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Author Topic: Rebuild DNA structures based on 28 parameters  (Read 93 times)

Offline Akhilesh Mishra

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Rebuild DNA structures based on 28 parameters
« on: October 28, 2017, 08:56:54 am »
Respected Xiang Sir,
                               I have calculated 28 structural parameter values on the basis of crystal structures of DNA, including 5 base pair axis parameter (X Disp., Y Disp., Inclination, Tip and Ax-Bend), 6 Intra base pair parameter (Shear, Stretch, Stagger, Buckle, Propel and Opening), 8 Inter base pair parameter (Shift, Slide, Rise, Tilt, Roll, Twist, H-Rise and H-Twist) and 9 backbone parameter (Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Chi, Phase and Amplitude).

I want to rebuild DNA structure on the basis of these all 28 parameters to get an average DNA structure according to my calculated values. I tried to use rebuild function but I am only able to use 12 parameters at a time through .par file. Further, in this project, I want to give some extra attention on backbone angles and thus want to change accordingly.

May you please guide me that how can I change all the 28 parameter value for a DNA structure at once or any step by step process to achieve the same.

                                                                Thank You!!
Your Sincerely
Akhilesh Mishra
Research Scholar,
c/o Prof B. Jayaram,
SCFBio, IIT Delhi, INDIA.       

Offline xiangjun

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Re: Rebuild DNA structures based on 28 parameters
« Reply #1 on: October 28, 2017, 07:03:37 pm »
Dear Akhilesh Mishra,

No, you cannot build DNA structures based on the 28 listed parameters simultaneously. At least in my understanding, they are not fully independent.

The 3DNA rebuild program can rigorously reconstruct the base-pair geometry using either of two sets of 12 parameters: 6 base-pair parameters (propeller, buckle, etc.) + 6 step parameters (roll, slide, etc.), or 6 base-pair parameters (propeller, buckle, etc.) + 6 helical parameters (x-displacement, inclination, etc.). The 2003 3DNA NAR paper provides details on the relationship between the step and helical parameters, in the section "Dimer step parameters". Fig. 4 and Table 1 taken from the 2003 3DNA NAR paper are shown below, for completeness.






So the answer is no, this feature request cannot be fulfilled.

Xiang-Jun
« Last Edit: October 28, 2017, 07:07:48 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Akhilesh Mishra

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Re: Rebuild DNA structures based on 28 parameters
« Reply #2 on: November 01, 2017, 09:03:45 am »
Thank You, Sir!!

As an alternative, is it possible that first I would modify the DNA structure by modifying bp_step.par file, then reanalyze the structure which will produce new bp_step.par and bp_helical.par file. In the second step, I would modify bp_helical.par file with my parameter values. This may generate the modified DNA structure with 18 modified parameters. Is this approach is correct?

Further Sir, I am trying my best to modify DNA backbone angles of a DNA structure separately but I am not getting any success. May you please guide me in this regard.
                 Thanks Again!! 

 

Offline xiangjun

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Re: Rebuild DNA structures based on 28 parameters
« Reply #3 on: November 02, 2017, 10:32:51 am »
Quote
As an alternative, is it possible that first I would modify the DNA structure by modifying bp_step.par file, then reanalyze the structure which will produce new bp_step.par and bp_helical.par file. In the second step, I would modify bp_helical.par file with my parameter values. This may generate the modified DNA structure with 18 modified parameters. Is this approach is correct?

Interesting idea. Please have a try and let us informed what you get.

Quote
Further Sir, I am trying my best to modify DNA backbone angles of a DNA structure separately but I am not getting any success. May you please guide me in this regard.

3DNA is of not much help here, sorry. You may try NAB (Nucleic Acid Builder), from the David Case lab at Rutgers. NAB “provides a programming environment for geometric and force-field manipulations of nucleic acids (and proteins as well).”

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

Offline Akhilesh Mishra

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Re: Rebuild DNA structures based on 28 parameters
« Reply #4 on: November 06, 2017, 09:06:39 am »
Respected Sir,
                     Is it possible to modify the rebuild code in such a manner that it starts to consider one ".par" file considering 18 parameters at once instead of two ".par" file (bp_step.par & bp_helical.par file) considering 12 parameters each?

Further Sir, I read the NAB manual but I do not get any clue that, "How could I change the backbone angle with my parameter values?" It might be, I am not focusing at right place may you please guide me to the place from where I can start.
                                   Thank You!!

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.