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Dear Dr. Lu,
For the PDB file 4YLN, a bps file can be made, however, an output file that analyzes the bps file can not be created.
The error message reads:
residue serial number 1144911546 or 0 <= 0
Are there some modifications that need to be done to the bps file before it can be analyzed? How can an output file for 4YLN be created?
Thanks,
Ashay
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Hi Ashay,
You've identified a bug in find_pair
output when the serial number of a nucleotide is 5-digit long, as in 4yln.
7660 7697 9 # 72 x ....>5:..16_:[.DC]C-----g[GTP]:..13_:6<.... 2.42 1.72 8.66 9.27 3.28
1144911546 0 # 73 | ....>7:..11_:[.DA]A-----T[.DT]:..52_:8<.... 1.27 1.16 40.25 8.64 2.60
The field "1144911546" should be "11449 11546". There is no residue with a serial number that big.
The bug has been fixed in 3DNA v2.3-2017feb08. Please download it and report back if you have further questions.
Thanks for reporting!
Xiang-Jun
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.