Probe could not be detected on your system.

[Gliese436c]

Hi,

I've installed cctbx-base using conda. I copied chem_data directory to ${CONDA_PREFIX}/lib/python3.11/site-packages/ and i had to export the variable $CLIBD_MON for the monomers library.

I'm trying to run the following command:

import mmtbx.model
from mmtbx.validation import molprobity
import iotbx.pdb

pdb_inp = iotbx.pdb.input(file_name=file)
model = mmtbx.model.manager(model_input = pdb_inp)
a=molprobity.molprobity(model)
a.molprobity_score()

but i get the following error:

RuntimeError: Probe could not be detected on your system.  Please make sure Probe is in your path. Probe is available at http://kinemage.biochem.duke.edu/

I tried to move the probe binary in ${CONDA_PREFIX}/bin which is in the path but it didn't work. How can i fix it?

[nwmoriarty]

Does

molprobity.probe input.pdb

work?

Cheers

Nigel

---

Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : @.*** Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

On Wed, Sep 20, 2023 at 3:08 AM Gliese436c @.***> wrote:

Hi,

I've installed cctbx-base using conda. I copied chem_data directory to ${CONDA_PREFIX}/lib/python3.11/site-packages/ and i had to export the variable $CLIBD_MON for the monomers library.

I'm trying to run the following command:

import mmtbx.modelfrom mmtbx.validation import molprobityimport iotbx.pdb pdb_inp = iotbx.pdb.input(file_name=file)model = mmtbx.model.manager(model_input = pdb_inp)a=molprobity.molprobity(model)a.molprobity_score()

but i get the following error:

RuntimeError: Probe could not be detected on your system. Please make sure Probe is in your path. Probe is available at http://kinemage.biochem.duke.edu/

I tried to move the probe binary in ${CONDA_PREFIX}/bin which is in the path but it didn't work. How can i fix it?

— Reply to this email directly, view it on GitHub https://github.com/cctbx/cctbx_project/issues/928, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAHYQPHGA7NV4SYP5AGDSPTX3K6BJANCNFSM6AAAAAA47U3CHU . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[Gliese436c]

I don't have molprobity.probe, just molprobity.probescore_ligand.

I forgot to say that I'm using conda from mambaforge.

Thanks Davide