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Author Topic: Question on Multiplets  (Read 2811 times)

Offline febos

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Question on Multiplets
« on: January 28, 2014, 01:10:51 pm »
Good Afternoon, Dr. Lu

I found out that multiplets in DSSR (beta-r29-on-20140106) can intersect each other, example in 2RSK (model 8 ):
Code: [Select]
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List of 4 multiplet(s)
   1 nts=4 GGGG [8.A.G.2.+8.A.G.5.+8.A.G.8.+8.A.G.11.]
   2 nts=4 GGGG [8.B.G.14.+8.B.G.17.+8.B.G.20.+8.B.G.23.]
   3 nts=7 GAGAGAG [8.A.G.1.+8.A.A.3.+8.A.G.4.+8.A.A.6.+8.A.G.7.+8.A.A.9.+8.A.G.10.]
   4 nts=10* AAAGAGAGAG [8.A.A.3.+8.A.A.6.+8.A.A.9.+8.B.G.13.+8.B.A.15.+8.B.G.16.+8.B.A.18.+8.B.G.19.+8.B.A.21.+8.B.G.22.]

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Here nts 8.A.A.3.;8.A.A.6.;8.A.A.9. are in both №3 and №4 multiplets.

Considering this issue I'd like to know what is Your definition of Multiplet? And also what does symbol "*" in " nts=10* " mean?

I'm sorry if You already described it somewhere else.

Best regards,
Eugene
« Last Edit: January 28, 2014, 01:13:05 pm by febos »

Offline xiangjun

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Re: Question on Multiplets
« Reply #1 on: January 28, 2014, 04:59:03 pm »
Hi Eugene,

That's the expected behavior right now. The "*" as in the 4th multiplet "nts=10*" means boundary cases where some bases are 'stacking' instead of being co-planar. Visualizing this multiplet in Jmol/PyMOL, you will notice that 8.A.A.3./8.A.A.6./8.A.A.9. are not far off, especially when 8.B.A.15. and 8.B.A.21. are not taken into consideration. In future releases of DSSR, I may consider to refine the algorithm to avoid any nt belonging to more then one multiplet.

Regarding the definition, more details will be available in the coming DSSR mauscript. Right now, suffice it to say that "DSSR detects triplets and higher-order base associations by searching horizontally in the plane of the associated bp for further H-bonding interactions" as put in the DSSR webpage and output from the -h (--help) option.

Users are strongly encouraged to upgrade to DSSR v1.0-2014jan25, which contains improved notes and formats in the output .

HTH,

Xiang-Jun
« Last Edit: January 28, 2014, 05:29:01 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline febos

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Re: Question on Multiplets
« Reply #2 on: January 29, 2014, 12:38:41 am »
Dr.Lu,

I looked at this file in Jmol and now I understand Your definition.

Thanks for Your help.

Best regards,
Eugene

Offline xiangjun

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Re: Question on Multiplets
« Reply #3 on: January 31, 2014, 03:12:39 pm »
Hi Eugene,

I've refined the algorithm for multiplets detection, now 2RSK (model #8) contains what one would expect:

Quote
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List of 4 multiplets
   1 nts=4 GGGG 8:A.G2,8:A.G5,8:A.G8,8:A.G11
   2 nts=4 GGGG 8:B.G14,8:B.G17,8:B.G20,8:B.G23
   3 nts=7 GAGAGAG 8:A.G1,8:A.A3,8:A.G4,8:A.A6,8:A.G7,8:A.A9,8:A.G10
   4 nts=7 GAGAGAG 8:B.G13,8:B.A15,8:B.G16,8:B.A18,8:B.G19,8:B.A21,8:B.G22

An image of multiplet #4 is attached below for your reference.

Please check out DSSR v1.0.1-2014jan31 for the update.

Xiang-Jun
« Last Edit: February 02, 2014, 01:23:15 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.