosure atom cs1 sphere 4.5 cut [enter] - then press the VIEW button (CUT will generate all the atoms that lie within the defined volume)
To examine the co-ordination around the Cs1 atom, type
|
