[phenixbb] refine double conformations of a glycan

22 Feb 2012

      Hi all,

In my structure, the ASN and the linked NAG has two conformations. The pdb:
ATOM   3685  C1 ANAG A2061       4.069   2.862  24.649  0.47 31.33
 C
ANISOU 3685  C1 ANAG A2061     3426   4664   3813   -664    421    625
 C
ATOM   3686  C1 BNAG A2061       9.105   0.384  22.719  0.53 40.81
 C
ANISOU 3686  C1 BNAG A2061     5087   5333   5084     24    -72   -116
 C
ATOM   3690  C2 ANAG A2061       4.508   1.905  25.749  0.47 34.38
 C
ANISOU 3690  C2 ANAG A2061     3953   4727   4383   -441    142    473
 C
ATOM   3691  C2 BNAG A2061       8.311  -0.893  22.808  0.53 40.91
 C
ANISOU 3691  C2 BNAG A2061     5087   5438   5018     13    -55    -37
 C
ATOM   3694  N2 ANAG A2061       5.010   0.727  25.059  0.47 35.56
 N
ANISOU 3694  N2 ANAG A2061     4185   4888   4437   -466    149    254
 N
ATOM   3695  N2 BNAG A2061       7.220  -0.767  23.761  0.53 40.82
 N
ANISOU 3695  N2 BNAG A2061     5159   5512   4836    246   -144   -112
 N
ATOM   3698  C7 ANAG A2061       6.312   0.507  24.874  0.47 34.61
 C
ANISOU 3698  C7 ANAG A2061     4357   4653   4141   -406    202    282
 C
ATOM   3699  C7 BNAG A2061       5.974  -1.172  23.460  0.53 41.98
 C
ANISOU 3699  C7 BNAG A2061     5327   5677   4943    117      8   -149
 C
ATOM   3700  O7 ANAG A2061       7.194   1.236  25.322  0.47 35.05
 O
ANISOU 3700  O7 ANAG A2061     4292   4626   4396   -724    290    343
 O
ATOM   3701  O7 BNAG A2061       5.625  -1.665  22.371  0.53 44.02
 O
ANISOU 3701  O7 BNAG A2061     5616   5774   5335      6   -122   -208
 O
ATOM   3702  C8 ANAG A2061       6.699  -0.698  24.067  0.47 33.30
 C
ANISOU 3702  C8 ANAG A2061     4119   4700   3832   -193     57    303
 C
ATOM   3703  C8 BNAG A2061       4.933  -0.984  24.514  0.53 42.31
 C
ANISOU 3703  C8 BNAG A2061     5260   5612   5203    157     -4   -125
 C
ATOM   3710  C3 ANAG A2061       3.357   1.608  26.717  0.47 34.94
 C
ANISOU 3710  C3 ANAG A2061     3903   4950   4420   -528    289    456
 C
ATOM   3711  C3 BNAG A2061       9.296  -2.001  23.171  0.53 40.83
 C
ANISOU 3711  C3 BNAG A2061     5144   5347   5021     31   -211    -83
 C
ATOM   3714  O3 ANAG A2061       3.801   0.844  27.813  0.47 37.07
 O
ANISOU 3714  O3 ANAG A2061     4043   5387   4655   -327    106    508
 O
ATOM   3715  O3 BNAG A2061       8.608  -3.231  23.147  0.53 41.68
 O
ANISOU 3715  O3 BNAG A2061     5286   5504   5046   -142   -263     97
 O
ATOM   3718  C4 ANAG A2061       2.696   2.880  27.229  0.47 33.38
 C
ANISOU 3718  C4 ANAG A2061     3490   4870   4323   -715    378    575
 C
ATOM   3719  C4 BNAG A2061      10.480  -2.021  22.187  0.53 39.61
 C
ANISOU 3719  C4 BNAG A2061     4854   5338   4854     85   -226    -13
 C
ATOM   3722  O4 ANAG A2061       1.507   2.534  27.956  0.47 35.04
 O
ANISOU 3722  O4 ANAG A2061     3669   4878   4766   -843    393    668
 O
ATOM   3723  O4 BNAG A2061      11.583  -2.708  22.745  0.53 37.22
 O
ANISOU 3723  O4 BNAG A2061     4397   5524   4220    146   -644     59
 O
ATOM   3726  C5 ANAG A2061       2.336   3.744  26.026  0.47 34.15
 C
ANISOU 3726  C5 ANAG A2061     3749   4890   4334   -733    503    550
 C
ATOM   3727  C5 BNAG A2061      11.003  -0.643  21.780  0.53 39.23
 C
ANISOU 3727  C5 BNAG A2061     4886   5258   4760     33   -165    -30
 C
ATOM   3730  C6 ANAG A2061       1.625   5.025  26.471  0.47 35.40
 C
ANISOU 3730  C6 ANAG A2061     4140   4847   4461   -657    269    378
 C
ATOM   3731  C6 BNAG A2061      11.764  -0.744  20.462  0.53 39.76
 C
ANISOU 3731  C6 BNAG A2061     5000   5228   4877     79   -185   -106
 C
ATOM   3736  O6 ANAG A2061       2.432   5.674  27.428  0.47 37.10
 O
ANISOU 3736  O6 ANAG A2061     4302   5083   4710   -773    428    205
 O
ATOM   3737  O6 BNAG A2061      10.918  -1.227  19.435  0.53 40.11
 O
ANISOU 3737  O6 BNAG A2061     4599   5472   5169    313    -83   -277
 O
ATOM   3740  O5 ANAG A2061       3.507   4.032  25.210  0.47 33.36
 O
ANISOU 3740  O5 ANAG A2061     3905   4796   3974   -742    445    909
 O
ATOM   3741  O5 BNAG A2061       9.974   0.304  21.624  0.53 39.18
 O
ANISOU 3741  O5 BNAG A2061     5023   5184   4676   -220    -99   -108
 O
ATOM   1157  N   ASN A  61       8.496   4.626  20.319  1.00 26.85
 N
ANISOU 1157  N   ASN A  61     3029   4695   2476  -1809   -655   1273
 N
ATOM   1158  CA AASN A  61       7.080   4.398  20.655  0.50 24.65
 C
ANISOU 1158  CA AASN A  61     2996   4000   2368  -1776   -634    980
 C
ATOM   1159  CA BASN A  61       7.083   4.446  20.752  0.50 25.61
 C
ANISOU 1159  CA BASN A  61     3174   4178   2376  -1622   -618    912
 C
ATOM   1162  CB AASN A  61       6.952   3.807  22.077  0.50 23.96
 C
ANISOU 1162  CB AASN A  61     2901   3704   2497  -1862   -440   1083
 C
ATOM   1163  CB BASN A  61       7.016   4.118  22.260  0.50 26.04
 C
ANISOU 1163  CB BASN A  61     3226   4291   2376  -1605   -554    824
 C
ATOM   1168  CG AASN A  61       5.499   3.653  22.494  0.50 27.33
 C
ANISOU 1168  CG AASN A  61     3048   4420   2914  -1388   -585    598
 C
ATOM   1169  CG BASN A  61       7.882   2.975  22.608  0.50 27.64
 C
ANISOU 1169  CG BASN A  61     3195   4695   2612  -1576   -444    650
 C
ATOM   1170  OD1AASN A  61       4.659   3.204  21.697  0.50 27.73
 O
ANISOU 1170  OD1AASN A  61     3349   4200   2986  -1314   -644    873
 O
ATOM   1171  OD1BASN A  61       8.908   3.141  23.291  0.50 30.84
 O
ANISOU 1171  OD1BASN A  61     3734   4991   2990  -1345   -880    129
 O
ATOM   1172  ND2AASN A  61       5.182   4.096  23.716  0.50 34.27
 N
ANISOU 1172  ND2AASN A  61     3736   5474   3811   -832   -539    234
 N
ATOM   1173  ND2BASN A  61       7.512   1.797  22.152  0.50 34.10
 N
ANISOU 1173  ND2BASN A  61     5062   4644   3251  -1031   -186    246
 N

I put link in .def file like this:
   apply_cif_link {
     data_link = "NAG-ASN"
     residue_selection_1 = chain A and resname ANAG and resid 2061
     residue_selection_2 = chain A and resname AASN and resid 61
   }
   apply_cif_link {
     data_link = "NAG-ASN"
     residue_selection_1 = chain A and resname BNAG and resid 2061
     residue_selection_2 = chain A and resname BASN and resid 61
   }
but when I run the .def file, I got an error message:
couldn't find :residue_selection_1 = chain A and resname ANAG and resid 2061

Is there any wrong in my file?

Thank you very much!

yamei

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[phenixbb] refine double conformations of a glycan

Qiang Chen