[NewChapter] rebuild is very slow and sometimes not finding anything

Started by Timo van der Laan

jflat06 Staff Lv 1

Also, when you are trying to Rebuild, are you attempting to do it while the helix is stretched out, with cut bands enabled?

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When I open devprev today I have build 20140203-a31a342de8-win_x86-devprev. I did not check the build number when I was having errors last night, but I did get a binary update last night. It's possible I did not get a full update, since I had a non-updated client running in the background, and possibly it was using some file and didn't get a new copy. This is on win 7 64.

I am not having the same errors today as yesterday. The backbone is not going through itself, and existing helices are not being severely deformed. The rate of finding rebuild has not improved much; it's about 3 per minute on my machine.

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I was rebuilding an already-existing helix. Auntdeen was trying to build a helix from an extended chain, something which many many people have had trouble with since newchapter went live. People have come up with a variety of techniques to make it work, but those techniques were not working for auntdeen last night.

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Here is some data comparing the Rebuild tool in the latest devprev release of newchapter (Feb 13) to earlier newchapter releases and to pre-newchapter devprev. I was only able to test one puzzle in common across these releases, but it looks like the latest Rebuild is finding poses at least as good as the pre-newchapter software, and better than the earlier newchapter releases. I have also noticed that it finds rebuild poses faster than the earlier newchapter releases.

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I tried increasing the number of rebuilds tried on each area from 10 to 20 (data on 10 rebuilds is attached to previous post). This increased the number of rebuilds with a positive score increase, from 41 to 80. It increased the number of areas of the protein improved by the script from 12 to 19 (out of 31 tried). The average improvement from each rebuild did not change, but with more areas being improved it did add up. The overall score increase went from 962 points (with 10 rebuilds per area) to 1181 points (with 20 rebuilds per area). There were still some areas where 20 rebuilds did not find an increase even though a previous test run of 10 rebuilds had found one. Still, as expected, trying more rebuilds results in better gains from a script run, because of better coverage of the areas where score increases are possible.