Messages

1

General discussions (Q&As) / Re: Shift and Tilt values of Z-DNA : 3DNA and Curves+

« on: May 13, 2018, 10:18:16 pm »

Dear Dr. Xiang-Jun Lu,
I am really thankful for such a detailed reply.  It is very reassuring to know that there are "No right or wrong parameters here" 
I will surely report back discrepancies If I observe any in the further analysis. Thanks a lot once again.

Best Regards,
Mandar Kulkarni

2

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