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Questions and answers => General discussions (Q&As) => Topic started by: mauricio esguerra on December 01, 2011, 05:45:21 am

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Title: std_curved parameters seems not to work in 3DNA V2.1
Post by: mauricio esguerra on December 01, 2011, 05:45:21 am

Dear Xiang-Jun,

In previous versions of 3DNA e.g. up to version:
3DNA v2.0 [August 2007] (by Dr. Xiang-Jun Lu; 3dna.lu@gmail.com (http://mailto:3dna.lu@gmail.com))

Changing the value of this parameter (i.e. <std_curved>) seems not to affect the analyze program.

I am fine using the August 2007 version for getting the global helical axis, but thought useful to report the bug.

Thanks for devoting so much of your spare time to 3DNA,

Mauricio

Title: Re: std_curved parameters seems not to work in 3DNA V2.1
Post by: xiangjun on December 01, 2011, 06:53:11 am

Greetings Mauricio!

It was (still is) a bug, but see thread "Global Helical Axis Information Missing (http://http://3dna.rutgers.edu:8080/forum/viewtopic.php?f=1&t=180&p=495&hilit=std_curved)". It's well worths repeating that for a word-around (for the time being), please do the following:

Code: [Select]

<std_curved >0.6</std_curved >   # add a space in the end of the tag!Just to clarify, [red:298epu6t][mono:298epu6t]3DNA v2.0 [August 2007][/mono:298epu6t][/red:298epu6t] was a pre-release for testing of v2.0 (beta) before the 2008 3DNA Nature Protocols paper was published; [red:298epu6t][mono:298epu6t]3DNA v2.0 [June 8, 2008][/mono:298epu6t][/red:298epu6t] is the currently distributed version. 3DNA [red:298epu6t]v2.1[/red:298epu6t] is not out yet, but I am planning to release it in the near future -- by early next year!

Thanks for reporting the bug! As always, the more bug reports, the merrier!

Xiang-Jun

Title: Re: std_curved parameters seems not to work in 3DNA V2.1
Post by: mauricio esguerra on December 01, 2011, 07:22:47 am

Ohh...! Great!
I usually pay attention to the forum but I didn't see this one.
Thanks!

Mauricio

Title: Re: std_curved parameters seems not to work in 3DNA V2.1
Post by: xiangjun on December 01, 2011, 11:25:51 am

I certainly should have made such cases more explicit -- I will add a new section to the forum, titled "Bug reports and feature requests", by the end of the week. As I am working on improving 3DNA, do you have any desired features or suggestions to make the software more useful? Do not be shy!

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