[phenixbb] refining nucleic acids, formats?

[Thomas C. Terwilliger]

Hi Todd,

I think that you are using the AutoBuild Wizard (based on the error
message you are getting)...if that isn't right, then please ask again...

The AutoBuild wizard can deal with building PROTEIN or RNA or DNA, but
only one at a time. The others have to be treated as a ligand with
"input_lig_file_list" and are added just before refinement.

I think that what is happening in your case is that there is more protein
than nucleic acid, and it is ignoring the nucleic acid.

Solutions:

1. If you just want to refine the structure, you can use phenix.refine
directly and there should be no problem at all.

2. If you do want to use AutoBuild, then split your model into PROTEIN and
RNA, and alternately build one and the other.  See

http://www.phenix-online.org/documentation/autobuild.htm#anch157

for some hints on how to do this.

All the best,
Tom T


> 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
>
> ***********************************
> 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']
> ***********************************
>
> 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
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