[phenixbb] .cif file created by Jligand for used in phenix.model_vs_data

Nigel Moriarty nwmoriarty at lbl.gov
Tue Jul 5 09:59:03 PDT 2016


You can link a ligand be placing it in the model and using



Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Mon, Jul 4, 2016 at 10:53 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> 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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