1226
General discussions (Q&As) / Re: Helices and Isolates in output of find_pair
« on: July 15, 2012, 09:36:07 am »
Thanks for providing detailed info about a mis-assigned helix by find_pair. As shown in the attached image, in PDB entry 1z58, nucleotides 336-338 and 346-348 should indeed be assigned into a helix. While the helix assignment algorithm of find_pair works elegantly for the majority of cases, it is clearly not sophisticated enough to properly handle complicated structures such as 1z58 (the large ribosomal subunit from the eubacterium Deinococcus radiodurans): if you pay close attention to the output from find_pair, you will see warning messages in such cases.
I'm interested in refining 3DNA on those complicated structures, and your reported example is a concrete case to start with. Do you have more examples? The more varied and detailed cases I have, the easier to test find_pair against, and the more 3DNA can work for you in the end.
Xiang-Jun
I'm interested in refining 3DNA on those complicated structures, and your reported example is a concrete case to start with. Do you have more examples? The more varied and detailed cases I have, the easier to test find_pair against, and the more 3DNA can work for you in the end.
Xiang-Jun