On 10/07/2018 09:32, Grandi, E. wrote:
Dear all,
Hello Eleanora,
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.
> I also tried to use the new lib.cif file mentioned as the input file but it did not work. OK.. there are a few clarifications needed if I am to understand exactly what went on here modified structure "tried to use" But perhaps I don't need to understand. The protocol is: Try to find the 3-letter-code of your ligand using Ligand Expo or some such If you find it, just use File -> Get Monomer. Now fit your ligand. If not, (1) use Lidia to make a chemical diagram, press "Apply" to run Acedrg Or (2) use Lidia to determine the SMILES string and use the "Make a Ligand" task in CCP4i2 Also, Grade is highly regarded: http://grade.globalphasing.org/ Paul. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
