- This topic has 3 replies, 3 voices, and was last updated 5 years, 1 month ago by Anonymous.
November 16, 2014 at 6:26 pm #2068Anonymous
I am using pmut_scan_parallel.linuxgccrelease to mutate a residue with a mutant list file. There are two PDB outputs for the point mutant. The two outputs are of slight difference at the mutated region. Can I ask why there are two outputs, and which one should I choose?
The original PDB and two outputs are attached.
My command line is:
~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/pmut_scan_parallel.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -s /home/lanselibai/Cheng/test/input/original.pdb -ex1 -ex2 -extrachi_cutoff 1 -use_input_sc -ignore_unrecognized_res -no_his_his_pairE -multi_cool_annealer 10 -mute basic core -output_mutant_structures -mutants_list /home/lanselibai/Cheng/test/input/mutants_list.txt
November 18, 2014 at 5:35 pm #10597Anonymous
What does your mutants_list.txt file look like? (And your log file.) I’m guessing it’s (accidentally) telling pmut_scan to make a “double” mutant where the two mutations happen to be the same. The slight differences are just because of the stochastic packing/minimization procedure used in relaxing the mutant.
November 19, 2014 at 4:01 pm #10606Anonymous
Hi R Moretti,
I just tested on our cluster with 1) without “-double_mutant_scan”, and 2) with “-double_mutant_scan”
So superising, in both cases, there is only one output for each mutant I specified in the file.
I am not sure why it happened differently previously on Ubuntu. But do not worry. This has been solved now.
The command line I am using is:
# part of the .sh file for cluster job submission:
pmut_scan_parallel.linuxgccrelease -s /home/ucbechz/Scratch/20141119_4_mutants/input/C226S.pdb -ex1 -ex2 -extrachi_cutoff 1 -use_input_sc -ignore_unrecognized_res -no_his_his_pairE -multi_cool_annealer 10 -mute basic core -output_mutant_structures -double_mutant_scan -mutants_list /home/ucbechz/Scratch/20141119_4_mutants/input/mutants_list.txt -constant_seed -jran 11111111 > 4_mutant.log
The mutants file is:
L L 50 K
H K 133 M
H K 65 M
H S 75 K
October 18, 2018 at 12:31 pm #14472Anonymous
Do you get also log file with ddG scores?
When I am using same method, I get two mutations pdbs but without energy score:
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 6.31 seconds
protocols.pmut_scan.PointMutScanDriver: go(): DONE with pmut scan.
and pdbs I get are:
and I am using mutant file
H W 33 A
H K 59 A
is there anything wrong in my script?
pmut_scan_parallel.linuxclangrelease -s ab_complex.pdb -ex1 -ex2 -extrachi_cutoff 1 -use_input_sc -ignore_unrecognized_res -no_his_his_pairE -multi_cool_annealer 10 -mute basic core -output_mutant_structures -mutants_list mutant.txt -constant_seed -jran 11111111 | tee double-mutant.log
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