molprobity coot TODO python script
Hello, 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? Another molprobity related question: us there a phenix script that produces a list of NQH flip candidates? Thank you, Wolfram Tempel Attached image: Clicking in the white areas on the window in the attached screen grab will move the center of the coot display, but labels for the problem areas are not shown in the window's columns.
On Thu, Jun 19, 2014 at 12:50 PM, wtempel
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, however.) -Nat
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Nathaniel Echols -
wtempel