nelse003
commented
6 years ago Alice: Please refer your users to the below discussion on using cofactors.
Alice: I will look at the dataset for “X0034 should have a hit, that is actually sitting in another pocket….”, and report back separately.
Nick: Thanks for your comments on using libcheck, they are added to https://github.com/xchem/XChemExplorer/issues/49.
Tobias, Rachael: Given that these errors are accounted for , and that the other recent error with Janine’s datasets discussed on XCHEMBB are likely due to inconsitent folder management, I will close issue: https://github.com/xchem/XChemExplorer/issues/88 . I will post a summary on XCHEMBB of the below, and ask for anyone else with such issues to let us know, so they can be cateogorised.
Thanks
Elliot
Co-factors are not well supported in the XCE interface:
Currently any co-factor restraints need to be supplied by adjusting the cif file of the bound ligand. This is awkward as it cannot be done within the xce interface, and is inconsistent with crystallographic protocol. See https://github.com/xchem/XChemExplorer/issues/49
This is the same issue discussed with Matthew rodriguez https://github.com/xchem/XChemExplorer/issues/50 : Issue: Dimple is behaving inconsistently due to the lack of definition of cif restraints for a cofactor. Follow up from #24 Solution:
- Generate cif file for cofactor.
- Merge cif file for cofactor into each supplied ligand cif
- Rerun dimple
- Check dimple logs that cofactor is being dealt with properly
- Rerun pandda
- Continue analysis
- Check refinement works well w.r.t cofactor @tkrojer: Should be able to assist with adjustment of cif files if needed. User: Matthew Rodriquez Data: /dls/labxchem/data/2017/lb16946-1/ Longer term solution: We are looking to add the ability to define cif files for cofactors: #49 User’s solution: The pandda.export seems to be working fine now. I edited my initial model so that chain D would not require a cif file and would instead be covered by the CCP4 standard library. I then re-ran dimple, re-ran pandda.analyse in a new folder and pandda.inspect.
Issue
Free.mtz files are being reported as missing, when pandda.export is run from XCE.
The files generated by pandda.export directly are moved from the pandda directory to the initial model directory in most cases
Some of the following programs run, but not in all cases
the path to the free.mtz is correct in
Actions:
1) Test with pre code cleanup version of pandda export to determine whether it is @nelse003 qsubbed code part, or @reskyner code cleanup
pre code cleanup version of XCE for testing: /dls/science/groups/i04-1/software/XChemExplorer/XChemExplorer/XChemExplorer
2) Look at Alice's test cases:
Very simple: They selected their good structures through inspect and then just went to export them. They then could only see 1 data selectable in the refinement tab, which is a random one which they did not even mark as interesting. Visit number I can’t remember for the American so would need to look it up but Christian was using lb18145-43 with OTUB2A. we had 5 hits that he modelled properly and I wanted to see them refined. The Amricans had the same problem.
I did not yet try to run in command line and will try that on Monday. We did not modify anything, just took the pipeline as it came. It failed on complaining that it could not find some mtz file for a data that we were not interested anyway…. I can try again on Monday and see what exactly it failed on. 1st day of shutdown and Friday so I want to leave now.
Cheers
Alice
3) Check Janine's test case is still valid . Given her use of folder paths this could be misleading and difficult to diagnose
Pandda.export is currently broken.
Symptoms: 1) Once you click on the button in XCE, It start to run 2) Move pandda files in the intital_model directory for some datasets (!) 3) Build the ensemble model 4) Build the refinement restraints for both phenix and Refmac 5) Stop without notice
Troubleshooting 6) Xce.log file is not really helpful here
2017-10-18 18:25:21 ==> XCE: XX02KALRNA-x0899: not in interesting_datasets; updating database... 2017-10-18 18:25:22 ==> XCE: XX02KALRNA-x0901: not in interesting_datasets; updating database... 2017-10-18 18:25:22 ==> XCE: XX02KALRNA-x0903: not in interesting_datasets; updating database... 2017-10-18 18:25:22 ==> XCE: XX02KALRNA-x0906: not in interesting_datasets; updating database... 2017-10-18 18:25:22 ==> XCE: XX02KALRNA-x0907: not in interesting_datasets; updating database... 2017-10-18 18:25:22 ==> XCE: XX02KALRNA-x0908: not in interesting_datasets; updating database... 2017-10-18 18:25:22 ==> XCE: XX02KALRNA-x0909: not in interesting_datasets; updating database... 2017-10-18 18:25:22 ==> XCE: XX02KALRNA-x0910: not in interesting_datasets; updating database... 2017-10-18 18:25:23 ==> XCE: XX02KALRNA-x0912: not in interesting_datasets; updating database... 2017-10-18 18:25:23 ==> XCE: XX02KALRNA-x0914: not in interesting_datasets; updating database... 2017-10-18 18:25:23 ==> XCE: finding out which PanDDA models need to be exported 2017-10-18 18:25:28 ==> XCE: XX02KALRNA-x0179-pandda-model.pdb was created on 2017-10-18 18:17:26 2017-10-18 18:25:28 ==> XCE: XX02KALRNA-x0515-pandda-model.pdb was created on 2017-10-18 18:19:32 2017-10-18 18:25:28 ==> XCE: checking which PanDDA models were newly created or updated 2017-10-18 18:25:28 ==> XCE: exporting XX02KALRNA-x0179 -> first time to be exported and refined 2017-10-18 18:25:28 ==> XCE: exporting XX02KALRNA-x0515 -> first time to be exported and refined 2017-10-18 18:25:28 ==> XCE: updating database for XX02KALRNA-x0179 setting time model was created to 2017-10-18 18:17:26 and RefinementOutcome to 2 - PANDDA model 2017-10-18 18:25:28 ==> XCE: updating database for XX02KALRNA-x0515 setting time model was created to 2017-10-18 18:19:32 and RefinementOutcome to 2 - PANDDA model 2017-10-18 18:25:28 ==> XCE: running pandda.export with the following settings: source /dls/science/groups/i04-1/software/XChemExplorer_new/XChemExplorer/setup-scripts/pandda.setup-sh pandda.export pandda_dir=/dls/labxchem/data/2017/lb18145-17/processing/analysis/panddas_all export_dir=/dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP XX02KALRNA-x0179 XX02KALRNA-x0515 generate_restraints=True
2017-10-18 18:26:37 ==> XCE: ERROR!!! XX02KALRNA-x0477: cannot start refinement because XX02KALRNA-x0477.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0477 2017-10-18 18:26:37 ==> XCE: ERROR!!! XX02KALRNA-x0481: cannot start refinement because XX02KALRNA-x0481.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0481 2017-10-18 18:26:37 ==> XCE: ERROR!!! XX02KALRNA-x0482: cannot start refinement because XX02KALRNA-x0482.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0482 2017-10-18 18:26:37 ==> XCE: ERROR!!! XX02KALRNA-x0492: cannot start refinement because XX02KALRNA-x0492.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0492 2017-10-18 18:26:37 ==> XCE: ERROR!!! XX02KALRNA-x0510: cannot start refinement because XX02KALRNA-x0510.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0510 2017-10-18 18:26:37 ==> XCE: ERROR!!! XX02KALRNA-x0515: cannot start refinement because XX02KALRNA-x0515.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0515 2017-10-18 18:26:37 ==> XCE: ERROR!!! XX02KALRNA-x0522: cannot start refinement because XX02KALRNA-x0522.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0522 2017-10-18 18:26:37 ==> XCE: ERROR!!! XX02KALRNA-x0523: cannot start refinement because XX02KALRNA-x0523.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0523 2017-10-18 18:26:37 ==> XCE: ERROR!!! XX02KALRNA-x0524: cannot start refinement because XX02KALRNA-x0524.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0524 2017-10-18 18:26:37 ==> XCE: ERROR!!! XX02KALRNA-x0525: cannot start refinement because XX02KALRNA-x0525.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0525 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0526: cannot start refinement because XX02KALRNA-x0526.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0526 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0528: cannot start refinement because XX02KALRNA-x0528.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0528 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0529: cannot start refinement because XX02KALRNA-x0529.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0529 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0530: cannot start refinement because XX02KALRNA-x0530.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0530 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0531: cannot start refinement because XX02KALRNA-x0531.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0531 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0533: cannot start refinement because XX02KALRNA-x0533.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0533 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0534: cannot start refinement because XX02KALRNA-x0534.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0534 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0535: cannot start refinement because XX02KALRNA-x0535.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0535 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0536: cannot start refinement because XX02KALRNA-x0536.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0536 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0537: cannot start refinement because XX02KALRNA-x0537.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0537 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0538: cannot start refinement because XX02KALRNA-x0538.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0538 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0539: cannot start refinement because XX02KALRNA-x0539.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0539 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0540: cannot start refinement because XX02KALRNA-x0540.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0540 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0541: cannot start refinement because XX02KALRNA-x0541.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0541 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0543: cannot start refinement because XX02KALRNA-x0543.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0543 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0544: cannot start refinement because XX02KALRNA-x0544.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0544 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0545: cannot start refinement because XX02KALRNA-x0545.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0545 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0546: cannot start refinement because XX02KALRNA-x0546.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0546 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0547: cannot start refinement because XX02KALRNA-x0547.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0547 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0548: cannot start refinement because XX02KALRNA-x0548.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0548 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0552: cannot start refinement because XX02KALRNA-x0552.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0552 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0565: cannot start refinement because XX02KALRNA-x0565.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0565 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0566: cannot start refinement because XX02KALRNA-x0566.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0566 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0569: cannot start refinement because XX02KALRNA-x0569.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0569 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0571: cannot start refinement because XX02KALRNA-x0571.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0571 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0577: cannot start refinement because XX02KALRNA-x0577.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0577 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0580: cannot start refinement because XX02KALRNA-x0580.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0580 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0581: cannot start refinement because XX02KALRNA-x0581.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0581 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0595: cannot start refinement because XX02KALRNA-x0595.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0595 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0606: cannot start refinement because XX02KALRNA-x0606.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0606 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0607: cannot start refinement because XX02KALRNA-x0607.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0607 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0608: cannot start refinement because XX02KALRNA-x0608.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0608 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0614: cannot start refinement because XX02KALRNA-x0614.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0614 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0617: cannot start refinement because XX02KALRNA-x0617.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0617 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0618: cannot start refinement because XX02KALRNA-x0618.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0618 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0619: cannot start refinement because XX02KALRNA-x0619.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0619 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0623: cannot start refinement because XX02KALRNA-x0623.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0623 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0625: cannot start refinement because XX02KALRNA-x0625.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0625 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0629: cannot start refinement because XX02KALRNA-x0629.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0629 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0630: cannot start refinement because XX02KALRNA-x0630.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0630 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0631: cannot start refinement because XX02KALRNA-x0631.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0631 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0632: cannot start refinement because XX02KALRNA-x0632.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0632 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0633: cannot start refinement because XX02KALRNA-x0633.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0633 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0634: cannot start refinement because XX02KALRNA-x0634.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0634 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0637: cannot start refinement because XX02KALRNA-x0637.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0637 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0638: cannot start refinement because XX02KALRNA-x0638.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0638 2017-10-18 18:26:38 ==> XCE: ERROR!!! XX02KALRNA-x0639: cannot start refinement because XX02KALRNA-x0639.free.mtz is missing in /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_GDP/XX02KALRNA-x0639 Etc.
7) Ensemble_model_generation.log file looks fine:
############################################## <~~~> ###############################################
Validating input parameters and input files
############################################## <~~~> ###############################################
----------------------------------------------- ------------------------------------------------ --- Processed merging parameters --- ----------------------------------------------- ------------------------------------------------
input { major = "/dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_lb18145-37/XX02KALRNA-x0510/XX02KALRNA-x0510-pandda-input.pdb" minor = "/dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_lb18145-37/XX02KALRNA-x0510/XX02KALRNA-x0510-pandda-model.pdb" pdb = None } options { minor_occupancy = 0.5 major_occupancy = 0.5 prune_duplicates_rmsd = 0.1 reset_all_occupancies = False } output { pdb = "/dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_lb18145-37/XX02KALRNA-x0510/XX02KALRNA-x0510-ensemble-model.pdb" log = "/dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_lb18145-37/XX02KALRNA-x0510/XX02KALRNA-x0510-ensemble-model.log" make_restraints = True } settings { overwrite = True verbose = False }
----------------------------------------------- ------------------------------------------------ --- Reading input files --- ----------------------------------------------- ------------------------------------------------
----------------------------------------------- ------------------------------------------------ --- Updating input occupancies prior to merging --- ----------------------------------------------- ------------------------------------------------
Multiplying occupancies of input.major by 0.5 Multiplying occupancies of input.minor by 0.5
----------------------------------------------- ------------------------------------------------ --- Post-processing occupancies --- ----------------------------------------------- ------------------------------------------------
Setting all main-conf occupancies to 1.0 Writing output structure to /dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_lb18145-37/XX02KALRNA-x0510/XX02KALRNA-x0510-ensemble-model.pdb
############################################## <~~~> ###############################################
Parameters for generating restraints
############################################## <~~~> ###############################################
restraints { output { phenix = "/dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_lb18145-37/XX02KALRNA-x0510/XX02KALRNA-x0510-ensemble-model.restraints-phenix.params" refmac = "/dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_lb18145-37/XX02KALRNA-x0510/XX02KALRNA-x0510-ensemble-model.restraints-refmac.params" log = "/dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_lb18145-37/XX02KALRNA-x0510/XX02KALRNA-x0510-ensemble-model.log" } modes { all = False peptide_bond_links = True duplicated_atom_restraints = True local_structure_restraints = False occupancy_groups = True b_factor_restraints = False } duplicates { make_for = *all protein het rmsd_cutoff = 0.1 sigma_xyz = 0.02 } peptide_bonds { suffix = ".link.pdb" } local_restraints { altlocs = "C,D" max_distance = 4.2 min_distance = 1.6 sigma_xyz = 0.1 } occupancy { resname = "DRG,FRG,LIG,UNK,UNL" group_dist = 5 overlap_dist = 2 complete_groups = True simple_groups = False exclude_altlocs = None } b_factors { resname = None contact_dist = 4 sigma_b = 1 } }
############################################## <~~~> ###############################################
Generating restraints
############################################## <~~~> ###############################################
----------------------------------------------- ------------------------------------------------ --- Checking the continuity of the protein backbone --- ----------------------------------------------- ------------------------------------------------
No breaks in the backbone - hooray! (nothing needs to be done here)
----------------------------------------------- ------------------------------------------------ --- Generating restraints for duplicated conformers --- ----------------------------------------------- ------------------------------------------------
Found 6 duplicated conformers consisting of 52 atoms
----------------------------------------------- ------------------------------------------------ --- Generating occupancy-constrained groups --- ----------------------------------------------- ------------------------------------------------
No matching residues were found (no occupancy constraints created)
############################################## <~~~> ###############################################
FINISHED
############################################## <~~~> ###############################################
############################################## <~~~> ###############################################
Final Parameters
############################################## <~~~> ###############################################
input { major = "/dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_lb18145-37/XX02KALRNA-x0510/XX02KALRNA-x0510-pandda-input.pdb" minor = "/dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_lb18145-37/XX02KALRNA-x0510/XX02KALRNA-x0510-pandda-model.pdb" pdb = None } options { minor_occupancy = 0.5 major_occupancy = 0.5 prune_duplicates_rmsd = 0.1 reset_all_occupancies = False } output { pdb = "/dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_lb18145-37/XX02KALRNA-x0510/XX02KALRNA-x0510-ensemble-model.pdb" log = "/dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_lb18145-37/XX02KALRNA-x0510/XX02KALRNA-x0510-ensemble-model.log" make_restraints = True } restraints { output { phenix = "/dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_lb18145-37/XX02KALRNA-x0510/XX02KALRNA-x0510-ensemble-model.restraints-phenix.params" refmac = "/dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_lb18145-37/XX02KALRNA-x0510/XX02KALRNA-x0510-ensemble-model.restraints-refmac.params" log = "/dls/labxchem/data/2017/lb18145-17/processing/analysis/initial_model_lb18145-37/XX02KALRNA-x0510/XX02KALRNA-x0510-ensemble-model.log" } modes { all = False peptide_bond_links = True duplicated_atom_restraints = True local_structure_restraints = False occupancy_groups = True b_factor_restraints = False } duplicates { make_for = *all protein het rmsd_cutoff = 0.1 sigma_xyz = 0.02 } peptide_bonds { suffix = ".link.pdb" } local_restraints { altlocs = "C,D" max_distance = 4.2 min_distance = 1.6 sigma_xyz = 0.1 } occupancy { resname = "DRG,FRG,LIG,UNK,UNL" group_dist = 5 overlap_dist = 2 complete_groups = True simple_groups = False exclude_altlocs = None } b_factors { resname = None contact_dist = 4 sigma_b = 1 } } settings { overwrite = True verbose = False }
4) Assess qsub code in XChemRefine.py, lines 870-959