Bob Hansen said: > Aidan asked: > >> In a previous email you said >> >> "Bonds are not projected into symmetry-generated atoms when there is >> bonding indicated already in the file." >> >> Is there a reason why this is so?
> Yes, because some of the atoms in a bond may be in special > positions and > others may not be, so when symmetry is applied, the number of bonds > may > not be a multiple of the number of new atoms. I think.... > > But you can still do this, I think. Show me the file. And also: > Actually, it's just: > > set minbonddistance 0.9 > load xxxxx.xxx Thanks for the suggestions, but this does not work for this example: http://rsc.anu.edu.au/~aidan/PCNB_lowsymm_packed.mol2 which is an extreme example of the sort of substitutional disorder we commonly encounter. Could there be a user settable flag to attempt to use as much bonding information from the "base atoms" as possible? If this is not possible, could you point out to me where in the code I would implement this change and I could have a go at making my own patched version of Jmol. I tried to find where the symmetry expansion is done, but to be honest I couldn't find it. This is a real show- stopper for me and I am in the middle of making a javascript application using Jmol to define intermolecular contact vectors. Cheers Aidan ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
