<div>Could you try this?</div><div><br></div><div> apply_cif_link {</div><div> data_link = "NAG-ASN"</div><div> residue_selection_1 = chain A and resname NAG and resid 2061</div><div> residue_selection_2 = chain A and resname ASN and resid 61</div>
<div> }</div><div><br></div>I hope this works for both conformers.<div>Off the top of my head I'm not sure anymore how exactly we handle the conformers. If the above doesn't work insert "and altloc A", with a copy for "and altloc B", similar to what you tried.</div>
<div><br></div><div>Ralf</div><div><br><div class="gmail_quote">On Tue, Feb 21, 2012 at 5:15 PM, Qiang Chen <span dir="ltr"><<a href="mailto:chen@red.dfci.harvard.edu">chen@red.dfci.harvard.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi all,<br>
<br>
In my structure, the ASN and the linked NAG has two conformations. The pdb:<br>
ATOM 3685 C1 ANAG A2061 4.069 2.862 24.649 0.47 31.33<br>
C<br>
ANISOU 3685 C1 ANAG A2061 3426 4664 3813 -664 421 625<br>
C<br>
ATOM 3686 C1 BNAG A2061 9.105 0.384 22.719 0.53 40.81<br>
C<br>
ANISOU 3686 C1 BNAG A2061 5087 5333 5084 24 -72 -116<br>
C<br>
ATOM 3690 C2 ANAG A2061 4.508 1.905 25.749 0.47 34.38<br>
C<br>
ANISOU 3690 C2 ANAG A2061 3953 4727 4383 -441 142 473<br>
C<br>
ATOM 3691 C2 BNAG A2061 8.311 -0.893 22.808 0.53 40.91<br>
C<br>
ANISOU 3691 C2 BNAG A2061 5087 5438 5018 13 -55 -37<br>
C<br>
ATOM 3694 N2 ANAG A2061 5.010 0.727 25.059 0.47 35.56<br>
N<br>
ANISOU 3694 N2 ANAG A2061 4185 4888 4437 -466 149 254<br>
N<br>
ATOM 3695 N2 BNAG A2061 7.220 -0.767 23.761 0.53 40.82<br>
N<br>
ANISOU 3695 N2 BNAG A2061 5159 5512 4836 246 -144 -112<br>
N<br>
ATOM 3698 C7 ANAG A2061 6.312 0.507 24.874 0.47 34.61<br>
C<br>
ANISOU 3698 C7 ANAG A2061 4357 4653 4141 -406 202 282<br>
C<br>
ATOM 3699 C7 BNAG A2061 5.974 -1.172 23.460 0.53 41.98<br>
C<br>
ANISOU 3699 C7 BNAG A2061 5327 5677 4943 117 8 -149<br>
C<br>
ATOM 3700 O7 ANAG A2061 7.194 1.236 25.322 0.47 35.05<br>
O<br>
ANISOU 3700 O7 ANAG A2061 4292 4626 4396 -724 290 343<br>
O<br>
ATOM 3701 O7 BNAG A2061 5.625 -1.665 22.371 0.53 44.02<br>
O<br>
ANISOU 3701 O7 BNAG A2061 5616 5774 5335 6 -122 -208<br>
O<br>
ATOM 3702 C8 ANAG A2061 6.699 -0.698 24.067 0.47 33.30<br>
C<br>
ANISOU 3702 C8 ANAG A2061 4119 4700 3832 -193 57 303<br>
C<br>
ATOM 3703 C8 BNAG A2061 4.933 -0.984 24.514 0.53 42.31<br>
C<br>
ANISOU 3703 C8 BNAG A2061 5260 5612 5203 157 -4 -125<br>
C<br>
ATOM 3710 C3 ANAG A2061 3.357 1.608 26.717 0.47 34.94<br>
C<br>
ANISOU 3710 C3 ANAG A2061 3903 4950 4420 -528 289 456<br>
C<br>
ATOM 3711 C3 BNAG A2061 9.296 -2.001 23.171 0.53 40.83<br>
C<br>
ANISOU 3711 C3 BNAG A2061 5144 5347 5021 31 -211 -83<br>
C<br>
ATOM 3714 O3 ANAG A2061 3.801 0.844 27.813 0.47 37.07<br>
O<br>
ANISOU 3714 O3 ANAG A2061 4043 5387 4655 -327 106 508<br>
O<br>
ATOM 3715 O3 BNAG A2061 8.608 -3.231 23.147 0.53 41.68<br>
O<br>
ANISOU 3715 O3 BNAG A2061 5286 5504 5046 -142 -263 97<br>
O<br>
ATOM 3718 C4 ANAG A2061 2.696 2.880 27.229 0.47 33.38<br>
C<br>
ANISOU 3718 C4 ANAG A2061 3490 4870 4323 -715 378 575<br>
C<br>
ATOM 3719 C4 BNAG A2061 10.480 -2.021 22.187 0.53 39.61<br>
C<br>
ANISOU 3719 C4 BNAG A2061 4854 5338 4854 85 -226 -13<br>
C<br>
ATOM 3722 O4 ANAG A2061 1.507 2.534 27.956 0.47 35.04<br>
O<br>
ANISOU 3722 O4 ANAG A2061 3669 4878 4766 -843 393 668<br>
O<br>
ATOM 3723 O4 BNAG A2061 11.583 -2.708 22.745 0.53 37.22<br>
O<br>
ANISOU 3723 O4 BNAG A2061 4397 5524 4220 146 -644 59<br>
O<br>
ATOM 3726 C5 ANAG A2061 2.336 3.744 26.026 0.47 34.15<br>
C<br>
ANISOU 3726 C5 ANAG A2061 3749 4890 4334 -733 503 550<br>
C<br>
ATOM 3727 C5 BNAG A2061 11.003 -0.643 21.780 0.53 39.23<br>
C<br>
ANISOU 3727 C5 BNAG A2061 4886 5258 4760 33 -165 -30<br>
C<br>
ATOM 3730 C6 ANAG A2061 1.625 5.025 26.471 0.47 35.40<br>
C<br>
ANISOU 3730 C6 ANAG A2061 4140 4847 4461 -657 269 378<br>
C<br>
ATOM 3731 C6 BNAG A2061 11.764 -0.744 20.462 0.53 39.76<br>
C<br>
ANISOU 3731 C6 BNAG A2061 5000 5228 4877 79 -185 -106<br>
C<br>
ATOM 3736 O6 ANAG A2061 2.432 5.674 27.428 0.47 37.10<br>
O<br>
ANISOU 3736 O6 ANAG A2061 4302 5083 4710 -773 428 205<br>
O<br>
ATOM 3737 O6 BNAG A2061 10.918 -1.227 19.435 0.53 40.11<br>
O<br>
ANISOU 3737 O6 BNAG A2061 4599 5472 5169 313 -83 -277<br>
O<br>
ATOM 3740 O5 ANAG A2061 3.507 4.032 25.210 0.47 33.36<br>
O<br>
ANISOU 3740 O5 ANAG A2061 3905 4796 3974 -742 445 909<br>
O<br>
ATOM 3741 O5 BNAG A2061 9.974 0.304 21.624 0.53 39.18<br>
O<br>
ANISOU 3741 O5 BNAG A2061 5023 5184 4676 -220 -99 -108<br>
O<br>
ATOM 1157 N ASN A 61 8.496 4.626 20.319 1.00 26.85<br>
N<br>
ANISOU 1157 N ASN A 61 3029 4695 2476 -1809 -655 1273<br>
N<br>
ATOM 1158 CA AASN A 61 7.080 4.398 20.655 0.50 24.65<br>
C<br>
ANISOU 1158 CA AASN A 61 2996 4000 2368 -1776 -634 980<br>
C<br>
ATOM 1159 CA BASN A 61 7.083 4.446 20.752 0.50 25.61<br>
C<br>
ANISOU 1159 CA BASN A 61 3174 4178 2376 -1622 -618 912<br>
C<br>
ATOM 1162 CB AASN A 61 6.952 3.807 22.077 0.50 23.96<br>
C<br>
ANISOU 1162 CB AASN A 61 2901 3704 2497 -1862 -440 1083<br>
C<br>
ATOM 1163 CB BASN A 61 7.016 4.118 22.260 0.50 26.04<br>
C<br>
ANISOU 1163 CB BASN A 61 3226 4291 2376 -1605 -554 824<br>
C<br>
ATOM 1168 CG AASN A 61 5.499 3.653 22.494 0.50 27.33<br>
C<br>
ANISOU 1168 CG AASN A 61 3048 4420 2914 -1388 -585 598<br>
C<br>
ATOM 1169 CG BASN A 61 7.882 2.975 22.608 0.50 27.64<br>
C<br>
ANISOU 1169 CG BASN A 61 3195 4695 2612 -1576 -444 650<br>
C<br>
ATOM 1170 OD1AASN A 61 4.659 3.204 21.697 0.50 27.73<br>
O<br>
ANISOU 1170 OD1AASN A 61 3349 4200 2986 -1314 -644 873<br>
O<br>
ATOM 1171 OD1BASN A 61 8.908 3.141 23.291 0.50 30.84<br>
O<br>
ANISOU 1171 OD1BASN A 61 3734 4991 2990 -1345 -880 129<br>
O<br>
ATOM 1172 ND2AASN A 61 5.182 4.096 23.716 0.50 34.27<br>
N<br>
ANISOU 1172 ND2AASN A 61 3736 5474 3811 -832 -539 234<br>
N<br>
ATOM 1173 ND2BASN A 61 7.512 1.797 22.152 0.50 34.10<br>
N<br>
ANISOU 1173 ND2BASN A 61 5062 4644 3251 -1031 -186 246<br>
N<br>
<br>
I put link in .def file like this:<br>
apply_cif_link {<br>
data_link = "NAG-ASN"<br>
residue_selection_1 = chain A and resname ANAG and resid 2061<br>
residue_selection_2 = chain A and resname AASN and resid 61<br>
}<br>
apply_cif_link {<br>
data_link = "NAG-ASN"<br>
residue_selection_1 = chain A and resname BNAG and resid 2061<br>
residue_selection_2 = chain A and resname BASN and resid 61<br>
}<br>
but when I run the .def file, I got an error message:<br>
couldn't find :residue_selection_1 = chain A and resname ANAG and resid 2061<br>
<br>
Is there any wrong in my file?<br>
<br>
Thank you very much!<br>
<br>
yamei<br>
<br>
<br>
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</blockquote></div><br></div>