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Questions and answers => General discussions (Q&As) => Topic started by: ashay on February 07, 2017, 02:39:14 pm

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Title: No Output File Created
Post by: ashay on February 07, 2017, 02:39:14 pm

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

Title: Re: No Output File Created
Post by: xiangjun on February 07, 2017, 06:41:59 pm

Hi Ashay,

You've identified a bug in

Code: [Select]

find_pair output when the serial number of a nucleotide is 5-digit long, as in 4yln.

Code: [Select]

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

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