3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: drboer on February 04, 2013, 02:26:53 am

Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Video Overview · DSSR v2.5.1 (DSSR Manual) · Homepage

Title: How to include dotted line along helical axis in figure?
Post by: drboer on February 04, 2013, 02:26:53 am

Dear all,

I'd like to add the helical axis as a dotted line in the 3dna-generated figures. Despite searching for it in NP08 and in the forums and website, I couldn't find how to do it.  I did see that the  stack2img help message mentions  a LISTFILE (LISTFILE  pairs of atom serial numbers for drawing a dotted line), but I can't find the format for this file, nor how to provide it to stack2img on the command line.

Any help would be highly appreciated,
Thanks in advance,
Roeland Boer.

Title: Re: How to include dotted line along helical axis in figure?
Post by: xiangjun on February 04, 2013, 06:28:28 pm

Could you be specific on what you mean by adding "the helical axis as a dotted line in the 3dna-generated figures"? As always, a concrete example would help clarify your point.

Fig. 3 (recipe #2) of the 3DNA NP08 paper shows a dotted line contacting bp centers, but I sense that's not what you want. Does the thread "defining a local helix axis (http://forum.x3dna.org/general-discussions/defining-a-local-helix-axis/)" help?

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University