Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Download/Licensing · {Video Overview of DSSR}

Author Topic: std_base  (Read 6615 times)

Offline maryatx3dna

  • with-posts
  • *
  • Posts: 27
    • View Profile
std_base
« on: March 13, 2014, 03:18:42 am »
Sir,
I tried the std_base -fit option with xdna as in a earlier post. I tried the same with another modification. It works for A and G but not with C and T modification. I am attaching herewith C modification. I tried changing n2 to n1 ; but doesnt work.  Please look through what goes wrong.

Thanking you

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1616
    • View Profile
    • 3DNA homepage
Re: std_base
« Reply #1 on: March 13, 2014, 01:20:45 pm »
As shown in the attached image, the modified W is far off from a normal C. There is no N1 atom. Changing N2 to N1 does not help because N2 in W is connected to C4 and C6, not C2 and C6 as is the norm for N1 in pyrimidines. Thus, up to 3DNA v2.1 released on 2013jul10, W is not recognized a nucleotide, as can be verified by the following command:
Code: [Select]
find_pair -s W.pdb stdout

W.pdb
W.outs
    1      # single helix
    0      # number of bases
    1    1 # explicit bp numbering/hetero atoms

So the reported behavior is as expected in the current 3DNA distributions. I will check if it is feasible to refine 3DNA's definition to include such modified cases in future releases. Alternatively, you may want to try the NUPARM/NUCGEN programs from the Bansal lab.

Xiang-Jun

« Last Edit: March 13, 2014, 01:36:10 pm by xiangjun »

Offline maryatx3dna

  • with-posts
  • *
  • Posts: 27
    • View Profile
Re: std_base
« Reply #2 on: March 14, 2014, 12:36:27 am »
Sir,
So it means i couldnt get analysis of a modified DNA containing such a residue? No trick is possible?
Also
I didnt get NUCPARM . Is it available.? Could nucgen and nucparm can be used to analyze modified residues?

Thanking you for your valuable suggestions,

mary

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1616
    • View Profile
    • 3DNA homepage
Re: std_base
« Reply #3 on: March 14, 2014, 12:55:22 am »
Quote
No trick is possible?
You could try changing C5Y to N1, then std_base would work. Just be careful with calculated parameters.

Quote
I didnt get NUCPARM . Is it available.? Could nucgen and nucparm can be used to analyze modified residues?
Just google NUPARM, you will find more information.

HTH,

Xiang-Jun

Offline maryatx3dna

  • with-posts
  • *
  • Posts: 27
    • View Profile
Re: std_base
« Reply #4 on: March 14, 2014, 07:18:55 am »
Sir,
Thank you very much.
I think that's working.
Hope the overall structural parameters would not be affected by this change in atom. The analysis will not be completed without helical parameter; after all other analysis done.

Thank you very much

mary

 

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.