On Tue, Feb 21, 2012 at 5:15 PM, Qiang Chen <chen@red.dfci.harvard.edu> wrote:

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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