[phenixbb] which monlib in refinement?

[Konrad Bergen]

Hello phenixbb,

i was recently refining a DCT and was a bit puzzled  when i got outliers in torsion angles (readout from the final .geo file). The DCT was built in coot (using the ccp4 monomer library) and seems to fit these restraints. A closer look gave me a discrepancy in the torsion angles between the ccp4 (ver 6.3.0) and the corresponding phenix (dev1325) file

/usr/local/ccp4-6.3.0/ccp4-6.3.0/lib/data/monomers/d/DCT.cif

_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 DCT      var_1    O3G    PG     O3B    PB       -60.011   20.000   1
 DCT      var_2    PG     O3B    PB     O3A     -179.960   20.000   1
 DCT      var_3    O3B    PB     O3A    PA      -179.992   20.000   1
 DCT      var_4    PB     O3A    PA     "O5'"    179.964   20.000   1
 DCT      var_5    O3A    PA     "O5'"  "C5'"    179.986   20.000   1
 DCT      var_6    PA     "O5'"  "C5'"  "C4'"   -179.998   20.000   1
 DCT      var_7    "O5'"  "C5'"  "C4'"  "O4'"     65.696   20.000   3
 DCT      var_8    "C5'"  "C4'"  "C3'"  "C2'"   -150.000   20.000   3
 DCT      var_9    "C4'"  "C3'"  "C2'"  "C1'"     30.000   20.000   3
 DCT      var_10   "C5'"  "C4'"  "O4'"  "C1'"    150.000   20.000   1
 DCT      var_11   "C4'"  "O4'"  "C1'"  N1      -150.000   20.000   1
 DCT      var_12   "O4'"  "C1'"  "C2'"  "C3'"      0.000   20.000   3
 DCT      var_13   "O4'"  "C1'"  N1     C6      -121.764   20.000   1
 DCT      CONST_1  "C1'"  N1     C2     N3       180.000    0.000   0
 DCT      CONST_2  "C1'"  N1     C6     C5       180.000    0.000   0
 DCT      CONST_3  N1     C6     C5     C4         0.000    0.000   0
 DCT      CONST_4  C6     C5     C4     N3         0.000    0.000   0
 DCT      CONST_5  C5     C4     N4     HN41     179.773    0.000   0
 DCT      CONST_6  C5     C4     N3     C2         0.000    0.000   0
 DCT      CONST_7  C4     N3     C2     O2       180.000    0.000   0


/usr/local/phenix.test/latest/chem_data/mon_lib/d/DCT.cif

_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 DCT      var_3    O1G    PG     O3B    PB         2.570   20.000   1
 DCT      var_4    PG     O3B    PB     O3A       83.412   20.000   1
 DCT      var_6    O3B    PB     O3A    PA      -132.456   20.000   1
 DCT      var_7    PB     O3A    PA     O5*      -51.566   20.000   1
 DCT      var_9    O3A    PA     O5*    C5*     -166.199   20.000   1
 DCT      var_10   PA     O5*    C5*    C4*      135.553   20.000   1
 DCT      var_11   O5*    C5*    C4*    C3*       12.096   20.000   3
 DCT      var_12   C5*    C4*    O4*    C1*      143.686   20.000   1
 DCT      var_13   C5*    C4*    C3*    C2*     -117.819   20.000   3
 DCT      var_14   C4*    C3*    C2*    C1*      -21.471   20.000   3
 DCT      var_15   C3*    C2*    C1*    N1       150.776   20.000   3
 DCT      var_16   C3*    C2*    C1*    O4*       32.781   20.000   3
 DCT      var_17   C2*    C1*    N1     C2       121.270   20.000   1
 DCT      var_18   C2*    C1*    N1     C6       -65.572   20.000   1
 DCT      CONST_1  C1*    N1     C2     N3       180.000    0.000   0
 DCT      CONST_2  N1     C2     N3     C4         0.000    0.000   0
 DCT      CONST_3  C2     N3     C4     C5         0.000    0.000   0
 DCT      var_19   N3     C4     N4     HN41       0.000   20.000   1
 DCT      CONST_4  N3     C4     C5     C6         0.000    0.000   0
 DCT      CONST_5  C4     C5     C6     N1         0.000    0.000   0

I am just wondering which values/library to use or if i got something completely wrong. 
Best regards
Konrad