std_base

[maryatx3dna]

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

[xiangjun]

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

[maryatx3dna]

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

[xiangjun]

No trick is possible?

You could try changing C5Y to N1, then std_base would work. Just be careful with calculated parameters.

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

[maryatx3dna]

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