[phenixbb] molprobity vs validation_cryoem

Roberto Marabini roberto at cnb.csic.es
Fri Apr 26 06:11:35 PDT 2019


Sorry, In the previous email I sent a wrong link for the pdb file. The
rigth one is:

https://drive.google.com/open?id=0B_i_LJfUN1z7dEF6MHhzNEJvUEo2eUJCZmNRYUpfVFFLZy1j

On Fri, Apr 26, 2019 at 10:51 AM Roberto Marabini <roberto at cnb.csic.es>
wrote:

> Hi guys,
>
>    We are using phenix version 1.15.2-3472. We have executed molprobity
> using the command line:
>
> phenix.python_1.15.2-3472
> /usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/command_line/molprobity.py
> "path_to_pdb"/refmac-refined.pdb pickle=True
> nproc=4
>
> We have also executed validation_cryoem (here we have used both the GUI
> and the command line and both interfaces return the same result)
>
> phenix.python_1.15.2-3472
> ./phenix/phenix/command_line/validation_cryoem.py
> "path_to_pdb"/refmac-refined.pdb "path_to_map"/molprobity.mrc
> resolution=3.2 pickle=True
>
> What we do not fully understand is why the two commands return different
> results for molprobity. Are the default parameters different?
>
> For example, validation_cryoem reports as number of outliers "34" in the
> molprobity tab (model.geometry.angle.outliers) while molprobity reports 21
>
> The test files are available at:
>
> 3Dmap:
> https://drive.google.com/open?id=0B_i_LJfUN1z7amoyM1B2N1U0Y2VYODB6LWdLY1pwai04RWxz
> pdb file: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093775/
>
>     Thanks for the help
>
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