pmut_scan does not produce log file

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    • #1730

        Hi all,

        I am trying to get ddG estimates for mutations on a interface. I run successfully pmut application with several different parameters, but contrary to what I understand should happen no log file is produced with the ddG info. The mutated pdb file is indeed produced with a lot of information after the coordinates are written.

        But I cannot find the ddG info there….

        Should a log file be produced then?

        Everything seems to run fine, but as I said I cannot find the ddG info.

        I should also mention that I am looking for a specific double mutant, which seems to be OK, and also the run seems to finish OK:

        fabian@fabians-imac { ..pmut }-> /Users/fabian/TOOLS/rosetta/rosetta-3.5/rosetta_source/bin/pmut_scan_parallel.macosgccrelease -database /Users/fabian/TOOLS/rosetta/rosetta-3.5/rosetta_database -s 3NQ0.pdb.gz -mutants_list mutants.txt -output_mutant_structures -ex1 -ex2 -ex3 -extrachi_cutoff 1 -use_input_sc -ignore_unrecognized_res -no_his_his_pairE -multi_cool_annealer 10 -mute basic core
        protocols.pmut_scan.PointMutScanDriver: go(): master node
        protocols.pmut_scan.PointMutScanDriver: mutation mutation_PDB_numbering average_ddG average_total_energy
        protocols.pmut_scan.PointMutScanDriver: main(): whole protocol took 6.56751 seconds
        protocols.pmut_scan.PointMutScanDriver: go(): DONE with pmut scan.
        fabian@fabians-imac { ..pmut }->

        BUT not output file that I can see…..

        For example this is one of the mutations I am after:

        A N 270 A A N 270 A

        Thanks a lot,

        Technion, Israel

      • #9428

          As the whole protocol is only taking 6.5 seconds, it doesn’t look like it’s evaluating any mutations. A likely possibility is that there’s something wrong with your mutants.txt list of possible mutations. If, for some reason, it’s malformated (e.g. it’s empty, or all the lines are commented out with “#”), it may be that pmut_scan thinks there’s no mutations to try. Try omitting the “-mutants_list mutants.txt” to do a complete scan, and see if that gives you something. (You don’t need to let it finish, just check that it runs for at least several minutes, and starts to give you mutant output.) If that’s the issue, you can post the mutants.txt file here as an attachment, and we can figure out what’s wrong.

          The actual tabular output wouldn’t get put to an output file, but instead will be printed to standard output (i.e. the terminal, or a log file if you redirect stdout). That’s what that “mutation mutation_PDB_numbering average_ddG average_total_energy” line is – it’s the header for the table that would be output if there were any mutations calculated.

        • #14471

            This is the same problem I have shared earlier. I tried without mutant.txt and pmut_scan works fine. However, it does not show ddG for all resiudes in the protein. I get output structures for all residues but not every residue change gives me energy score.

            Besides, I also wanted to know if there is any way to mutate only specific residue with all 19 residues. Since, one way is mentioned to give mutant.txt and it will generate mutations on specific residue, only if it works. Second do I need to write all desired mutations one by one in the file?

            Looking for helpfull hints

            kind regards


          • #14475

              You want the ddG of all combinations regardless of whether they are above the threshold of -1.0 ddG?

              In that case use the argument to get all possible outputs.

              -DDG_cutoff 999

              It is super handy…

              If you are going to copy paste the output tables, say transition state vs. bound, do be aware that if you have a NCAA, such as a protonated aspartate, and you are scanning, it will mutate also try the mutation to aspartate, so you’ll get an extra line.

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