Hello All-
I'm trying to refine some RNA and I can't seem to get phenix to read in my pdb file as it seems to not recognize the the nucleic acid as nucleic acid, as opposed to protein. By comparison to another pdb from the rcsb site(3b31) I seem to be following the same convention. Any suggestions on what I am doing wrong? I do have protein in the pdb as well. The protein has a different chain id.
I am running phenix-1.24.1b, my next move if I can't figure this out is to upgrade. Do I have the format of the RNA wrong?
Here is the error message and below that is an example of the first residue of the rna.
Cheers-
Todd
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sorry the PDB file xxx.pdb has an incomplete residue (or conformer/residue combination) in conformer '' chain R residue U 1 because this conformer is missing the following main-chain atoms: ['N', 'CA', 'C']
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ATOM 18243 O5' U R 1 50.409 12.832 14.548 1.00144.33 O
ATOM 18244 C5' U R 1 49.763 12.566 15.794 1.00144.88 C
ATOM 18245 C4' U R 1 49.745 13.804 16.678 1.00145.19 C
ATOM 18246 O4' U R 1 49.036 13.579 17.920 1.00145.17 O
ATOM 18247 C1' U R 1 49.400 14.624 18.811 1.00145.36 C
ATOM 18248 N1 U R 1 49.443 14.148 20.242 1.00145.47 N
ATOM 18249 C2 U R 1 48.886 14.949 21.229 1.00145.51 C
ATOM 18250 O2 U R 1 48.347 16.024 21.005 1.00145.55 O
ATOM 18251 N3 U R 1 48.976 14.439 22.507 1.00145.32 N
ATOM 18252 C4 U R 1 49.555 13.242 22.895 1.00145.27 C
ATOM 18253 O4 U R 1 49.558 12.920 24.081 1.00145.43 O
ATOM 18254 C5 U R 1 50.118 12.468 21.816 1.00145.29 C
ATOM 18255 C6 U R 1 50.045 12.940 20.562 1.00145.32 C
ATOM 18256 C2' U R 1 50.735 15.197 18.331 1.00145.42 C
ATOM 18257 O2' U R 1 50.561 16.545 17.935 1.00145.28 O
ATOM 18258 C3' U R 1 51.102 14.243 17.192 1.00145.51 C
ATOM 18259 O3' U R 1 51.827 14.863 16.146 1.00146.05 O