Not sure about the selection problem but the missing commands are likely molprobity.reduce and molprobity.probe. Chris, you should be able to change that.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty@LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


On Mon, Aug 12, 2019 at 11:43 AM Charitha Belluru Shetty <charitha-belluru.b.shetty@gsk.com> wrote:

Hi Christopher/Nigel,

 

We downloaded the molprobity after the patch and ran the configure.sh and setup scripts. Now things got worst.

 

Can you please help us on this.

 

Here is the output we are getting.

 

 

 

 

 

 

When we press the “Click here” button, below log file is generated.

 

[PLACE YOUR COMMENTS HERE]

 

==================================================

  USER / SERVER INFORMATION

==================================================

User IP       : 11.27.95.128

User browser  : Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/76.0.3809.100 Safari/537.36

Session ID    : c2h8n399dagb0ggfn8kpla6fu4

Session URL   : http://uptus002vm.corpnet2.com/molprobity/index.php?MolProbSID=c2h8n399dagb0ggfn8kpla6fu4

 

MolProb. ver. : 4.4

Server name   : uptus002vm.corpnet2.com

Server time   : 2019 Aug 12    18:24:41

 

==================================================

  ERRORS FROM THIS SESSION

==================================================

 

 

sh: phenix.reduce: command not found

sh: phenix.reduce: command not found

sh: phenix.reduce: command not found

sh: phenix.probe: command not found

sh: phenix.probe: command not found

sh: phenix.reduce: command not found

sh: phenix.reduce: command not found

sh: phenix.probe: command not found

sh: phenix.probe: command not found

 

Starting phenix.clashscore

on Mon Aug 12 13:50:31 2019 by appmgmt

===============================================================================

 

Processing files:

-------------------------------------------------------------------------------

 

  Files not used by program:

  --------------------------

  /hpc/apps/2018/molprobity/v4.4.app/MolProbity/public_html/data/c2h8n399dagb0ggfn8kpla6fu4/coordinates/1irkFH.pdb

 

Processing PHIL parameters:

-------------------------------------------------------------------------------

 

  Adding command-line PHIL:

  -------------------------

    b_factor_cutoff=40

    clash_cutoff=-0.4

 

Final processed PHIL parameters:

-------------------------------------------------------------------------------

  data_manager {

    default_output_filename = "cctbx_program"

  }

  b_factor_cutoff = 40

 

 

Starting job

===============================================================================

Sorry: 0 model(s) found. Expected at least 1.

chartClashlist ran for 5 seconds

do Charts ran for 0 seconds

sh: phenix.probe: command not found

do Kinemage ran for 0 seconds

 

Traceback (most recent call last):

  File "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/../modules/cctbx_project/mmtbx/command_line/mp_geo.py", line 7, in <module>

    mp_geo.run(sys.argv[1:])

  File "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/validation/molprobity/mp_geo.py", line 132, in run

    pdb_hierarchy.models()[0].chains():

IndexError: list index out of range

 

 

 

 

sh: phenix.reduce: command not found

 

sh: phenix.reduce: command not found

 

sh: phenix.reduce: command not found

 

sh: phenix.probe: command not found

 

sh: phenix.probe: command not found

 

sh: phenix.reduce: command not found

 

sh: phenix.reduce: command not found

 

sh: phenix.probe: command not found

 

sh: phenix.probe: command not found

 

 

 

Starting phenix.clashscore

 

on Mon Aug 12 13:50:31 2019 by appmgmt

 

===============================================================================

 

 

 

Processing files:

 

-------------------------------------------------------------------------------

 

 

 

  Files not used by program:

 

  --------------------------

 

  /hpc/apps/2018/molprobity/v4.4.app/MolProbity/public_html/data/c2h8n399dagb0ggfn8kpla6fu4/coordinates/1irkFH.pdb

 

 

 

Processing PHIL parameters:

 

-------------------------------------------------------------------------------

 

 

 

  Adding command-line PHIL:

 

  -------------------------

 

    b_factor_cutoff=40

 

    clash_cutoff=-0.4

 

 

 

Final processed PHIL parameters:

 

-------------------------------------------------------------------------------

 

  data_manager {

 

    default_output_filename = "cctbx_program"

 

  }

 

  b_factor_cutoff = 40

 

 

 

 

 

Starting job

 

===============================================================================

 

Sorry: 0 model(s) found. Expected at least 1.

 

chartClashlist ran for 5 seconds

 

do Charts ran for 0 seconds

 

sh: phenix.probe: command not found

 

do Kinemage ran for 0 seconds

 

 

 

Traceback (most recent call last):

 

  File "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/../modules/cctbx_project/mmtbx/command_line/mp_geo.py", line 7, in <module>

 

    mp_geo.run(sys.argv[1:])

 

  File "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/validation/molprobity/mp_geo.py", line 132, in run

 

    pdb_hierarchy.models()[0].chains():

 

IndexError: list index out of range

 

 

 

 

 

sh: phenix.reduce: command not found

 

sh: phenix.reduce: command not found

 

sh: phenix.reduce: command not found

 

sh: phenix.probe: command not found

 

sh: phenix.probe: command not found

 

sh: phenix.reduce: command not found

 

sh: phenix.reduce: command not found

 

sh: phenix.probe: command not found

 

sh: phenix.probe: command not found

 

 

 

Starting phenix.clashscore

 

on Mon Aug 12 13:50:31 2019 by appmgmt

 

===============================================================================

 

 

 

Processing files:

 

-------------------------------------------------------------------------------

 

 

 

  Files not used by program:

 

 --------------------------

 

  /hpc/apps/2018/molprobity/v4.4.app/MolProbity/public_html/data/c2h8n399dagb0ggfn8kpla6fu4/coordinates/1irkFH.pdb

 

 

 

Processing PHIL parameters:

 

-------------------------------------------------------------------------------

 

 

 

  Adding command-line PHIL:

 

  -------------------------

 

    b_factor_cutoff=40

 

    clash_cutoff=-0.4

 

 

 

Final processed PHIL parameters:

 

-------------------------------------------------------------------------------

 

  data_manager {

 

    default_output_filename = "cctbx_program"

 

  }

 

  b_factor_cutoff = 40

 

 

 

 

 

Starting job

 

===============================================================================

 

Sorry: 0 model(s) found. Expected at least 1.

 

chartClashlist ran for 5 seconds

 

do Charts ran for 0 seconds

 

sh: phenix.probe: command not found

 

do Kinemage ran for 0 seconds

 

 

 

Traceback (most recent call last):

 

  File "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/../modules/cctbx_project/mmtbx/command_line/mp_geo.py", line 7, in <module>

 

    mp_geo.run(sys.argv[1:])

 

  File "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/validation/molprobity/mp_geo.py", line 132, in run

 

    pdb_hierarchy.models()[0].chains():

 

IndexError: list index out of range

 

 

 

 

 

 

 

 

 

sh: phenix.reduce: command not found

 

 

 

sh: phenix.reduce: command not found

 

 

 

sh: phenix.reduce: command not found

 

 

 

sh: phenix.probe: command not found

 

 

 

sh: phenix.probe: command not found

 

 

 

sh: phenix.reduce: command not found

 

 

 

sh: phenix.reduce: command not found

 

 

 

sh: phenix.probe: command not found

 

 

 

sh: phenix.probe: command not found

 

 

 

 

 

 

 

Starting phenix.clashscore

 

 

 

on Mon Aug 12 13:50:31 2019 by appmgmt

 

 

 

===============================================================================

 

 

 

 

 

 

 

Processing files:

 

 

 

-------------------------------------------------------------------------------

 

 

 

 

 

 

 

  Files not used by program:

 

 

 

  --------------------------

 

 

 

  /hpc/apps/2018/molprobity/v4.4.app/MolProbity/public_html/data/c2h8n399dagb0ggfn8kpla6fu4/coordinates/1irkFH.pdb

 

 

 

 

 

 

 

Processing PHIL parameters:

 

 

 

-------------------------------------------------------------------------------

 

 

 

 

 

 

 

  Adding command-line PHIL:

 

 

 

  -------------------------

 

 

 

    b_factor_cutoff=40

 

 

 

    clash_cutoff=-0.4

 

 

 

 

 

 

 

Final processed PHIL parameters:

 

 

 

-------------------------------------------------------------------------------

 

 

 

  data_manager {

 

 

 

    default_output_filename = "cctbx_program"

 

 

 

  }

 

 

 

  b_factor_cutoff = 40

 

 

 

 

 

 

 

 

 

 

 

Starting job

 

 

 

===============================================================================

 

 

 

Sorry: 0 model(s) found. Expected at least 1.

 

 

 

chartClashlist ran for 5 seconds

 

 

 

do Charts ran for 0 seconds

 

 

 

sh: phenix.probe: command not found

 

 

 

do Kinemage ran for 0 seconds

 

 

 

 

 

 

 

Traceback (most recent call last):

 

 

 

  File "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/../modules/cctbx_project/mmtbx/command_line/mp_geo.py", line 7, in <module>

 

 

 

    mp_geo.run(sys.argv[1:])

 

 

 

  File "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/validation/molprobity/mp_geo.py", line 132, in run

 

 

 

    pdb_hierarchy.models()[0].chains():

 

 

 

IndexError: list index out of range

 

 

Best Regards,

Charitha Shetty

 

From: Robert Nolte
Sent: Sunday, August 11, 2019 12:39 PM
To: Nigel Moriarty (nwmoriarty@lbl.gov) <nwmoriarty@lbl.gov>; cctbxbb@phenix-online.org
Cc: Charitha Belluru Shetty <charitha-belluru.b.shetty@gsk.com>
Subject: Molprobity / CCTBX incompatibility

 

We are trying to reinstall our internal molprobity server, and have hit an issue with the github version where it appears to be a version conflict with the version of cctbx that is currently being downloaded by configuration script in the master branch of molprobity. We are getting errors when we run the validation routine such as

 

Unrecogized PHIL parameter: data_version=8000

 

or

 

Unrecognized PHIL parameter: clash_cutoff=-0.4

 

The analysis for clashscore, rotalyze, are failing to run and we get a number of divide by zero errors for several of the other ‘visualize’ and ‘eff_resolution’ routines.

 

Can you help get this working.

                Thanks,

                Bob Nolte

 

 

 

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