Hello Kazem 

I do not think that Jmol is your best tool for that, since I am 
guessing there will be a lot of (repetitive) silica groups to which 
the new groups must be added. Removal of groups is probably easy.
For just one addition it could be done, although still not the best 
choice. 
Although Jmol has some editing capabilities now, its design is of a 
viewer, so building models is harder. An exception is the Model Kit 
application like e.g. in Chemagic.com - but that's for single, small, 
molecules and so far from your needs I think.
·
 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28871 Alcalá de Henares  (Madrid), Spain


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