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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
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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:
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
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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
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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
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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
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University