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Messages - Akhilesh Mishra

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Feature requests / Re: Rebuild DNA structures based on 28 parameters
« 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!!

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Feature requests / Re: Rebuild DNA structures based on 28 parameters
« 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!! 

 

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Feature requests / 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.       

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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.