Konrad

The DCT entry in the phenix copy monomer library is from an earlier version of the monomer library. The newer version of monomer library is likely better but it's not immediately clear that the older version is wrong. Can you send my the .geo file off-list?

Cheers

Nigel

On Tue, Apr 2, 2013 at 9:21 AM, Konrad Bergen <Konrad.Bergen@uni-konstanz.de> wrote:
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
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--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
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