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Author Topic: How to calculate groove parameters  (Read 595 times)

Offline lvelve0901

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How to calculate groove parameters
« on: August 22, 2016, 02:35:23 pm »
Hi,

Can we calculate groove parameters (like major groove width, minor groove depth etc.) in dssr?

Best,
Honglue

Offline xiangjun

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Re: How to calculate groove parameters
« Reply #1 on: August 22, 2016, 02:52:24 pm »
Hi Honglue,

Thanks for using DSSR, and for posting on the 3DNA Forum.

Quote
Can we calculate groove parameters (like major groove width, minor groove depth etc.) in dssr?

Not yet in DSSR. However, you may try 3DNA v2.3 which implement a method based on El Hassan and Calladine for the calculation of groove widths (but not depths). Given a PDB file (e.g., 355d.pdb), the command is:

Code: [Select]
find_pair 355d.pdb | analyze
and the output is in file 355d.out. For a complete description of groove dimensions, you may want to give Curves+ a try.


I've been thinking about incorporating key features of the 3DNA analyze program into DSSR. In addition to groove parameters, are there other features to would like to be made available in DSSR?

Best regards,

Xiang-Jun
« Last Edit: August 22, 2016, 02:54:19 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline lvelve0901

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Re: How to calculate groove parameters
« Reply #2 on: August 23, 2016, 09:41:59 pm »
Hi, xiangjun,

I think I only need groove parameters for now. I will let you know if I have some further need.

Thank you so much.

Best,
Honglue

 

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.