chainRef is not defined

[nuwoo]

Hello, i have a problem with step 6, which following the error, after check the code , i see that probable cause is REFERENCE_DIR not exist, but refer the README I can't find which step it should be created.

# Running on pdb 5V1U
refmono : []
refmulti : []
Traceback (most recent call last):
  File "6_RunCapri.py", line 126, in <module>
    print(chainRef)
NameError: name 'chainRef' is not defined

thanks a lot for any suggestions or references.

[jessica-andreani]

Hello, thanks for your interest.

Indeed, the script does not find the reference complex. REFERENCE_DIR is defined in the config.ini file. For the demo, it points to the ref_capri_curated directory (in data_demo). In this directory, the script should find the reference file 5V1U_A-E.pdb for evaluation of 5V1U.

However, you are right, I will add this step to the pipeline in the README as these files should be prepared by the user for non-demo test cases.

[nuwoo]

thanks for your reply, i also use the dada_demo to test, but after use ref_capri_curated directory( alson defined in config.ini) , i meet another problem in step 6, execute sh cmd_run_capri_all_models.sh , output dir caprieval_on_cutmodels have named prefix with protocls, but content are none as below:

# file RMSAvsA RMSBvsB RMSABvsAB LRMSA LRMSB FRNAT FRNNAT FRIR IRMS CAPRIrank DockQ DockQrank ref_index

If run this command multiple times, some of the file has normal output, but nothing like the data_demo output. the cutomodels abd af2_runs has the normal output, please give any tips or suggestions to find the reason.

[jessica-andreani]

Thanks for your feedback. Can you please check if the cut models were generated in directory cutmodels_for_caprieval? If the files are there, the most likely explanation is that the ProFit software is either not found or not working properly. Could you please check your ProFit installation and configuration? (see ProFit section of the README)