Open martinfalk opened 4 years ago
Thank you for pointing this out.
I introduced these flags (fast_clash and condensed_probe) to optimize the runtime of this utility. For technical reasons in some corner cases you can get slightly more clashes and almost negligible increase of clashscore itself (when using faster version). I believe these new clashes highlight areas that researchers should investigate. This code is used both in Phenix suite and in Molprobity website (http://molprobity.biochem.duke.edu/). We have already switched to a faster version in Phenix which you can see in model.py.
The discrepancy between web servers and Phenix package is the only result of these options. We (@chrissciwilliams) are investigating the possibilities of moving Molprobity web service to use the Phenix package options, but there is some inertia for such a visible service as Molprobity.
Got it. This slight difference actually caused me to investigate this. In particular since there is no obvious way in Phenix to access these parameters in order to reproduce the results with Molprobity and/or scripts.
There is an inconsistency regarding the default arguments of
clashscore.py
, in particularcondensed_probe
. Running the python script on a molecule produces slightly different results than running the validation in PHENIX.The default args for the command line are
False
. See here https://github.com/cctbx/cctbx_project/blob/34685978dccbf7a194fe99be48a51c2c99244c07/mmtbx/programs/clashscore.py#L12-L26 and https://github.com/cctbx/cctbx_project/blob/34685978dccbf7a194fe99be48a51c2c99244c07/mmtbx/programs/clashscore.py#L43-L46When looking for
condensed_probe
within mmtbx, I came acrossmodel.py
where it is defaulted toTrue
https://github.com/cctbx/cctbx_project/blob/34685978dccbf7a194fe99be48a51c2c99244c07/mmtbx/model/model.py#L3020-L3023When running clashscore.py on the command line using
condensed_probe=True
it produces the same results as when run within PHENIX.