Gents
You can link a ligand be placing it in the model and using
link_ligands=True.
Cheers
Nigel
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Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
On Mon, Jul 4, 2016 at 10:53 PM, Pavel Afonine
Hello Lu,
However, as this structure had been solved and the cif file is then created by ReadySet. My question is that how to use ReadySet or eLBOW to generate a cif file to describe the ligand that is covalently link to my protein.
Custom restraints is what you are looking for. Phenix provides with a possibility to define bonds, angles etc restraints between any atoms, as many as you like. For instance, you can define a bond between any pair of atoms, any number of pairs. Same with angle. This is described in the documentation. Please get back to me if you have any questions or have any problems with this.
I can load the ligand in REEL. I guess the next step is to add the atom (or the whole residue?) to the ligand and then run optimization. I did what I thought but the program output some errors and I have sent them to the developer. Is there any tutorial?
No idea. I'm interested too. Hope some one explains this.
I guess we can solve this issue using simple command line/nasty-file-editing practices. However, let's see if other developers suggest a solution. If not.. get back to me and we will solve this one way or another.
Pavel
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