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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Aug 12, 2019 at 11:43 AM Charitha Belluru Shetty < [email protected]> 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=c2h8n399dagb0...

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 ([email protected]) ; [email protected] *Cc:* Charitha Belluru Shetty *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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