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General discussions (Q&As) / Shift and Tilt values of Z-DNA : 3DNA and Curves+
« on: April 30, 2018, 09:50:09 am »
Dear Dr. Xiang-Jun Lu,
I am analyzing Z-DNA duplex (PDB ID: 1I0T.pdb) using 3DNA (v2.3-2017feb08) and Curves+ both. I have removed water and other molecule from PDB and only DNA coordinates are present. The input for Curves+ is generated using find_pair -c+ option.
3DNA command:
find_pair 1I0T.pdb stdout | analyze -c stdin
Curves+ command:
find_pair -c+ 1I0T.pdb curves_1I0T.inp
./Cur+ < curves_1I0T.inp
I observed that the Shift and TIlt values for dinucleotide steps have similar values but exactly opposite signs. Also, X-displacement, Y-displacement, Inclination values are totally different (ignoring terminal base pairs) compared to 3DNA results.
What could be the possible reason for such difference? I have searched the forum, but I did not find any discussions related to such discrepancy.
I have attached PDB file and both output files to the mail. Thanks in advance. I look forward to your reply.
Best Regards,
Mandar Kulkarni
I am analyzing Z-DNA duplex (PDB ID: 1I0T.pdb) using 3DNA (v2.3-2017feb08) and Curves+ both. I have removed water and other molecule from PDB and only DNA coordinates are present. The input for Curves+ is generated using find_pair -c+ option.
3DNA command:
find_pair 1I0T.pdb stdout | analyze -c stdin
Curves+ command:
find_pair -c+ 1I0T.pdb curves_1I0T.inp
./Cur+ < curves_1I0T.inp
I observed that the Shift and TIlt values for dinucleotide steps have similar values but exactly opposite signs. Also, X-displacement, Y-displacement, Inclination values are totally different (ignoring terminal base pairs) compared to 3DNA results.
What could be the possible reason for such difference? I have searched the forum, but I did not find any discussions related to such discrepancy.
I have attached PDB file and both output files to the mail. Thanks in advance. I look forward to your reply.
Best Regards,
Mandar Kulkarni