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.
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