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Questions and answers => General discussions (Q&As) => Topic started by: mauricio esguerra on October 26, 2007, 02:13:03 pm

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Title: Silly helical regions question.
Post by: mauricio esguerra on October 26, 2007, 02:13:03 pm

Hello Dr. Xin,

I write again to bother with a similar question that I asked a while ago.
I am wondering if in 3DNA the standard helical regions are the ones that get a poc_haxis.r3d file created, and the ones that do not generate one after running analyze on them are the quasi-continuous ones.

Thanks,

Mauricio

Title:
Post by: yrxin on October 27, 2007, 01:41:54 pm

Hi Mauricio,

I think the poc_haxis.r3d file may be related to the curve of the helix as it is commented in the file. If the helix is not strongly bent, you will get this r3d file after running analyze. The helix could be a conventional or a quasi-continuous one. However, I don't exactly know the numerical criteria of the bend. Is it related to the parameter "std_curved"? I am sure Xiang-Jun knows it very well, and he may answer the question better.

Xiang-Jun, could you please help to explain it? Thank you.

Yurong

Title:
Post by: xiangjun on October 28, 2007, 11:50:43 pm

As Yurong pointed out, the "poc_haxis.r3d" file is produced when "analyze" finds the structure being analyzed is not "too curved" (check "misc_3dna.par" for default setting of the parameter). It corresponds directly to the "Global linear helical axis defined ..." section from the "analyze" main output file. It does not matter if the helical region is "quasi-continuous" or not.

To make it more concrete, here is an example:

Code: [Select]

find_pair bdl084.pdb stdout | analyzeYou will get file "poc_haxis.r3d" with contents as follows:

Code: [Select]

###
### Linear global helical axis if not strongly curved
#5
#   17.536   25.713   25.665    9.424   12.911   15.677   -9.080    9.424    1.000    0.000    1.000
#5
#   17.536   25.713   25.665    6.368   12.911   15.677   -9.080    6.368    1.000    0.000    1.000
#5
#   17.536   25.713   25.665    5.849   12.911   15.677   -9.080    5.849    1.000    0.000    1.000
5
   17.536   25.713   25.665    0.060   12.911   15.677   -9.080    0.060    1.000    0.000    1.000Check also the following section from "bdl084.out":

Code: [Select]

Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 3.30(0.52)
Helix:    -0.127  -0.275  -0.953
HETATM 9998  XS    X X 999      17.536  25.713  25.665
HETATM 9999  XE    X X 999      12.911  15.677  -9.080
Average and standard deviation of helix radius:
      P: 9.42(0.82), O4': 6.37(0.85),  C1': 5.85(0.86)
BTW, the poc in file "poc_haxis.r3d" stands for P (phosphorus), O4', and C1' atoms.

HTH,

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