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

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error--rosetta fragment‐based refinement protocol for refinement against EM density
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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,

AttachmentSize
A_asymm_refine.txt2.74 KB
Category: 
Post Situation: 
Thu, 2016-06-30 11:06
gsuchunli

Why is this in the Rosetta++ subforum?

 

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 08:54
smlewis

The application dos2unix is useful for the line ending conversion - it's likely installed on your machine already.

Unfortunately, the RosettaScripts parser is rather simple, and so it doesn't have much error reporting capability. Having it report an error on "<ROSETTASCRIPTS>" may just mean that there's an unmatched tag somewhere. I can't see if from your output, but it's something you want to double-check.

Another thing I'd highly suggest is to make sure that there's a space between the last option and the closing slash of the tag. The simple parser can sometimes get confused, and will think the slash is part of the option if they're all smashed together. (Resulting in mis-matched tags and the above error message.) Adding a space between the last option and the slash normally fixes that.  -- Or putting quotes around the option values. That's always asafe thing to do, especially with variable substitution. 

Tue, 2016-07-12 08:17
rmoretti