[phenixbb] command line molprobity tools
pafonine at lbl.gov
Wed May 1 13:31:32 PDT 2013
On 5/1/13 12:51 PM, Nathaniel Echols wrote:
> We have discussed making a unified program ("phenix.molprobity") that
> would do something like this. There aren't any technical obstacles;
> the only reason it hasn't happened is that this really needs to happen
> as a part of a more comprehensive refactoring of both the validation
> tools in the Phenix GUI, and of the MolProbity server itself.
> Otherwise we will inevitably end up with another jumbled mess with
> lots of code duplication.
What an excellent idea for someones todo list -:)
I would elaborate on this some more... Since validation in this context
is not only checking model quality, but also checking data and
model-to-data fit qualities, existing tools should probably be logically
grouped into three:
- data validation (phenix.xtriage, etc..)
- model validation (all these numerous jiffies mentioned in this
- model-to-data fit validation (phenix.model_vs_data,
phenix.real_space_correlation, phenix.polygon, etc).
Since all these tools were developed incrementally, there is duplication
in what they output, duplication in relevant code, and there could be
even inconsistencies... So that's right - to be healthy every programs
needs a rewrite every so often!
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