Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL

Author Topic: How does 3DNA calculate rise  (Read 1294 times)

Offline Auffinger

  • Verified Member
  • *
  • Posts: 108
    • View Profile
How does 3DNA calculate rise
« on: May 21, 2019, 05:07:44 am »
Hi Xiang-Jun,

I just have a silly question but I am unable to
find a simple description of how you calculate the rise values
and, incidentally, all other values.

Thanks,

Pascal
pascal auffinger
ibmc-cnrs
15, rue rené descartes
67084 strasbourg cedex
france

web sites:
http://www-ibmc.u-strasbg.fr/arn/Westho ... er_pub.HTM
http://www-ibmc.u-

Offline xiangjun

  • Administrator
  • Verified Member
  • *****
  • Posts: 1528
    • View Profile
    • 3DNA homepage
Re: How does 3DNA calculate rise
« Reply #1 on: May 21, 2019, 09:43:37 am »
Hi Pascal,

Have a look of $X3DNA/doc/tech-details.pdf, and/or read the source code.

HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

* Click "NOTIFY" to receive email notifications
* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite

Offline Auffinger

  • Verified Member
  • *
  • Posts: 108
    • View Profile
Re: How does 3DNA calculate rise
« Reply #2 on: July 03, 2019, 04:10:05 am »
Hi Xiang-Jun,

I found this definition regarding rise in the Calladine 1995 JMB paper:

Rise, Dz , is simply the component along the global
helix axis of the vector joining the mid points of
successive C6-C8 lines.

Is it calculated the same way in 3DNA ?
Sorry, I am not good at looking at the code.

Best,

Pascal
pascal auffinger
ibmc-cnrs
15, rue rené descartes
67084 strasbourg cedex
france

web sites:
http://www-ibmc.u-strasbg.fr/arn/Westho ... er_pub.HTM
http://www-ibmc.u-

Offline xiangjun

  • Administrator
  • Verified Member
  • *****
  • Posts: 1528
    • View Profile
    • 3DNA homepage
Re: How does 3DNA calculate rise
« Reply #3 on: July 03, 2019, 10:37:57 am »
Quote
I found this definition regarding rise in the Calladine 1995 JMB paper:

Rise, Dz , is simply the component along the global
helix axis of the vector joining the mid points of
successive C6-C8 lines.

I was puzzled by your above finding of 'Rise definition' in the Calladine 1995 JMB paper, titled The Assessment of the Geometry of Dinucleotide Steps in Double-Helical DNA; a New Local Calculation Scheme". Checking carefully, I noticed that the above citation comes from the "Appendix: NEWHELIX Definitions" (p.662) which uses a global helical axis, as further described below:

Quote
The expressions for Rise and Twist are clearly defined in a global sense, and they therefore depend on the overall conformation of an oligomer. Thus while these expressions are probably valid for, say, B-DNA oligomers where all base-pairs are nearly perpendicular to the overall fitted helix axis, they may not be appropriate for the analysis of other oligomers such as those that adopt the ‘‘A’’ form. It should be noted that since the magnitude of Helical Twist is in general substantially greater than the inclination of the base-pairs to the average best-fit helix-axis, the NH-values for Helical Twist are unlikely to be very different from those given by CEHS.

The CEHS definition of translational parameters (Shift-Dx, Slide-Dy, and Rize-Dz) comes on p.654:

Quote
The displacements: Dx, Dy and Dz can now be obtained by resolving the vector joining the origins of the two original base-pair triads into components along the axes of the mid-step triad.

Yes, that's the definition used in 3DNA as well.

HTH,

Xiang-Jun
« Last Edit: July 03, 2019, 10:40:05 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

* Click "NOTIFY" to receive email notifications
* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite

 

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.