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Author Topic: strange exception  (Read 367 times)

Offline xiangjun

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Re: strange exception
« Reply #25 on: July 08, 2019, 02:21:16 pm »
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It seems the new version (Jul8) works very well for all my trajectory for now.

Glad to hear that the updated version works. I've just released DSSR v1.9.4-2019jul08.

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By the way I am benchmarking your new version using a ribosomal structure (PDB 1FFK).
Here I attached the output using version 2017jan22 (x3dna-dssr-old) and 2019jul08 (x3dna-dssr).

Here is the output:
...
For example, it seems the new version detect less base pairs, less multiplets, is that because you adjust the criteria for base pair or something?

If you think this post should be in a separate topic, could you please help move it to a proper place?

DSSR has been under continuous development and delivery. I maintain an extensive test set that includes all known buggy cases (such as your attached examples in this thread). For each release, I test DSSR against all nucleic-acid structures in the PDB to ensure that it does not crash. Except for boundary cases, DSSR is stable from version 1.0 and backward compatible, especially with the JSON output. I am confident that DSSR is a solid software product, with robust performances in real-world applications.

If you are interested in knowing the details between the two versions you tested, please start a new thread. Please provide concrete examples (base pairs, multiplets, etc.) where the differences really bother you.

Best regards,

Xiang-Jun

« Last Edit: July 08, 2019, 08:24:26 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.