[phenixbb] molprobity vs validation_cryoem

Roberto Marabini roberto at cnb.csic.es
Sun Apr 28 06:59:27 PDT 2019


Thanks for the explanation.

  roberto

On Fri, Apr 26, 2019 at 4:03 PM Oleg Sobolev <osobolev at lbl.gov> wrote:

> Hi Roberto,
>
> The difference occurs because of using/not using CDL
> (conformation-dependent library) modifications. In case of molprobity, CDL
> is not used since it is not mentioned the pdb file header which lead us to
> assume that it was refined without CDL. In case of cryoem_validation it is
> used. To turn it off use "cdl=False" command-line parameter or locate this
> flag in GUI. To turn it on for molprobity, add line
> REMARK   3 CDL
> to your pdb file.
>
> Best regards,
> Oleg Sobolev.
>
> On Fri, Apr 26, 2019 at 6:14 AM Roberto Marabini <roberto at cnb.csic.es>
> wrote:
>
>> 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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