3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: rparkesh on November 06, 2010, 02:30:49 pm

Title: Re:stacking diagrm
Post by: rparkesh on November 06, 2010, 02:30:49 pm: Hi
My question was something specific about the generating the stacking diagram. How we can generate different color diagram other than the default and also how one can hide hydrogen atoms in the generated stacking diagram. I was trying to search in the manual but couldn't locate it.

I will appreciate any help.

Regards
Raman
Title: Re: Re:stacking diagrm
Post by: xiangjun on November 06, 2010, 08:03:17 pm: Hi Raman,

Thanks for posting questions related to stacking diagrams. You are actually the first to ask such details, and the documentation is sketchy, thus no wonder you "couldn't locate it".

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How we can generate different color diagram other than the default

Assuming you are using 3DNA v2.0, the config files are stored in the [mono:24t3qvd3]$X3DNA/config[/mono:24t3qvd3] directory, named [mono:24t3qvd3]ps_image.par[/mono:24t3qvd3], [mono:24t3qvd3]fig_image.par[/mono:24t3qvd3] and [mono:24t3qvd3]raster3d.par[/mono:24t3qvd3] for PostScript, Xfig, and Raster3D formats, respectively. They are pure ASCII text files and should not be that difficult to follow. You may copy a chosen-format-config file to a local directory for the stacking diagrams and tweak it as you see fit. Note the format is rigid -- make your change by directly overwriting the default one. [See FAQ http://3dna.rutgers.edu/x3dna/faqs#find_pair (http://3dna.rutgers.edu/x3dna/faqs#find_pair) on local vs global effects for a config file.]

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how one can hide hydrogen atoms in the generated stacking diagram.
You can run "[mono:24t3qvd3]get_part -d[/mono:24t3qvd3]" to remove H atoms first, and then feed the resulting PDB file to [mono:24t3qvd3]stack2img[/mono:24t3qvd3].

[hr:24t3qvd3][/hr:24t3qvd3]
Needless to say, the above-outlined procedures are not that user-friendly. However, they should work as expected, and allow for reproducible results with a script. Given an opportunity, I'd make the config file more flexible in future versions of 3DNA.

Have a try and report back if you have any problem.

Xiang-Jun