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BGSU-RNA / FR3D

The official repository for "Find RNA 3D" (FR3D), a suite of programs for searching RNA 3D structures.
http://rna.bgsu.edu/main/software/fr3d/
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Infinite loop zBorderSS #10

Open michal-zurkowski opened 7 years ago

michal-zurkowski commented 7 years ago

I encountered a problem while reading file 488D.pdb. It enters infinite loop in file zBorderSS at line 121 and newer leaves. Used zAddNTData to read file.

clzirbel commented 7 years ago

Hi,

I recently fixed a situation like this with a different file. The problem was that one base was making two cWW basepairs (GC or AU or GU), and that got it stuck in a loop. This was fixed by improving the program that checks for one base using the Watson-Crick edge more than once. This was pushed to the dev branch, and now 488D loads without the infinite loop. Hopefully this helps you, too.

Craig

Craig L. Zirbel Professor and Graduate Coordinator Department of Mathematics and Statistics BGSU | Bowling Green State University Bowling Green, OH 43403 +1-419-372-7466; zirbel@bgsu.edu mailto:zirbel@bgsu.edu http://www-math.bgsu.edu/~zirbel http://www-math.bgsu.edu/%7Ezirbel

On 12/21/2016 8:39 PM, Michał Żurkowski wrote:

I encountered a problem while reading file 488D.pdb. It enters infinite loop in file zBorderSS at line 121 and newer leaves. Used zAddNTData to read file.

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michal-zurkowski commented 7 years ago

Hi, Unfortunately I still have this problem even on dev branch. I tried octave and newest MatLab to be sure and it still locks in the same loop. I'm using 488D.pdb from http://www.rcsb.org and trying to read with "File = zAddNTData(pdb_id);"

Mchal

clzirbel commented 7 years ago

Oops, my fault, haven't updated dev recently. Sorry about that. Lots to commit, I'll get working on it soon.

Craig L. Zirbel Professor and Graduate Coordinator Department of Mathematics and Statistics BGSU | Bowling Green State University Bowling Green, OH 43403 +1-419-372-7466; zirbel@bgsu.edu mailto:zirbel@bgsu.edu http://www-math.bgsu.edu/~zirbel http://www-math.bgsu.edu/%7Ezirbel

On 12/22/2016 10:11 AM, Michał Żurkowski wrote:

Hi, Unfortunately I still have this problem even on dev branch. I tried octave and newest MatLab to be sure and it still locks in the same loop. I'm using 488D.pdb from http://www.rcsb.org and trying to read with "File = zAddNTData(pdb_id);"

Mchal

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