My software notes

June 7, 2011

[CSRosetta] one bug found for 3.1 on Mac

Filed under: softwares and scripts — kpwu @ 3:45 pm
Tags: , ,

When I use CSRosetta 3.1 on my iMac, I always meet an error that the runCSrescore3.com can’t work properly. The best_model is not selected, therefore the script doesn’t generate a 3-column name.rms.rescore.txt at the end.

I might find where the bug is although it’s quite confused to me.

1. The extract_pdb3.com used in runCSrescore3.com contains only one line to extract all PDBs simulated from Rosetta 3.1 but the total number of extracted PDBs are not matched to the real number of simulated PDB. For example, I have 500 structures in the “silent.out“, the extract_pdb3.com only extracts the first 499 PDBs to the directory “output”. The latest PDB in silent.out is never extracted.

2. The way to fix is quite weird to me but it works. I edited the “silent.out” file, remove the latest line and save as a new file. Then re-run runCSrescore3.com, everything works smoothly.

Here is the last 2 lines in silent.out, one of my CSRosetta project:

132 L -89.994 0.000 0.000 -18.305 11.572 -10.761 -170.644 70.854 0.000 0.000 S_j001_00000020 
rm temp.default.out.list

I deleted the line containing “rm temp.default.out.list” and ran “runCSrescores3.com”, everything works as it should be.

NOTE: I also tested CSRosetta 3.1 on a Linux cluster, it’s not necessary for me to do such edition and there is no such error message I met. Very weird to me. Hope this found bug can help Mac users to run CSRosetta 3.x well.

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