how to bypass/deactivate dictionnary check for restraints in phenix.refine
Hello All, I am refining an unusual complex moiety in a protein xl with neutron data. Does anyone know if it is possible to bypass/deactivate dictionnary .cif check i got the blocking error message "it looks like angle and bond restraints are conflicting." and Phenix.refine stops. but really it s not conflicting: my .cif file works great in coot to model the complex. it is hydrogen based, so i really need restraints to get it optimal. any clues welcome, many thanks in advance. Dr. Maxime Cuypers Post-Doctoral Research Associate, Structural Biology St Jude Children s Research Hospital, 262 Danny Thomas Place Memphis, TN 38105-3678, USA
Hi Maxime, could you please send us PDB file so that we investigate and start from there? Alternatively, you can create your own cif file for the ligand in question and provide it to refinement, then it will be used instead of the default one. Pavel On 2/2/18 07:36, Maxime Cuypers wrote:
Hello All,
I am refining an unusual complex moiety in a protein xl with neutron data. Does anyone know if it is possible to bypass/deactivate dictionnary .cif check i got the blocking error message "it looks like angle and bond restraints are conflicting." and Phenix.refine stops. but really it s not conflicting: my .cif file works great in coot to model the complex. it is hydrogen based, so i really need restraints to get it optimal.
any clues welcome, many thanks in advance.
Dr. Maxime Cuypers Post-Doctoral Research Associate, Structural Biology St Jude Children s Research Hospital, 262 Danny Thomas Place Memphis, TN 38105-3678, USA
Hi Maxime,
Can you send the model and the cif file, so we can investigate?
(Reply only to me, so the file is not shared to the entire list.)
Best wishes,
Dorothee
On Fri, Feb 2, 2018 at 7:36 AM, Maxime Cuypers
Hello All,
I am refining an unusual complex moiety in a protein xl with neutron data. Does anyone know if it is possible to bypass/deactivate dictionnary .cif check i got the blocking error message "it looks like angle and bond restraints are conflicting." and Phenix.refine stops. but really it s not conflicting: my .cif file works great in coot to model the complex. it is hydrogen based, so i really need restraints to get it optimal.
any clues welcome, many thanks in advance.
Dr. Maxime Cuypers Post-Doctoral Research Associate, Structural Biology St Jude Children s Research Hospital, 262 Danny Thomas Place Memphis, TN 38105-3678, USA
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participants (3)
-
Dorothee Liebschner -
Maxime Cuypers -
Pavel Afonine