Hi, Does phenix.refine restrain cis peptide? How do I know if the refined pdb file contain any cis peptide? Thanks. -- Jianghai
Hi Jianghai,
Does phenix.refine restrain cis peptide?
Yes, controlled via this parameter scope: peptide_link { cis_threshold = 45 discard_psi_phi = True omega_esd_override_value = None }
How do I know if the refined pdb file contain any cis peptide?
In theory you could tell by inspecting the .geo file, but it is difficult to pin-point the cis peptide restraints. Probably, it is better to use e.g. the pdb deposition tools or something similar to get a listing of the cis peptides. I'll add "list cis peptides" to our to-do list. Ralf
Hi Jianghai, Coot can detect the residues with cis peptides bonds . Good luck! liu Ralf W. Grosse-Kunstleve wrote:
Hi Jianghai,
Does phenix.refine restrain cis peptide?
Yes, controlled via this parameter scope:
peptide_link { cis_threshold = 45 discard_psi_phi = True omega_esd_override_value = None }
How do I know if the refined pdb file contain any cis peptide?
In theory you could tell by inspecting the .geo file, but it is difficult to pin-point the cis peptide restraints. Probably, it is better to use e.g. the pdb deposition tools or something similar to get a listing of the cis peptides.
I'll add "list cis peptides" to our to-do list.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thanks, Ralf, It would be very nice if phenix.refine could output this kind information onto the pdb head, just like refmac5 does. Another feature I would like to request is the phase smearing in MLHL refinement, which turned out to be very important in one of my recent cases. -- Jianghai On Nov 8, 2008, at 10:13 PM, Ralf W. Grosse-Kunstleve wrote:
Hi Jianghai,
Does phenix.refine restrain cis peptide?
Yes, controlled via this parameter scope:
peptide_link { cis_threshold = 45 discard_psi_phi = True omega_esd_override_value = None }
How do I know if the refined pdb file contain any cis peptide?
In theory you could tell by inspecting the .geo file, but it is difficult to pin-point the cis peptide restraints. Probably, it is better to use e.g. the pdb deposition tools or something similar to get a listing of the cis peptides.
I'll add "list cis peptides" to our to-do list.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (3)
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Jianghai Zhu -
junfeng liu -
Ralf W. Grosse-Kunstleve