error–rosetta fragment‐based refinement protocol for refinement against EM density

[Anonymous]

I am trying to use rosetta fragment‐based refinement protocol for refinement against EM density. My script is attached.

It always complaints:

core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.434133 seconds to load from binary

core.pack.pack_rotamers: built 185 rotamers at 21 positions.

core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph

core.pack.interaction_graph.interaction_graph_factory: IG: 27768 bytes

protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=A_asymm_refine.xml

protocols.rosetta_scripts.RosettaScriptsParser: Variable substitution will occur with the following values: ‘%%denswt%%’=’25’;  ‘%%map%%’=’half1_34A.mrc’;  ‘%%reso%%’=’3.4’;  ‘%%rms%%’=’1.5’;  ‘%%testmap%%’=’half2_34A.mrc’;  

protocols.rosetta_scripts.RosettaScriptsParser: Substituted script:

<ROSETTASCRIPTS>

 <SCOREFXNS>

    <cen weights=”score4_smooth_cart”>

    <Reweight scoretype=elec_dens_fast weight=20/>

    </cen>

    <dens_soft weights=”soft_rep”>

    <Reweight scoretype=cart_bonded weight=0.5/>

    <Reweight scoretype=pro_close weight=0.0/>

    <Reweight scoretype=fa_sol weight=0.0/> # remove this line if not a membrane protein

    <Reweight scoretype=elec_dens_fast weight=”25″/>

    </dens_soft>

    <dens weights=“talaris2014_cart”>

    <Reweight scoretype=elec_dens_fast weight=”25″/>

    <Reweight scoretype=fa_sol weight=0.0/> # remove this line if not a membrane protein

    <Set scale_sc_dens_byres=”R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88″/>

    </dens>

 </SCOREFXNS>

 <MOVERS>

    <SetupForDensityScoring name=setupdens/>

    <LoadDensityMap name=loaddens mapfile=”half1_34A.mrc”/>

    <SwitchResidueTypeSetMover name=tocen set=centroid/>

    <MinMover name=cenmin scorefxn=cen type=lbfgs_armijo_nonmonotone max_iter=200 tolerance=0.00001 bb=1 chi=1 jump=ALL/>

    <CartesianSampler name=cen5_50 automode_scorecut=-0.5 scorefxn=cen mcscorefxn=cen fascorefxn=dens_soft strategy=”auto” fragbias=”density” rms=1.5 ncycles=200 fullatom=0 bbmove=1 nminsteps=25 temp=4 fraglens=7 nfrags=25/>

    <CartesianSampler name=cen5_60 automode_scorecut=-0.3 scorefxn=cen mcscorefxn=cen fascorefxn=dens_soft strategy=”auto” fragbias=”density” rms=1.5 ncycles=200 fullatom=0 bbmove=1 nminsteps=25 temp=4 fraglens=7 nfrags=25/>

    <CartesianSampler name=cen5_70 automode_scorecut=-0.1 scorefxn=cen mcscorefxn=cen fascorefxn=dens_soft strategy=”auto” fragbias=”density” rms=1.5 ncycles=200 fullatom=0 bbmove=1 nminsteps=25 temp=4 fraglens=7 nfrags=25/>

    <CartesianSampler name=cen5_80 automode_scorecut=0.0 scorefxn=cen mcscorefxn=cen fascorefxn=dens_soft strategy=”auto” fragbias=”density” rms=1.5 ncycles=200 fullatom=0 bbmove=1 nminsteps=25 temp=4 fraglens=7 nfrags=25/>

   <ReportFSC name=report testmap=”half2_34A.mrc” res_low=10.0 res_high=3.4/>

   <BfactorFitting name=fit_bs max_iter=50 wt_adp=0.0005 init=1 exact=1/>

   <FastRelax name=relaxcart scorefxn=dens repeats=1 cartesian=1/>

 </MOVERS>

 <PROTOCOLS>

   <Add mover_name=setupdens/>

   <Add mover_name=loaddens/>

   <Add mover_name=tocen/>

   <Add mover_name=cenmin/>

   <Add mover_name=relaxcart/>

   <Add mover_name=cen5_50/>

   <Add mover_name=relaxcart/>

   <Add mover_name=cen5_60/>

   <Add mover_name=relaxcart/>

   <Add mover_name=cen5_70/>

   <Add mover_name=relaxcart/>

   <Add mover_name=cen5_80/>

   <Add mover_name=relaxcart/>

   <Add mover_name=relaxcart/>

   <Add mover_name=fit_bs/>

   <Add mover_name=report/>

 </PROTOCOLS>

 <OUTPUT scorefxn=dens/>

</ROSETTASCRIPTS>

Error: ERROR: Exception caught by JobDistributor while trying to get pose from job ‘3j5p_transmem_A_sym_0001’

Error: Tag::read – parse error, printing backtrace.

 

Tag::read – parse error – file:istream line:1 column:1 – <ROSETTASCRIPTS>

Tag::read – parse error – file:istream line:1 column:1 – ^

Error: 

Error: Treating failure as bad input; canceling similar jobs

protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: 3j5p_transmem_A_sym_0001

protocols.jd2.JobDistributor: no more batches to process… 

protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 5 seconds

Error: ERROR: Exception caught by rosetta_scripts application:1 jobs failed; check output for error messages

Error: 

 

My flags is the following:

-in:file:s 3j5p_transmem_A.pdb

-database /Applications/rosetta_2016/main/database

-out:suffix _sym

-ignore_unrecognized_res

-edensity:mapreso 3.4

-edensity:cryoem_scatterers

-parser:script_vars denswt=25 rms=1.5 reso=3.4 map=half1_34A.mrc testmap=half2_34A.mrc

-crystal_refine

-default_max_cycles 200

-overwrite

-parser:protocol A_asymm_refine.xml

Thanks,

if it’s failing on the first tag, it’s probably some sort of character or endline encoding problem.  Google “windows to unix endlines” and try to fix the endlines to the posix/unix standard; that’s the most likely problem off the top of my head.

Fri, 2016-07-01 11:54

smlewis

 

 I fixed “windows to unix endlines, but it still came out the same error

 

[Anonymous]

See the thread here for some answers/suggestions.

[Author]

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