Why there are two outputs using pmut_scan_parallel.linuxgccrelease with a mutant list file?

[Anonymous]

Dear friends,
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

Thank you.

Yours sincerely
Cheng

[Anonymous]

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.

[Anonymous]

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.

Thank you.

Yours sincerely
Cheng

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

[Anonymous]

Hi Cheng,

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:

ab_complex.H-K169A.pdb

ab_complex.H-W143A.pdb

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

kind regards

Mustafa

[Author]

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