ERROR: Assertion Fdensity.u2 and Fdensity.u3 failed

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December 6, 2017 at 3:38 pm #2808

Anonymous

I’m using “rosetta_src_2017.36.59679_bundle”. I’m trying to fit some strucutres to an EM density map. My script exited with the below error. Please help me troubleshoot it and let me know if you need further details.

This is the script that’s I’m running:



<ROSETTASCRIPTS>

<SCOREFXNS>

<ScoreFunction name="cen" weights="score4_smooth_cart">

<Reweight scoretype="elec_dens_fast" weight="20"/>

</ScoreFunction>

<ScoreFunction name="dens_soft" weights="beta_soft">

<Reweight scoretype="cart_bonded" weight="0.5"/>

<Reweight scoretype="pro_close" weight="0.0"/>

<Reweight scoretype="elec_dens_fast" weight="%%denswt%%"/>

</ScoreFunction>

<ScoreFunction name="dens" weights="beta_cart">

<Reweight scoretype="elec_dens_fast" weight="%%denswt%%"/>

<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"/>

</ScoreFunction>

</SCOREFXNS>



<MOVERS>

<SetupForDensityScoring name="setupdens"/>

<LoadDensityMap name="loaddens" mapfile="%%map%%"/>



<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="%%rms%%" 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="%%rms%%" 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="%%rms%%" 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="%%rms%%" ncycles="200" fullatom="0" bbmove="1" nminsteps="25" temp="4" fraglens="7"

nfrags="25"/>



<ReportFSC name="report" testmap="%%testmap%%" res_low="10.0" res_high="%%reso%%"/>



<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="setupdens"/>

<Add mover="loaddens"/>

<Add mover="tocen"/>

<Add mover="cenmin"/>

<Add mover="relaxcart"/>

<Add mover="cen5_50"/>

<Add mover="relaxcart"/>

<Add mover="cen5_60"/>

<Add mover="relaxcart"/>

<Add mover="cen5_70"/>

<Add mover="relaxcart"/>

<Add mover="cen5_80"/>

<Add mover="relaxcart"/>

<Add mover="relaxcart"/>

<Add mover="report"/>

</PROTOCOLS>

<OUTPUT scorefxn="dens"/>



</ROSETTASCRIPTS>

This is the error I’m getting:



protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER ReportFSC - report=======================

rho_calc 6807 of 6807

core.scoring.electron_density.ElectronDensity: Forcing apix to 1.375,1.375,1.375

protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:

protocols.jd2.JobDistributor: [ ERROR ]



[ERROR] Exception caught by JobDistributor for job tubulin_PF_dep_noligand_0001



[ ERROR ] EXCN_utility_exit has been thrown from: src/core/scoring/electron_density/ElectronDensity.cc line: 1053

ERROR: Assertion `Fdensity.u1()==Fdensity2.u1() && Fdensity.u2()==Fdensity2.u2() && Fdensity.u3()==Fdensity2.u3()` failed.





protocols.jd2.JobDistributor: [ WARNING ] tubulin_PF_dep_noligand_0001 reported failure and will NOT retry

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

protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 30641 seconds

protocols::checkpoint: Deleting checkpoints of FastRelax

protocols::checkpoint: Deleting checkpoints of FastRelax

protocols::checkpoint: Deleting checkpoints of FastRelax

protocols::checkpoint: Deleting checkpoints of FastRelax

protocols::checkpoint: Deleting checkpoints of FastRelax

protocols::checkpoint: Deleting checkpoints of FastRelax

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

Error: [ ERROR ]

Loading alternate density map /home/labusr/Documents/tubulin_test_map_right.mrc



ERROR: Assertion `Fdensity.u1()==Fdensity2.u1() && Fdensity.u2()==Fdensity2.u2() && Fdensity.u3()==Fdensity2.u3()` failed.

ERROR:: Exit from: src/core/scoring/electron_density/ElectronDensity.cc line: 1053

BACKTRACE:

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0x27f) [0x7f02d445448f]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::scoring::electron_density::ElectronDensity::getFSC(ObjexxFCL::FArray3D<std::complex<double> > const&, ObjexxFCL::FArray3D<std::complex<double> > const&, unsigned long, double, double, utility::vector1<double, std::allocator<double> >&, bool)+0x213) [0x7f02d6a6b6e3]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.3.so(protocols::electron_density::ReportFSC::apply(core::pose::Pose&)+0x11fd) [0x7f02da4f9a6d]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const&)+0x22c) [0x7f02d924f30c]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair, std::allocator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair> > >)+0x3b) [0x7f02d924ff3b]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x1a7) [0x7f02d9250707]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool)+0xb78) [0x7f02d9313528]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xc1) [0x7f02d9314f71]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x4a) [0x7f02d92ec6ba]

/home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease() [0x403408]

/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f02d2449c05]

/home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease() [0x403d4b]

./Tublin_exercise_refine.sh: line 8: -ignore_unrecognized_res: command not found

December 11, 2017 at 4:30 pm #13946
Anonymous
I wish someone would help with this. Thanks a lot.
December 11, 2017 at 5:49 pm #13947
Anonymous
Hey sorry for the delay. It looks like you are trying to do an FSC calculation using two maps of different volume. You’ll need to make both maps the same size to get it to run. This should be doable in chimera without too much trouble.

-Brandon
- December 11, 2017 at 8:40 pm #13948
  Anonymous
  Thanks a lot. I’m still new to chimera, so I wodon’t mind at all if you tell me how to do it, or refer me to a tutorial. Thanks a lot.
- December 14, 2017 at 2:51 am #13955
  Anonymous
  I’m not actually sure I haven’t had to do it myself. I would check out this to see if there’s something you can use on there. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html
- December 18, 2017 at 7:51 pm #13962
  Anonymous
  Thanks. I actually have been trying a few stuff like using molmap and masking then fitting the two maps, however, I’m not entire sure what you mean by having the same volume. Could you please elaborate on that? I’m still getting that eror unless I use the exact same map.
- December 22, 2017 at 10:12 pm #13970
  Anonymous
  The maps are basically a 3 dimensional grid where every point has a value associated with it. The grid sizes need to be the same to run a FSC calculation. So if the size of your grid for the first map is 10x10x10 the size of the grid for the second map has to be the same. I believe the resample command is the one you want to use https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample
- January 22, 2018 at 5:01 am #14000
  Anonymous
  Thanks a lot. I looked into that, the two maps actually are taken from an original map by doing a 10 angstrom molmap and then masking. Because of that, they should have the same grid size. I tried 1) fitting in the two maps together 2) changing the origin index from map viewer->features_>coordinates to make them match, I still keep getting this error. I attached the two maps here, and I would appreciate if you take a look at them: https://drive.google.com/drive/folders/1Cfw3IB2DHezZ5j2zdnlY_J33dcUWVuGD?usp=sharing
- January 28, 2018 at 5:48 pm #14005
  Anonymous
  Any help would be appreciated.
- January 30, 2018 at 7:04 pm #14018
  Anonymous
  You ran it through with Rosetta using the maps with the same coordinates after aligning? I am not sure what the issue is but I will ask the author of the code to take a look.
  
  Have you tried running the chimera command vop resample #1 onGrid #2?
- February 27, 2018 at 5:00 pm #14059
  Anonymous
  I just tried vop resample, I think it worked, but let me try it one more time to verify it.
- March 5, 2018 at 6:50 pm #14062
  Anonymous
  Yep, to confirm this works. However, let me ask you, what is the FSC being done “between” exactly? The two map volumes? If so, why? It would make more sense to do some kind of other cross correlation to validate the model generated in the other map, not the map volumes themselves. Am I assuming something wrong here?
  
  Regards.
January 18, 2018 at 5:28 pm #14002
Anonymous
I would appreciate any prompt help.
March 8, 2018 at 5:28 pm #14091
Anonymous
Glad you got it working! The FSC is doing two calculations. One between a simulated map generated from the structure and the training map and the second between the simulated map testing map. What you want to see is that the correlation is similar between the two tests. If the correlation is much better between the simulated data and the training map compared to the correlation between the simulated map and the testing data you know that you have likely over fit your model to training data.

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