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Author Topic: xyz coordinates of O1P atoms  (Read 3956 times)

Offline ghzheng

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xyz coordinates of O1P atoms
« on: June 29, 2007, 12:21:53 pm »
How can I get the O1P and O2P atoms' coordinates w.r.t the middle frame of each dimer? After doing "find_pair -t *.pdb stdout | analyze", in the auxiliary.par files, we can see xyz coordinates of C1' atoms, xyz coordinates of P atoms w.r.t. the middle frame of each dimer, etc. But there are not datas for, xyz coordinates of O1P atoms w.r.t. the middle frame of each dimer.

I did find_pair after correction of o1p_o2p labeling. Bascially, if I try 1KX5.pdb, which has normal labels of O1P and O2P, I still have trouble to obtain coordinates of O1P and O2P w.r.t the middle frame of each dimer.

Can you let me know how I can obtain the information? Thanks.

Offline xiangjun

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« Reply #1 on: July 01, 2007, 10:58:56 am »
Thanks for using 3DNA.

Firstly, a detour: you mentioned the "o1p_o2p" utility program which was designed to check for correct labelling of the O1P and O2P atoms of nucleotides in a PDB file. The utility was initially written when I noticed the incorrect O1P/O2P labelling problem in the NDB entry adh008 (9dna) used as a test case in the 3DNA distribution.

To my surprise, even as of today, the problem is still there in the NDB (adh008) and PDB (9dna). To make it concrete, here is the except from corresponding data files in PDB format:

    NDB Asymmetric Unit coordinates
[pdb format, Unix compressed(.Z): pdb9dna.ent]:
Code: [Select]
ATOM     24  P     C A   2      35.309  46.286  11.717  1.00 28.71      9DNA  87
ATOM     25  O1P   C A   2      35.789  44.945  11.170  1.00 26.94      9DNA  88
ATOM     26  O2P   C A   2      36.213  47.108  12.492  1.00 25.98      9DNA  89
[/list]
    NDB Biological Unit coordinates
[pdb format: 9dna.pdb1]:
Code: [Select]
ATOM     20  P     C A   2      35.309  46.286  11.717  1.00 28.71           P  
ATOM     37  OP1   C A   2      36.213  47.108  12.492  1.00 25.98           O  
ATOM     38  OP2   C A   2      35.789  44.945  11.170  1.00 26.94           O  
[/list]
    PDB coordinates [
9DNA.pdb]:
Code: [Select]
ATOM     24  P     C A   2      35.309  46.286  11.717  1.00 28.71      9DNA  87
ATOM     25  O1P   C A   2      35.789  44.945  11.170  1.00 26.94      9DNA  88
ATOM     26  O2P   C A   2      36.213  47.108  12.492  1.00 25.98      9DNA  89
[/list]
Have you noticed the inconsistencies?

I am impressed you cared to run "o1p_o2p" to check for the correct O1P/O2P labelling in your interested DNA structures. From my limited experience, I feel those days people are much more interested in solving problems of "grand importance". Yet, whenever checked seriously, even "simple" issues claimed to have been resolved for so many years still have left so many details to be worked out. From SCHNAaP and SCHNArP, to resolving the discrepancies, to 3DNA and its continuous support/further refinements over the years (in my spare time), I have been trying to solve one specific problem that apparently has made a much bigger impact than I originally expected ten years ago.

Now, to answer your question. As of 3DNA v1.5, the auxiliary.par file does not contain the O1P (and O2P for that matter) xyz coordinates w.r.t. the middle frame. I am getting that info into v2.0 which hopefully could be released in the near future.

In the meantime, please check the file "stacking.pdb" which contains all the info you asked and much more. Of course, you need to have some (script) programming skills to extract the info you need and be careful about other technical details such as residue numbering, and direction of middle frame etc. I would say it's well worth the efforts ...

HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.