Dear all, A quick note to report the problems I have experienced (and a solution) with the refinement of a peptide containing both D- and L-amino-acids with refmac5.8 (Refmac_5.8.0073). This refinement was done with high resolution data, with hydrogens included in the model (important to remember !).
When using the standard dictionary for D-TRYPTOPHAN: $CLIBD_MON/d/DTR.cif, most of the geometrical definitions were altered after the inserted D-amino-acid. The geometrical Rms deviations are strongly increased already at the first cycle (see differences of two runs at the end of my message). The first solution was to generate a new cif dictionary from the standard TRP.cif file in the following way: sed -e 's/negativ/positiv/' -e 's/TRP/DTR/g' -e 's/L-peptide/D-peptide/' $CLIBD_MON/t/TRP.cif > DTRP.cif Running again refmac5 with this cif file using the LIBIN DTRP.cif instruction produced the more sensible results. It looked to me that the TRP and DTR cif definitions have diverged at some point. Looking more closely at the differences in this two files, pointed me to this: Hydrogen on the indole NE1 is named HE1 in TRP and HNE1 for DRT... Using a pdb file with HE1 renamed as HNE1 worked with the current DRT file, but with slightly worst results. The DTR.cif file probably needs to be updated (and maybe the other D-amino-acids cifs also revisited). Best regards, Pierre PS1. I can send the log and pdb files to developers if they are interested. PS2. I haven't checked with other D-amino-acids, since I have only this one in my structure. With modified TRP as DTRP.cif: < Initial Final < R factor 0.0865 0.0847 < R free 0.0913 0.0896 < Rms BondLength 0.0181 0.0175 < Rms BondAngle 2.2555 2.2407 < Rms ChirVolume 0.1131 0.1154 With standard DRT.cif file: > Initial Final > R factor 0.0865 0.1916 > R free 0.0913 0.2006 > Rms BondLength 2.4522 1.7415 > Rms BondAngle 33.3672 32.1460 > Rms ChirVolume 1.1972 1.0767 With DRT.cif and renamed HE1 as HNE1: > Initial Final > R factor 0.0865 0.0848 > R free 0.0913 0.0901 > Rms BondLength 0.0207 0.0200 > Rms BondAngle 2.4024 2.3884 > Rms ChirVolume 0.1122 0.1140
