[phenixbb] molprobity coot TODO python script

Nathaniel Echols nechols at lbl.gov
Thu Jun 19 13:42:14 PDT 2014

On Thu, Jun 19, 2014 at 12:50 PM, wtempel <wtempel at gmail.com> wrote:

> I noticed the following when loading a phenix-created python TODO script
> using the 4730 and 5100 Linux-x86_64-ubuntu-12.04.3-python-gtk2 coot builds.
> A "MolProbity to-do list" window opens. GUI functions such as "Show Probe
> dots" and "Overlap only" are working as expected. Clicking anywhere within
> the "C-beta outliers" or "Severe clashes" areas of the window moves the
> display center to problem areas of the structure.
> But:
> no text is visible in any of the columns ("Chain", "Residue", "Name", etc.
> of the "C-beta outliers area"; "Atom 1", Atom 2", "Overlap" of the "Severe
> clashes"). As a result, I cannot select a specific problem spot for
> centering.
> Any ideas?

That's strange - it's working fine for me, but I'm using the latest code.
 Which version are you using?  Could you please send me the script?

Another molprobity related question: us there a phenix script that produces
> a list of NQH flip candidates?

The version in the nightly build will output these, but they don't make it
into the to-do list yet.  (They have always appeared in the Phenix GUI,

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