3DNA Forum

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

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:
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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