Hi Oliver,
Just wondering whether there is any capacity to include DEN restraints in phenix.real_space_refine, e.g. as implemented in the program DireX (see ref below), or any possibility of implementing such in a future release of PHENIX?
do you have a specific example of a model *before* and *after* running through DireX that exemplifies the benefits? I would be very interested to see it (if you have one and choose to send me, please send it to my email address directly, not the whole phenixbb). phenix.real_space_refine has a number of options that allow to achieve very large convergence radius, such as model morphing, Simulated Annealing refinement, analog of MZ protocol (http://www.phenix-online.org/papers/dd5048_reprint.pdf) for rigid-body refinement, etc. These options are not enabled by default and so may escape user's attention.
Also, on a different but related topic, does anyone have any suggestions as to how to handle model validation (local and global) at low resolution in real-space? It seems as though there is not a solid consensus on how to handle this.
phenix.real_space_refine outputs block of text containing Molprobity statistics, as well as model to data (map) fit such as map correlation. You can also run Comprehensive Validation from Phenix GUI, although at the moment it would not accept map as a source of data. Pavel