Juanxun
Sorry for the slow response but you don't need to use the apply_cif_link
because the links are automatically applied in phenix.refine.
You can check this using the .geo file thus
elbow.refine_geo_display PHE-SEP-ARG_minimized.geo SEP !
The output (see below) shows the restraints between SEP and anything else.
The first RMS section is the entire model, the second is for the selection.
In the latest nightly builds, there is also a graphical representation
available via REEL.
phenix.reel PHE-SEP-ARG_minimized.pdb PHE-SEP-ARG_minimized.geo
Cheers
Nigel
RMS results for model
RMS(D/Z)
d-all d-none d-alt z-all
z-none z-alt
bond 0.001( 32) 0.001( 32) 0.000( 0) 0.024( 32)
0.024( 32) 0.000( 0)
angle 0.216( 42) 0.216( 42) 0.000( 0) 0.080( 42)
0.080( 42) 0.000( 0)
----- bonds ----- bonds ----- bonds ----- bonds ----- bonds ----- bonds
1 " C PHE C 3 " - " N SEP C 4 " ['1.329', '1.329', '-0.000',
'1.40e-02', '5.10e+03', '3.76e-04']
2 " C SEP C 4 " - " N ARG C 5 " ['1.329', '1.329', '-0.000',
'1.40e-02', '5.10e+03', '5.93e-05']
---- angles ---- angles ---- angles ---- angles ---- angles ---- angles
1 " C PHE C 3 " - " N SEP C 4 " - " CA SEP C 4 " ['121.70',
'121.80', '-0.10', '1.80e+00', '3.09e-01', '3.34e-03']
2 " CA PHE C 3 " - " C PHE C 3 " - " N SEP C 4 " ['116.20',
'116.25', '-0.05', '2.00e+00', '2.50e-01', '6.82e-04']
3 " C SEP C 4 " - " N ARG C 5 " - " CA ARG C 5 " ['121.70',
'121.73', '-0.03', '1.80e+00', '3.09e-01', '2.87e-04']
4 " CA SEP C 4 " - " C SEP C 4 " - " N ARG C 5 " ['116.20',
'116.23', '-0.03', '2.00e+00', '2.50e-01', '2.85e-04']
5 " O PHE C 3 " - " C PHE C 3 " - " N SEP C 4 " ['123.00',
'123.01', '-0.01', '1.60e+00', '3.91e-01', '1.81e-05']
6 " O SEP C 4 " - " C SEP C 4 " - " N ARG C 5 " ['123.00',
'123.00', '0.00', '1.60e+00', '3.91e-01', '5.79e-07']
---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals
---- dihedrals
1 " CA PHE C 3 " - " C PHE C 3 " - " N SEP C 4 " - " CA SEP
C 4 " ['180.00', '-179.13', '-0.87', '0', '5.00e+00', '4.00e-02',
'3.05e-02']
2 " CA SEP C 4 " - " C SEP C 4 " - " N ARG C 5 " - " CA ARG
C 5 " ['180.00', '-179.41', '-0.59', '0', '5.00e+00', '4.00e-02',
'1.38e-02']
---- chirals ---- chirals ---- chirals ---- chirals ---- chirals ----
chirals
RMS results for selection
RMS(D/Z)
d-all d-none d-alt z-all
z-none z-alt
bond 0.000( 2) 0.000( 2) 0.000( 0) 0.000( 2)
0.000( 2) 0.000( 0)
angle 0.054( 6) 0.054( 6) 0.000( 0) 0.029( 6)
0.029( 6) 0.000( 0)
Nigel
On Tue, May 21, 2013 at 10:51 PM, Jianxun Qi
refinement.pdb_interpretation { apply_cif_link { data_link = "SEPC-N" residue_selection_1 = "chain C and resname PHE and resid 3" residue_selection_2 = "chain C and resname SEP and resid 4" } apply_cif_link { data_link = "SEPC-N" residue_selection_1 = "chain C and resname SEP and resid 4" residue_selection_2 = "chain C and resname ARG and resid 5" } }
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov