score is 0 in the output? – RosettaScripts

[Anonymous]

Hello,

The following is my .xml script:

<ROSETTASCRIPTS>



<TASKOPERATIONS> You can control which parts you want to change from here



<ProteinInterfaceDesign name="pido" repack_chain1="1" repack_chain2="1" design_chain1="0" design_chain2="1" interface_distance_cutoff="7"/> task operation that designates which residues are designable and repackable at the interface

</TASKOPERATIONS>



<RESIDUE_SELECTORS>

<Chain name="chB" chains="B"/>

</RESIDUE_SELECTORS>



<SIMPLE_METRICS>

InteractionEnergyMetric name="interface_energy" scoretypes_only="talaris2014"

<RMSDMetric name="rmsd" rmsd_type="rmsd_protein_bb_heavy" residue_selector="chB" use_native="true"/>

<TotalEnergyMetric name="total" residue_selector="chB" scoretype="total_score" scorefxn="talaris2014"/>

<TimingProfileMetric name="clock"/>

</SIMPLE_METRICS>



<MOVERS>

<MutateResidue name="D63A" target="63A" new_res="ALA"/>

<MutateResidue name="E64A" target="64A" new_res="ALA"/>

<MutateResidue name="E67A" target="67A" new_res="ALA"/>



<RepackMinimize name="des1" scorefxn_repack="soft_rep" scorefxn_minimize="soft_rep" minimize_bb_ch1="0" minimize_bb_ch2="1" minimize_rb="0" task_operations="pido"/> This works

<RepackMinimize name="des2" scorefxn_repack="talaris2014" scorefxn_minimize="talaris2014" minimize_bb_ch1="0" minimize_bb_ch2="1" minimize_rb="0" task_operations="pido"/> This works

<RunSimpleMetrics name="metric1" metrics="clock,rmsd,total" prefix="m1_"/>

<RunSimpleMetrics name="metric2" metrics="clock,rmsd,total" prefix="m2_"/>

<ParsedProtocol name="design">



<Add mover_name="des1"/>

<Add mover_name="des2"/>

</ParsedProtocol>

<GenericMonteCarlo name="iterate" scorefxn_name="talaris2014" mover_name="design" trials="3"/> Iterate through design to find best solution. change trial numbers to higher for real application.

</MOVERS>



<PROTOCOLS>

<Add mover="D63A"/>

<Add mover="E64A"/>

<Add mover="E67A"/>

<Add mover="metric1"/>

<Add mover="iterate"/>

<Add mover="metric2"/>

</PROTOCOLS>

</ROSETTASCRIPTS>

 

When I examine the score.sc output file, it looks like this:

SCORE:     score        rms     maxsub       time        description

SCORE:     0.000      0.710    441.000    830.000 200ns1-101_AB_0001

SCORE:     0.000      0.709    441.000    763.000 200ns1-101_AB_0002

 

and the scores at the end of the PDB files look like this:

TER

maxsub 441

rms 0.71

score 0

silent_score 0

time 830

 

Why am I getting scores of zero?

To my understanding, the RunSimpleMetric movers should be scoring the pose at the point where I call them in the protocol for TotalEnergyMetric, RMSDMetric, and TimingProfileMetric. 

My intention there was to see the energy before and after the “iterate” mover (I realize there’s a way to calculate the delta energy directly, but I was trying to see how the RunSimpleMetrics movers work). Is that not how I’m supposed to do it?

[Author]

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