Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · G4 Structures · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Author Topic: Filter frayed ends or broken H bonds  (Read 84 times)

Offline RAHULRAH

  • regular
  • *
  • Posts: 2
    • View Profile
Filter frayed ends or broken H bonds
« on: October 10, 2019, 08:32:20 am »
Hello,

I am trying to process some X-ray protein-DNA crystal data. I am just focussing on the double-stranded DNA structure. But there are some snapshots/structure in which the H-bond doesn't seem to be okay i.e. say distance of acceptor and donor atoms in H-bond is more than 5 angstrom.

Are there any justified criteria for how to filter such bad snapshots?

Thanks in advance
Rahul

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1445
    • View Profile
    • 3DNA homepage
Re: Filter frayed ends or broken H bonds
« Reply #1 on: October 10, 2019, 09:09:46 am »
Hi Rahul,

Please use concrete examples to illustrate unambiguously what you want to achieve.

Thanks.

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

Offline RAHULRAH

  • regular
  • *
  • Posts: 2
    • View Profile
Re: Filter frayed ends or broken H bonds
« Reply #2 on: October 11, 2019, 08:18:34 am »
Hi Xiang,

Thanks for the reply. Sorry for not making it clear.

In simple words, how would I classify whether any H-bond in DNA is broken or how to identify base-pairs in DNA structure?

I want to use a Gaussian model similar to the one of Prof. Olson's coarse-grained model but also including intra-base parameters i.e. shear, stretch, stagger and Buckle, Propellor, opening. As you expect that some ends might be frayed due to which some of the helical parameters given by 3DNA are very weird. For example, very high opening or stretch which indicates H-bond is broken and I can see that in VMD as well.

Now the question is what shall be the criteria of such broken H-bonds? Is there any standard protocol in 3DNA? I have seen some articles using 4 angstroms as a cutoff in 3DNA, for example in, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879501/ and https://doi.org/10.1093/nar/gky599

Thanks
Rahul

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1445
    • View Profile
    • 3DNA homepage
Re: Filter frayed ends or broken H bonds
« Reply #3 on: October 11, 2019, 08:54:11 am »
See FAQ entry: "How to fix missing (superfluous) base pairs identified by find_pair?" (http://forum.x3dna.org/faqs/how-to-fix-missing-(superfluous)-base-pairs-identified-by-find_pair/)

Again, if you provide a concrete example, we could discuss the issue in more detail.

Best regards,

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

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.