On Sun, Jan 25, 2015 at 12:25 AM, Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote:
> Here, I subtracted the "Phenix and Refmac" entries from the total Phenix > count, because it seems likely that Phenix was used for other purposes than > refinement. > Actually, based on my skimming of methods sections in recent publications, it is relatively common for users to run multiple refinement programs over the course of a project. In fact it's far more common than the combinations in the "software" field indicate, because the PDB deposition process will automatically use whatever is indicated by the submitted PDB file - i.e. the last program run - and users usually won't update this to include previously run programs. One consequence of this is that CNS ends up being underrepresented in the software field, because it tends to be used earlier in refinement (DEN, for example), with Phenix or Refmac substituted when the model is closer to convergence. The other consequence is that you can't assume that entries tagged as just Phenix OR Refmac were really refined with only one program rather than a combination. The moral: when you deposit your structures, please indicate all software used, not just the very last program that you ran. (And, of course, include the relevant citations in the actual publication, which sadly doesn't always happen.) -Nat
