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Author Topic: w3DNA hanging on some structures  (Read 1121 times)

Offline nb0147

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w3DNA hanging on some structures
« on: May 12, 2016, 06:53:40 am »
Hello

I've been using w3DNA to analyse a family of structures (very useful and straightforward, thank you very much). However, it is just hanging with some of the structures.

They have non-natural bases in them, but this can't be the only reason, as I have two chemically identical structures in very slightly different conformations, one runs fine and the other hangs forever.

Any thoughts would be much appreciated,

Nick

Offline wolson

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Re: w3DNA hanging on some structures
« Reply #1 on: May 12, 2016, 12:27:54 pm »
The hangup on your submission is likely related to the nature of the unusual bases treated in your system. The 3DNA webserver is working. You may want to try the new DSSR software to treat systems with unusual bases. These are not treated as rigorously in the 3DNA code. DSSR reports the rigid-body parameters, torsion angles, virtual distances, etc. found with 3DNA. You can download the software and learn about these and other features of DSSR from our 2015 NAR paper and the DSSR Manual (see links on the forum pages).

Offline xiangjun

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Re: w3DNA hanging on some structures
« Reply #2 on: May 12, 2016, 03:22:43 pm »
Hi Nick,

Since I do not have direct access to the w3DNA server (other than the public interface as everyone does), I cannot help fix any server-related issue. However, the problem you experienced may be due to a bug in 3DNA per se. Please provide me with a sample file with non-natural bases so I can reproduce the 'hanging' issue.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline nb0147

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Re: w3DNA hanging on some structures
« Reply #3 on: May 17, 2016, 03:39:58 am »
Hello Xiang-Jun

Thank you very much for looking into this.

For the benefit of the forum: I sent Xiang-Jun the PDB files, which he checked with the latest version of x3DNA. They all ran fine. I installed the latest version locally (required an OS update: OSX Lion to OSX El Capitan, which I probably should have done anyway ;0) and they all ran fine for me as well.

Thanks again to Xiang-Jun for some lovely software and excellent tech support.

Nick

 

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.