How to calculate groove parameters

[lvelve0901]

Hi,

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

Best,
Honglue

[xiangjun]

Hi Honglue,

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

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

[lvelve0901]

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