Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Download/Licensing · {Video Overview of DSSR}

Author Topic: Global Helical Axis Information Missing  (Read 5584 times)

Offline slaw

  • with-posts
  • *
  • Posts: 19
    • View Profile
Global Helical Axis Information Missing
« on: September 23, 2010, 08:16:05 pm »
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

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1614
    • View Profile
    • 3DNA homepage
Re: Global Helical Axis Information Missing
« Reply #1 on: September 23, 2010, 09:57:20 pm »
That's because 1E3M is curved, thus fitting a global linear helical axis would be meaningless. More specifically, the section:

Code: [Select]
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'.

Code: [Select]
# 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

Offline slaw

  • with-posts
  • *
  • Posts: 19
    • View Profile
Re: Global Helical Axis Information Missing
« Reply #2 on: September 23, 2010, 11:47:08 pm »
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

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1614
    • View Profile
    • 3DNA homepage
Re: Global Helical Axis Information Missing
« Reply #3 on: September 24, 2010, 08:12:47 pm »
Quote from: "Sean"
...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:
Code: [Select]
<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.

 

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.