[cctbxbb] Molprobity / CCTBX incompatibility

Nigel Moriarty nwmoriarty at lbl.gov
Mon Aug 12 12:33:29 PDT 2019 

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 at 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 at 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 at lbl.gov) <nwmoriarty at lbl.gov>;
> cctbxbb at phenix-online.org
> *Cc:* Charitha Belluru Shetty <charitha-belluru.b.shetty at 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
>
>
>
>
>
>
>
> *GSK monitors email communications sent to and from GSK in order to
> protect GSK, our employees, customers, suppliers and business partners,
> from cyber threats and loss of GSK Information. GSK monitoring is conducted
> with appropriate confidentiality controls and in accordance with local laws
> and after appropriate consultation.*
>
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