Using fragment picker, I have generated a 9mer file, however I manipulated with it to include different number of fragments at each location, ranging from 1 to 25.
I have generated thousands of decoys without any errors. But the following message always appears "...finished reading top 25 9mers..." although the number of fragments is not 25 at each position. Does it mean that all went right (it took for each position the corresponding number of available fragments) or simply Rosetta ignored fragments where number is less than 25?
Thank you so much,
The number printed there is the maximum number of fragments read at any position in the protein. If you have less than 25 fragments at any position, it will read all the fragments for that position, but for the purpose of that diagnostic line the number of fragments will be overshadowed by the position where there are 25 fragments.
(The code in question is `n_frags = std::max( n_frags, frame->nr_frags() );`, run once for each position, where `n_frags` is only ever used in the display line. In each "frame" (position) the number of fragments is stored correctly and varies based on how many you actually have.)