.cif file created by Jligand for used in phenix.model_vs_data
Dear all, 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: Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 19 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Any suggestions how to do this would be greatly appreciated. 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. Best wishes! Lu -- 卢作焜 南开大学新生物站A202 Lu Zuokun, Ph.D. Candidate College of Life Science, Nankai University
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, Pavel
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?
Best!
Lu
--
卢作焜
南开大学新生物站A202
Lu Zuokun, Ph.D. Candidate
College of Life Science, Nankai University
在 2016-07-04 22:41:04，"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
Gents
You can link a ligand be placing it in the model and using
link_ligands=True.
Cheers
Nigel
---
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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participants (3)
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luzuok -
Nigel Moriarty -
Pavel Afonine