[phenixbb] command line molprobity tools

Pavel Afonine 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!


More information about the phenixbb mailing list