cis peptide and pdb head
Hi, How does phenix.refine treat cis peptide? Will it automatically detect it and restrain it like refmac5? or do I have to input the information somewhere? or generally how does phenix.refine treat the pdb head? I remember that some earlier version manual stated that all the head information are discarded, is that correct? Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++
Hi Jianghai,
How does phenix.refine treat cis peptide? Will it automatically detect it and restrain it like refmac5? or do I have to input the information somewhere?
Ralf is better person to answer since he implemented this... Anyway, from what I remember, phenix.refine tries to automatically detect cis/trans as following (Ralf, please confirm or deny): - if in input model it deviates within 45 degrees from cis, then phenix.refine considers it as cis; - if in input model it deviates within 45 degrees from trans, then phenix.refine considers it as trans.
or generally how does phenix.refine treat the pdb head? I remember that some earlier version manual stated that all the head information are discarded, is that correct?
The only information that phenix.refine picks up and uses from PDB file header is CRYST1 record. If data file in MTZ format is used then CRYST1 record is not mandatory. Pavel.
After phenix.refine detects the cis peptide, where does this information output? Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++ On Aug 20, 2007, at 10:56 PM, Pavel Afonine wrote:
Hi Jianghai,
How does phenix.refine treat cis peptide? Will it automatically detect it and restrain it like refmac5? or do I have to input the information somewhere?
Ralf is better person to answer since he implemented this... Anyway, from what I remember, phenix.refine tries to automatically detect cis/trans as following (Ralf, please confirm or deny): - if in input model it deviates within 45 degrees from cis, then phenix.refine considers it as cis; - if in input model it deviates within 45 degrees from trans, then phenix.refine considers it as trans.
or generally how does phenix.refine treat the pdb head? I remember that some earlier version manual stated that all the head information are discarded, is that correct?
The only information that phenix.refine picks up and uses from PDB file header is CRYST1 record. If data file in MTZ format is used then CRYST1 record is not mandatory.
Pavel. _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
After phenix.refine detects the cis peptide, where does this information output?
It gives you a count per chain in the indented pdb interpretation summary. Look for "CIS" and "PCIS" in the output. The definitve resource to find out more about the restraints is the .geo file. To pin-point restraints for certain atoms, copy the atom/residue/chain etc. labels from the PDB file, e.g. bond simple: (2, 4) " C GLY A 1 " " N ASN A 2 " distance_model: 1.33179 distance_ideal: 1.329 weight: 5102.04 This is a peptide bond. " C GLY A 1 " (without the quotes) is formatted exactly like in the ATOM record in the PDB file. Pavel's answer is correct in all points. Ralf
participants (3)
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Jianghai Zhu -
Pavel Afonine -
Ralf W. Grosse-Kunstleve