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RE: [ccp4bb]: unknown ligand
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*** CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html ***
If you able to fix some water molecule and have some
idea about the skelton, then you can use "BEILSTEIN
COMMANDER 2000" for possible ligand. It has several options
to search the small molecule data bank, which includes
a rough drawing of your molecule. This was suggested long
back in the CCP4 bulletin, if I am right.
You can get more information about BEILSTEIN by doing
general google search.
Hope this information helps u.