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Author Topic: 3DNA calculation for Bases that have two conformers in pdb  (Read 7121 times)

Offline kailsen

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3DNA calculation for Bases that have two conformers in pdb
« on: October 08, 2009, 12:29:46 am »
Dear Sir,
 I would like to know which of the two bases does 3DNA consider while calculating the parameters in cases where the pdb has two conformers for a single base
e.g from 437D.pdb
ATOM     47  O4'A  G A2648     -26.371  52.168 -12.884  0.58 13.58           O  
ATOM     48  O4'B  G A2648     -25.879  52.221 -11.854  0.42 16.38           O
ATOM     49  C3'A  G A2648     -24.982  50.605 -13.934  0.58 11.81           C  
ATOM     50  C3'B  G A2648     -24.120  50.873 -12.569  0.42 14.39           C

I some cases one of the bases is completely flipped out, while in some the bases overlap each other except for the few atoms. I note this happening mainly in RNA GA base pairs

Offline xiangjun

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Re: 3DNA calculation for Bases that have two conformers in pdb
« Reply #1 on: October 08, 2009, 06:58:09 pm »
This is a subtle point with regard to the ATOM or HETATM records of PDB format, and I am glad that you raised the issue. 3DNA has been designed with this in mind and works as it should.

In 3DNA v2.0, file misc_3dna.par contains the following section:

Code: PHP
  1. <span class="syntaxdefault"></span><span class="syntaxcomment"># Section 2&#58; alternative location in ATOM or HETATM records
  2. #   default to A or 1 (A1), and ' ' is always added
  3. </span><span class="syntaxkeyword"><</span><span class="syntaxdefault">alt_list</span><span class="syntaxkeyword">></span><span class="syntaxdefault">A1</span><span class="syntaxkeyword"></</span><span class="syntaxdefault">alt_list</span><span class="syntaxkeyword">></span><span class="syntaxdefault"> </span>
Thus, by default, only ATOM or HETATM records with alternative locations (column #17) of ' ', 'A' or '1' are processed. Of course, as pointed out in 3DNA FAQ, you could modify file misc_3dna.par to use other alternative locations: 'B', for example.

HTH,

Xiang-Jun

PS:
  • Every 3DNA user should upgrade to v2.0: you have nothing to lose (no backward compatibility issues) but to take advantage of a more refined piece of software.
  • Are you sure 437D.pdb has the ATOM records you listed?
    Code: [Select]
    e.g from 437D.pdb
    ATOM 47 O4'A G A2648 -26.371 52.168 -12.884 0.58 13.58 O
    ATOM 48 O4'B G A2648 -25.879 52.221 -11.854 0.42 16.38 O
    ATOM 49 C3'A G A2648 -24.982 50.605 -13.934 0.58 11.81 C
    ATOM 50 C3'B G A2648 -24.120 50.873 -12.569 0.42 14.39 C
    I cannot find them in 437D.pdb. It is not an important point here, but it would be helpful if you can clarify the discrepancy, just for the record.

Offline kailsen

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Re: 3DNA calculation for Bases that have two conformers in pdb
« Reply #2 on: October 10, 2009, 06:15:57 am »
Hi Lu,

 Thanks you for clarifying my doubt. Sorry for the discrepancy in the PDB ID. Pls  see 483d.pdb  instead. I had  removed the ANISOU lines for clarity.

ATOM     27  C4 A  U A2647     -28.663  57.538  -5.049  0.58 17.81           C  
ATOM     28  C4 B  U A2647     -29.492  57.317  -4.727  0.42 18.11           C  
ATOM     29  O4 A  U A2647     -29.141  58.325  -4.234  0.58 16.26           O  
ATOM     30  O4 B  U A2647     -30.281  57.919  -4.000  0.42 18.56           O

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.