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

luzuok luzuokun at 126.com
Mon Jul 4 21:14:45 PDT 2016

Dear Pavel,

ReadySet is used to generate the geometry restraint file and the program runs fluently.

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. 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?




Lu Zuokun, Ph.D. Candidate
College of Life Science, Nankai University

在 2016-07-04 22:41:04,"Pavel Afonine" <pafonine at lbl.gov> 写道:

Hi Lu,

    The protein was covalently linked by my ligand and I used JLigand to generate the link record and the .cif file. This file can be used in Refmac successfully. But the .cif file cannot be recognized by phenix.model_vs_data nor phenix.refine. The program runs with the following message:

Phenix has tools to deal with ligands, including tools to create CIF files, and other means to represent the restraints. The outcome of these tools should be compatible with other Phenix programs.
If you use external tools to do this (such as Jligand) then the resulting CIF may or may not work with Phenix tools, this is not unexpected.

Any suggestions how to do this would be greatly appreciated.

Use ReadySet or eLBOW to generate ligand-related files. If those still don't work for you then please get back to us with more details and someone here will investigate.

Another question is, how can I generate a restraints file for COOT to do real space refinement? The .cif file is imported in COOT, but when I do real space refinement, the link bond still takes apart.

See above. Also, you can do real-space refinement using phenix.real_space_refine, from command line or GUI.

All the best,
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