Hi I was wondering if there is a way to restrain the omega angles of the structure being refined to its starting values while allowing the phi and psi dihedral angles to vary? I was looking at omega_esd_override_value discard_omega in phenix.real_space_refine. Thank you, George
George, perhaps you can use reference model restraints machinery to do this..? Or perhaps you can tweak corresponding values in mon_lib/list/mon_lib_list.cif file..? Both ways may not be exactly what you want but may offer a reasonable work-around. Why you would like to do this? Pavel On 7/30/14, 11:53 AM, George Devaniranjan wrote:
Hi
I was wondering if there is a way to restrain the omega angles of the structure being refined to its starting values while allowing the phi and psi dihedral angles to vary?
I was looking at
omega_esd_override_value
discard_omega
in phenix.real_space_refine.
Thank you, George
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Hi Pavel,
Thank you, I will look into your suggestions.
*I am confused by omega_esd_override_value *
*What is it supposed to do? *
Why? Again curiosity of what phenix.real_space_refine can do. I am trying
to stretch it to the max and see where is breaks….
Thank you
On Wed, Jul 30, 2014 at 12:23 PM, Pavel Afonine
George,
perhaps you can use reference model restraints machinery to do this..? Or perhaps you can tweak corresponding values in mon_lib/list/mon_lib_list.cif file..? Both ways may not be exactly what you want but may offer a reasonable work-around.
Why you would like to do this?
Pavel
On 7/30/14, 11:53 AM, George Devaniranjan wrote:
Hi
I was wondering if there is a way to restrain the omega angles of the structure being refined to its starting values while allowing the phi and psi dihedral angles to vary?
I was looking at
omega_esd_override_value
discard_omega
in phenix.real_space_refine.
Thank you, George
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Hi George, On 7/30/14, 9:28 AM, George Devaniranjan wrote:
*I am confused by omega_esd_override_value * * * *What is it supposed to do? *
sources/cctbx_project % libtbx.find_files -g omega_esd_override_value ./mmtbx/monomer_library/pdb_interpretation.py: omega_esd_override_value = None ./mmtbx/monomer_library/pdb_interpretation.py: if (peptide_link_params.omega_esd_override_value is not None): ./mmtbx/monomer_library/pdb_interpretation.py: assert peptide_link_params.omega_esd_override_value > 0 ./mmtbx/monomer_library/pdb_interpretation.py: proxy.weight = 1/peptide_link_params.omega_esd_override_value**2 Hopefully this makes it clearer. Pavel
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George Devaniranjan -
Pavel Afonine