FRODO/crystalline structure visualisation

jgpletin at BE.AC.VUB jgpletin at BE.AC.VUB
Thu Jun 25 08:51:31 EST 1992


SA121 at phx.cam.ac.uk (S. Arrowsmith) writes:
|Does anyone have any experience with using FRODO for several
|molecules together, ie a whole (or partial) unit cell?  I've
|been using it to try and observe solvent channels, and either
|it or the display (Evans & Sutherland PS300) isn't really up
|to the job.  I'm curious to know if anybody has tried this
|sort of thing before, and if they've come to the same conclusions
|as I have.
 
We have been doing this kind of thing on FRODO. It can be fun to watch a
'crystal' composed of umphteen unit cells; and it gets easier to spot
solvent channels. Here is how we go about it (using FRODO 4.4 on a PS390):
You turn to MOL and make an object that contains a whole assymmetric unit.
Next you use the MOL-symm command to generate a full unit cell.
You can put all of these in a single object.
Finally, you construct a 'crystal' with the same symm command by translating
this 'unit cell' across the axes. Again, you can put everything in a single
object.
 
The commands would look somewhat like this :
mol
name mol2
zone *
name mol3
symm sn mol2       with n=1 to # symmetry relations
name mol4
symm +a mol3
symm -4a+b+2c mol3
........
 
You could, after having build a 3*3*3 unitcells~3 object start translating
that, etc.
The possibilities are NOT endless - FRODO gets significantly slower; but
it never crashed on me when i was doing this.
Hope this answers your question at least partly.
--
      Jurgen Pletinckx               Department of Ultrastructure
      Vrije Universiteit Brussel     Belgium
      *****************  Kwaliteit drijft boven  *****************
Disclaimer: I know Phil Evans nor Alwyn Jones.




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