Infinite loop zBorderSS

[michal-zurkowski]

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]

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

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______________________________________________________________________ *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; [email protected] <mailto:[email protected]> http://www-math.bgsu.edu/~zirbel <http://www-math.bgsu.edu/%7Ezirbel>

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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. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#10>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA8Pk_WmN1jOe0Gs7DTq5fG9kf_vl4-Qks5rKdTKgaJpZM4LTjkF>.

[michal-zurkowski]

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]

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

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______________________________________________________________________ *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; [email protected] <mailto:[email protected]> http://www-math.bgsu.edu/~zirbel <http://www-math.bgsu.edu/%7Ezirbel>

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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 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA8Pk8qgFJtNzzFk_y47qwy9h7c3yDaRks5rKpMPgaJpZM4LTjkF>.