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

Pavel Afonine pafonine at lbl.gov
Mon Jul 4 22:53:37 PDT 2016

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.


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