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General discussions (Q&As) / Re: helical Parameters of a Modified nucleic acids
« on: February 15, 2008, 11:53:00 pm »
Hi Mathew,
I have checked the files you uploaded. There are a few issues that are needed to be clarified to run 3DNA against your XDNA structure:
HTH,
Xiang-Jun
I have checked the files you uploaded. There are a few issues that are needed to be clarified to run 3DNA against your XDNA structure:
- Each Atomic_?.pdb file must be set with regard to the standard base reference frame, not just taken directly from a PDB file, as in your four attachments. Have a look (e.g., using RasMol of Atomic_A.pdb with the 3DNA distribution to see an example).
- For 3DNA to take a residue as a nucleotide, it must contain at least a six-membered ring with standard atom names common to A/C/G/T/U etc, including the " N1 " atom. In you modified Y bases (Atomic_Y-xty.pdb, Atomic_Z-xcs.pdb and Atomic_W-xae.pdb), you have atom " N " in place of " N1 ". In your cent02.pdb file, you also have atom " ND " in stead of " N1 " in residue XCS. That's why thay are not recognized by 3DNA. The modified R base, Atomic_X-xga.pdb, is fine.
- So to get to the bottom of it, you need to manually edit your cent02.pdb file to change " N " and " ND " to " N1 ", which I have done and attached as cent02_N1.pdb. Your Atomic_X-xga.pdb does not conform to PDB format (check Chain ID column), and you need to manually change atom name " N " to " N1 " in the other 3 Atomic_?-???.pdb files. I have modified "std_base" with option "-fit" to set a nucleotide with regard to the standard base reference frame to be used with 3DNA, and I have attached the re-oriented bases as Atomic_r.pdb and Atomic_y.pdb. You could also use Atomic_R.pdb and Atomi_Y.pdb, but the small case letter would lead 3DNA print out diagnostic message.
- You do not need to have a separate Atomic_?.pdb file for each modified base. In your case, two should be enough, and the updated baselist.dat is as follows:Code: [Select]
# for XDNA residues from Mathew
XTY y
XCS y
XT5 y
XAE r
XGA r
XA5 r
DT3 t
DA3 a - I have also attached the 3DNA 'analyze' output file cent02_N1.out (renamed cent02_N1.txt so it can be attached) for your reference.
- As I said in my previous email, I helped another 3DNA user on XDNA a while ago, and here is the URL for some of the info I provided: http://rutchem.rutgers.edu/~xiangjun/3D ... /xdna.html. Please download the updated 'std_base' program (Linux version) there. In the coming new release of 3DNA v2.0 (no specific date yet!), the "-fit" option comes as built in.
HTH,
Xiang-Jun