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Questions and answers => RNA structures (DSSR) => Topic started by: auffinger on January 31, 2014, 03:26:41 am

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Title: dssr corrupted double-linked list: issue
Post by: auffinger on January 31, 2014, 03:26:41 am
Hi Xiang-Jun,

With the file 2OIU.py.pdb (see attached, I get the following message and dssr freeze:

*** glibc detected *** x3dna-dssr: corrupted double-linked list: 0x0000000001604530 ***

Thanks for help and best wishes for the Horse year.

Best,

Pascal
Title: Re: dssr corrupted double-linked list: issue
Post by: xiangjun on January 31, 2014, 09:13:05 am
Hi Pascal,

Thanks for reporting the issue you experienced with DSSR. Could you be more specific to help me reproduce the bug? Which version, on what platform, with what options did you use? When I tried 2OIU.py.pdb on my iMac, DSSR seems to be working (see below):

Code: [Select]
Processing file '2OIU.py.pdb' [2OIU.py]

total number of base pairs: 74
total number of multiplets: 6
total number of helices: 6
total number of stems: 12
total number of hairpin loops: 6
total number of bulges: 2
total number of internal loops: 4
total number of junctions: 2
total number of non-loop single-stranded segments: 12
total number of kissing loops: 0
total number of A-minor (type I and II) motifs: 4
total number of ribose zippers: 8 (27)
total number of kink turns: 0

This is likely a bug that only shows up in rare cases, presumably associated with your non-standard PDB file (2OIU.py.pdb). I'll try my best to fix the bug as soon as I can clearly identify it.

Best regards,

Xiang-Jun
Title: Re: dssr corrupted double-linked list: issue
Post by: xiangjun on January 31, 2014, 03:24:51 pm
Hi Pascal,

As a follow up, I have checked the troublesome 2OIU.py.pdb on a Ubuntu Linux (64-bit) machine, and was able to reproduce the bug. Interesting, the issue did not show up with the original PDB entry 2oiu (http://www.rcsb.org/pdb/explore/explore.do?structureId=2oiu); otherwise, I've have caught it ;D. As noted in my previous reply, this bug did not show up on Mac OS X either. So in the future bug report, please remember to give sufficient details.

Anyway, thanks for using DSSR under 'extreme' conditions, which certainly helps to make the program more robust. In DSSR v1.0.1-2014jan31, this bug has been fixed, among a few other improvements. Have a try, and report back if you have further issues.

Best regards,

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.