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Hi All,
I am trying to find the vector that describes the global helical axis for 1E3M.pdb the 1E3M.out file does not give this information. I have tried using 3DNA on the classical 1BNA structure and I am able to obtain the global helical axis. Any assistance for obtaining the global helical axis for 1E3M.pdb would be greatly appreciated (and an explanation for not being able to get this value is also appreciated).
Thanks in advance!
Sean
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That's because 1E3M is curved, thus fitting a global linear helical axis would be meaningless. More specifically, the section:
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 3.04(1.34)
shows a "deviation" of 1.34, which is larger than the default cutoff of 0.6, as defined in file 'misc_3dna.par'.
# Section 4: is this double helix curved?
# criterion to decide if a helix is strongly curved.
# if relatively straight, 'analyze' will output a set of
# global parameters, the normalized axis vector, and the
# two end points the helical axis passes through
<std_curved>0.6</std_curved>
HTH,
Xiang-Jun
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Hi,
Thank you for your reply. I am only interested in generating a rough helical axis so high accuracy is not important so I tried changing the parameter from 0.6 to 2.0 but I am still unable to obtain the values for the helical axis. Does this mean that I should also change other parameters?
Sean
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...so I tried changing the parameter from 0.6 to 2.0 but I am still unable to obtain the values for the helical axis. Does this mean that I should also change other parameters?
You've identified a bug in 3DNA v2.0 :D, so a big thank you! No other parameters need to be changed.
Technically, the bug is related to the tag [mono:hqpg41e9]"std_curved"[/mono:hqpg41e9] match; in the source code, it was mistaken as [mono:hqpg41e9]"std_curved "[/mono:hqpg41e9], i.e., with an extra space in the end. I've fixed this bug in the source; so the next release of 3DNA won't have this issue. As a temporary work around, simply add a suffix space in the tag, as below and it will work as expected:
<std_curved >0.6</std_curved > # add a space in the end!As a side note, v1.5 does not have this bug.
HTH,
Xiang-Jun
[hr:hqpg41e9][/hr:hqpg41e9]
PS. As always, the more bugs reported, the merrier :) ! In future release of 3DNA, I will also add an acknowledgement list.
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