Last modified September, 1996 - Armel Le Bail
At this stage, you are supposed to have run STRUVIR once with the minimum default specifications (if not, go to the first step). To go further, you need to know more about interatomic distances in your structure. They are available in the struvir.imp file. You may associate an editor to all .imp files (WordPad is fine) so as to be able to edit struvir.imp by a double click on the file name in the file explorator. Edit struvir.imp, note that this file contains atomic coordinates for all atoms in the box specified (here by a default XYZR options). The file lists then inteatomic distances and angles, and the recognized polyhedra.
WARNING : In fact, the default XYZR
may not be sufficient for generating all atoms necessary for the completion
of coordinations, so you should edit pba2.dat and add the following XYZR
options, for instance :
XYZR -0.55 1.55 -0.55 1.55 -1.1 1.1
This option meaning that atoms for -0.55<x<1.55, -0.55<y<1.55 and -1.1<z<1.1 will be included. Run again STRUVIR and go to the interatomic distances in struvir.imp. Decide what you would like to show after having identified the specific building units in the structure. In the pba2.dat case, you will observe for the Al and K cations in struvir.imp (angles have been removed):
The AlF6 octahedra have been automatically recognized by the program
because the default OCTA options are:
OCTA 90 20 1.97 0.4
The options mean octahedra with octahedral angles 90+-20° and mean central atom to coordinated atoms 1.97+-0.4A. You should add the OCTA instruction with different options for cases out of the default limit values.
Looking in struvir.imp at K-F distances and F-K-F angles you may recognize that there are KF6 trigonal prisms (the seventh and next F atoms are at much more longer distances from the K atom than the first six F atoms). These prisms cannot be identified by the program by default values. Only octahedra and tetrahedra (instruction TETR) are included in the default search. Other polyhedra which may have from 3 to 12 vertices are handled by the BZRR instruction. In the present case, edit pba2.dat and add the following line between the TITL and END instructions :
BZRR 2.8 K
The options meaning a search for neighbouring atoms up to 2.8A around the K atom.
Re-run STRUVIR now. With the new XYZR conditions defined above, 32 AlF6 octahedra and 16 'Bizarre' KF6 trigonal prisms will be identified. Looking at the po.wrl file, you have now (selecting 'flat shading' and having lowered a bit the light with the 'lamp' button):
This .gif file was prepared by screen copy at 640x480 resolution. Of course, saving a final view at 1280x1024 resolution or more would be much better. Now you may run STRUVIR with the original pba2.dat as delivered with the package. Loading the new po.wrl into Netscape 3.0 you should see :
The only difference with the previous picture is the presence of O atoms
as circles generated by the CIRC instruction
with options :
CIRC 0.03 O
which is supposed to draw oxygen atoms as circles (spheres in VRML) with a radius R = 0.03A. In fact, the R value acts for the HPGL and POSTSCRIPT outputs, not for the VRML and POVRAY ones for which R is always fixed at 0.5A.
So the additional FORM, VIEW, TETR, SHAD instructions and the longer PARA instruction line were not really necessary in the original pba2.dat file because the default values were sufficient at least for the VRML output (however SHAD has no effect on the VRML and POVray outputs but it affects a lot the HPGL and POSTSCRIPT ones). These options are mainly there because pba2.dat was built from another preexisting data STRUVIR file by a copy-paste in a new one containing yet atomic coordinates. This will probably be your way too if you become a STRUVIR user. As I have published maybe 70 papers making use of STRUPLO (and a few using STRUVIR) as crystal structure drawing program, I will probably continue in spite of its imperfections. Better programs exist which you may consider to buy. The problem is that one license implies one equipped computer. If this computer is not on your desk, this may be a reason to choose STRUVIR...
You should now examine the detailed instructions list and see the other options meaning.