[phenixbb] which monlib in refinement?
Nigel Moriarty
nwmoriarty at lbl.gov
Tue Apr 2 10:20:13 PDT 2013
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 at 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
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
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