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Author Topic: misshapen base ring  (Read 4204 times)

Offline Damien

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misshapen base ring
« on: January 07, 2013, 10:25:54 am »
Dear all,

I have a long DNA 3D structure that contains 4 bases with misshapen rings. I detected them thanks to visual inspection.

How can I identify these structural deficiencies in a more automatic manner with Web 3DNA? From the list of numbers resulting from "Analysis", can I detect these misshapen bases?

Thanks for your help,

Damien

Offline xiangjun

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Re: misshapen base ring
« Reply #1 on: January 07, 2013, 10:45:36 am »
Could you post (attach) an example structure to make your point concreate?

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

Offline Damien

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Re: misshapen base ring
« Reply #2 on: January 07, 2013, 11:12:21 am »
Hi Xiang-Jun,

Here is the 280 bp circular structure. Bases 275 and 276 of chain E, and 7 and 8 of chain F pose problem.

Thanks

Damien

Offline xiangjun

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Re: misshapen base ring
« Reply #3 on: January 07, 2013, 11:55:26 am »
Hi Damien,

Thanks for providing a sample PDB file that illustrates the problem you are facing; it helped me to identify the issue.

As shown by the attached image for DT8 on chain F, the base is distorted beyond recognition. For example, C5--C6 distance is only 0.42 Å -- far too short for a covalent bond, whereas N1--C6 = 1.97 Å and C4--C5 = 2.16 Å are far too long. So 3DNA won't recognize it as a DNA base T at all. Same issues exist for the other three nucleotides.

It does not makes much sense to change 3DNA to accommodate such erroneous cases; rather, the mistakes should be fixed in any tool you used to generate this structure in the first place.

HTH,

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

Offline Damien

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Re: misshapen base ring
« Reply #4 on: January 07, 2013, 12:43:07 pm »
Many thanks Xiang-Jun for this reply!

No, I did not suggest to change anything in 3DNA. I'm just looking for a way to avoid the visual inspection of the bases one by one.

I have the answer to my question in your reply: Web 3DNA does not recognize these distorted bases. This explains why the analysis in Web 3DNA results in 277 bp and not 280 (it seems however  that one "bad" base is recognized, DT 8 F).

So, 277 instead of 280 is the indication that something goes wrong. Then, a look at the RMSD in parentheses from the Nucleic acid structural parameter summary file is also a relevant parameter.

Am I right?

Thanks

Damien

ps: the goal of all this is to repair only the distorted base rings (as minimization on such a long structure can be very very long)

Offline xiangjun

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Re: misshapen base ring
« Reply #5 on: January 07, 2013, 01:34:38 pm »
Hi Damien,

Thanks for your follow-up. Yes, you can certainly use 3DNA to detect anomaly in a structure; that happened a (long) while ago at the NDB.

Thanks for pointing out the "bad" pair involving DT8 on chain F. The issue is due to the very 'generous' distance criteria used, which work well for 'reasonable' cases but apparently fail for your severely distorted structure. I'll fix the issue and update 3DNA shortly.

Xiang-Jun
« Last Edit: January 07, 2013, 01:36:42 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Damien

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Re: misshapen base ring
« Reply #6 on: January 07, 2013, 02:13:38 pm »
Many thanks for your help Xiang-Jun! I appreciate.

Damien

Offline xiangjun

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Re: misshapen base ring
« Reply #7 on: January 08, 2013, 01:19:16 pm »
Hi Damien,

I've updated 3DNA v2.1 to 2013jan08, with an improved algorithm for nucleotide identification. Specifically, in its default setting, DT8 on chain F is no longer recognized as a nucleotide. For the record, in my yesterday's response with an attached image, I observed the missing pair issue via Jmol using the DT8 as a test case. However, I did not check carefully to notice that previous versions of 3DNA, by virtue of very general distance cutoffs, actually take it as a nucleotide! :-[

Note that the w3DNA web-server hosted at Rutgers is currently not yet updated to the latest version. So your best bet is to download the standard command-line version of 3DNA; it is the most efficient and convenient way to get your job done.

HTH,

Xiang-Jun
« Last Edit: January 08, 2013, 01:21:18 pm by xiangjun »
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]· 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.