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Author Topic: Segmentation fault  (Read 1366 times)

Offline Phosphoserine

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Segmentation fault
« on: May 21, 2016, 08:10:28 am »
Dear Dr. Xiang-Jun,

I have recently used the x64 Linux x3dna-snap binary to analyze the interactions in almost all available protein--DNA complexes, using the .pdb files as inputs. In over 3,700 of them, the program worked wonderfully, however, in four (PDB IDs 1LBG, 2VS7, 2VW9, 3T72) the program crashed with a segmentation fault. I was not able to observe any shared features in these complexes which could cause this unexpected behavior, nor do these complexes have any features which distinguish them from the structures for which the program worked (i.e., 1LBG is a C-alpha only structure, but the program did not crash for other CA structures).

This behavior was tested on Ubuntu 16.04 and Debian 8 machines and was reproduced under a Windows 10 environment with the .exe binary as well. Running the 32-bit Linux binary yields "program not found", so I can't test that. The web version of SNAP fails to process these structures as well.

It seems that it is beyond the scope of my knowledge to see what might be causing this behavior, but I thought you might appreciate this feedback and I hope it aids the development of this great tool.

Best regards,
David J.

Offline xiangjun

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Re: Segmentation fault
« Reply #1 on: May 21, 2016, 09:49:50 am »
Hi David,

Thank you so much for using SNAP, and the detailed bug report of the program's failure on some PDB structures. This post serves to acknowledge that I've noticed this issue. I strive to fix the segmentation fault ASAP, and report back my findings on the Forum.

Best regards,

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

Offline xiangjun

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Re: Segmentation fault
« Reply #2 on: May 21, 2016, 12:34:03 pm »
Hi David,

I've fixed the segmentation fault bug in the beta-r07-2016may21 release of SNAP. The bug was due to missing side-chain atoms in certain amino acids, leading to undefined (NULL pointer) for the corresponding reference frame. Please have a try, and report back how it goes.

As always, any comments, suggestions, and bug reports are appreciated.

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

Offline Phosphoserine

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Re: Segmentation fault
« Reply #3 on: May 21, 2016, 02:27:37 pm »
Dear Xiang-Jun,

thank you very much for the quick bug fix, the updated x64 Linux binary now runs without problems for virtually all protein--DNA complex structures there are available.

Best regards,
David J.

 

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.