Dear all,

I am recently working on a protein-ligand structure. The problem is that the ligand is not present in the library used by Refmac. Therefore, after having modified the structure on Coot I cannot run Refmac again because the ligand is not recognized. The program suggest me to use JLigand to solve this problem but I cannot open it on my Mac because I cannot install Java and I do not know why.

Here is the message from Refmac:

Important, Important, Important!!!!!

Your coordinate file has a ligand which has either minimum or no description in the library

A new ligand description has been added to lib.cif file

Picture of the new ligand can be viewed using postscript file. See above

Check description in this file and, if satisfied, use it as the input library

Otherwise either edit bond orders manually or use JLigand to view and edit the ligand

and create a library entry by running acedrg

It is strongly recommended that dictionary  entry should be checked carefully before using it

If you are happy with the library description then use the keyword (MAKE CHECK NONE)

I.e. do not check correctness of the coordinates

===> Error: New ligand has been encountered. Stopping now

I also tried to use the new lib.cif file mentioned as the input file but it did not work.

Does anyone have any suggestions?

Thank you very much for the help in advance.

Best regards,

Eleonora