[phenixbb] linking only one conformer to a thiol

Krzysztof Bzymek kbzymek at gmail.com
Thu Apr 5 17:13:50 PDT 2018


Hi,

I'm trying to refine a structure with a disulfide bond between a cysteine
and a thiol-containing peptide. There are two conformations for the
thiopeptide, in one of them the thiol is facing away from SG of the
cysteine (~7 A away). I defined the link as:

refinement.pdb_interpretation  {
  apply_cif_link {
    data_link = DRG-CYS
    residue_selection_1 = chain A and resname DRG and resid 10
    residue_selection_2 = chain B and resname CYS and resid 20
  }
}

I also tried:

refinement.pdb_interpretation  {
  apply_cif_link {
    data_link = DRG-CYS
    residue_selection_1 = chain A and resname DRG and resid 10 and altloc A
    residue_selection_2 = chain B and resname CYS and resid 20
  }
}

After refinement (with a corresponding data_link.eff file defining the
bonds and angles), the thiol of the other conformer that was facing away
from the cysteine moves out of the electron density and now faces the
cysteine (still about ~5.7 A away).

Is there a way to define a link between only one conformer and have the
other refine independently? I did try refinement without the above link
definition (relying on the proximity of the two cysteines and automatic
linking in phenix) but some of the bond and dihedral angles showed higher
deviation from ideal values expected for disulfide bonds.

Thanks,

Chris
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