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 <jxqi@im.ac.cn> wrote:

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 : NWMoriarty@LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov