RosettaCommons - Unsolved

READ THIS BEFORE YOU POST

Sergey — Thu, 03 Feb 2011 17:58:18 +0000

When posting build/install question please specify the following information about your system and PyRosetta version, this will allow us to answer your questions more accurate and faster:

- OS type,
- OS version
- OS arch (32 or 64bit)
for example: Ubuntu Linux 10.04 32Bit or Mac OS X 10.6

- Python version
- Python arch (32 or 64bit) if different from OS

- Version of PyRosetta including SVN revision number.

Thank you!

Post Situation:

Unsolved

Forums:

PyRosetta - Build/Install

FARFAR2 error: no edge found that contains seqpos!

mandar — Wed, 19 Jun 2024 01:39:06 +0000

Hi,

I am running MPI version of rna_denovo using command below using PDB, sequence, and secondary structure as inputs :

rna_denovo.mpi.linuxgccrelease -fasta rna_sequence.fasta -secstruct_general_file rna.secstruct -native 2CKY_1.pdb -align_pdb 2CKY_1.pdb -rmsd_screen 4.0 -cycles 20000 -minimize_rna true -nstruct 100 -out:file:silent FARFAR2_native_2CKY_1.out -use_legacy_job_distributor

However, this job is failed with no edge error as mentioned in ROSETTA_CRASH.log:

###################################

[FILE]: src/core/kinematics/FoldTree.cc
[LINE]: 2353
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: no edge found that contains seqpos!

#####################################

I could not trace origin of this error. Any suggestions to understand and solve this error would be of great help.

Thanks,

Mandar

Category:

Nucleic Acids

Forums:

Rosetta 3 - General

Post Situation:

Unsolved

Error with fragment picking

gserci — Tue, 18 Jun 2024 00:37:39 +0000

Hello everyone,

I'm very new to using Rosetta and I'm having problems generating 3mers and 9mers. I've followed the tutorials and the documentation, but I continue to receive an error.

I've created a directory (input_files) with the following files: a FASTA sequence, an ss2 file (generated using PsiPred), and a PDB file (I've tried using both the one generated by AlphaFold3 and the one generated by DMPFold prediction but it doesn't seem to make a difference). The protein has 322 amino acids and I've verified that all three input files have 322 amino acids.

This is the command I use in the shell:

../../rosetta.binary.ubuntu.release-371/main/source/build/src/release/linux/5.4/64/x86/gcc/7/static/fragment_picker.static.linuxgccrelease @flags

And this is the contenute of "flags":

# Input databases
-in::file::vall                 ../../rosetta.binary.ubuntu.release-371/main/tools/fragment_tools/vall.apr24.2008.extended.gz

# Query-related input files
#-in::file::checkpoint          input_files/0296.checkpoint
-in::file::fasta                input_files/0296.fasta
-in::file::s                    input_files/0296.pdb
-frags::ss_pred                 input_files/0296.psipred.ss2 predA

# Weights file
-frags::scoring::config         input_files/simple.wghts

# What should we do?
-frags::bounded_protocol

# three-mers and nine-mers
-frags::frag_sizes              3 9
-frags::n_candidates            200
-frags::n_frags                 200

# Output
-out::file::frag_prefix         output_files/frags
-frags::describe_fragments      output_files/frags.fsc

This is the simple.wghts file:

# score name          priority  wght   max_allowed  extras
RamaScore               400    2.0     -       predA
SecondarySimilarity     350     1.0            predA
FragmentCrmsd             0     0.0     -

and this is the error in crash report:

[FILE]: src/protocols/frag_picker/scores/SecondarySimilarity.hh
[LINE]: 99
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to find secondary structure prediction for psipred

Lines 97-99 of SecondarySimilarity.hh are:

core::fragment::SecondaryStructureOP query_prediction( picker->get_query_ss(prediction_id) );
                if ( ! query_prediction ) {
                        utility_exit_with_message("Unable to find secondary structure prediction for " + prediction_id );

If I use, instead of simple.wghts:

SecondarySimilarity      350     0.5 - predA
ProfileScoreL1           50      1 -
FragmentCrmsd            30      0.0 -
RamaScore                100     2.0 - predA

this is the error:

[FILE]: src/protocols/frag_picker/scores/SecondarySimilarity.cc
[LINE]: 136
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Assertion `query_prediction->total_residue() == query_len_` failed.

Can you please help me making this fragment picker work?

Category:

Fragment Generation

Forums:

Rosetta 3 - General

Post Situation:

Unsolved

Segmentation fault (core dumped) error when importing pyrosetta with Tensorflow

proteinstudio — Mon, 17 Jun 2024 15:00:22 +0000

Hi my workflow involves importing pyrosetta and tensorflow together in a single python script. And whenever I import both modules and run the program, I'm keep getting segmentation fault (core dumped) error. Here is my code:

import tensorflow as tf
from pyrosetta import *

If I put them other way around

from pyrosetta import *
import tensorflow as tf

I get Floating point exception (core dumped)

Here is my system information:

OS type: Fedora Linux 38 (64 bit)

Python: 3.11.4

Pyrosetta: pyrosetta-2023.45+release.a6d9ba8-cp311-cp311-linux_x86_64.whl

Below is the output I get from gdb debugger:

Thread 1 "python" received signal SIGFPE, Arithmetic exception.
0x00007fff7b1a4831 in std::__detail::_Map_base<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, void*>, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, void*> >, std::__detail::_Select1st, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, false, true>, true>::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&) () from /home/ju/.cache/pypoetry/virtualenvs/hercules-An2atp8I-py3.11/lib/python3.11/site-packages/tensorflow/python/platform/_pywrap_tf2.so
(gdb) backtrace
\#0 0x00007fff7b1a4831 in std::__detail::_Map_base<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, void*>, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, void*> >, std::__detail::_Select1st, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, false, true>, true>::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&) () from /home/ju/.cache/pypoetry/virtualenvs/hercules-An2atp8I-py3.11/lib/python3.11/site-packages/tensorflow/python/platform/_pywrap_tf2.so
#1 0x00007fff7b1a467f in pybind11::detail::local_internals::local_internals() () from /home/ju/.cache/pypoetry/virtualenvs/hercules-An2atp8I-py3.11/lib/python3.11/site-packages/tensorflow/python/platform/_pywrap_tf2.so
#2 0x00007fff7b1a6207 in pybind11::detail::loader_life_support::get_stack_tls_key() () from /home/ju/.cache/pypoetry/virtualenvs/hercules-An2atp8I-py3.11/lib/python3.11/site-packages/tensorflow/python/platform/_pywrap_tf2.so
#3 0x00007fff7b1a237c in pybind11::cpp_function::dispatcher(_object*, _object*, _object*) () from /home/ju/.cache/pypoetry/virtualenvs/hercules-An2atp8I-py3.11/lib/python3.11/site-packages/tensorflow/python/platform/_pywrap_tf2.so
#4 0x000000000055505b in ?? ()
#5 0x000000000052f0ec in _PyObject_MakeTpCall ()
#6 0x000000000053d28e in _PyEval_EvalFrameDefault ()
#7 0x0000000000613134 in ?? ()
#8 0x0000000000612797 in PyEval_EvalCode ()
#9 0x000000000062c513 in ?? ()
#10 0x000000000054adab in ?? ()
#11 0x00000000005458d7 in _PyEval_EvalFrameDefault ()
#12 0x0000000000565f23 in _PyFunction_Vectorcall ()
#13 0x0000000000553b10 in ?? ()
#14 0x0000000000583dc1 in PyObject_CallMethodObjArgs ()
#15 0x0000000000583860 in PyImport_ImportModuleLevelObject ()
#16 0x0000000000598d96 in ?? ()
#17 0x000000000054adab in ?? ()
#18 0x00000000005458d7 in _PyEval_EvalFrameDefault ()
#19 0x0000000000565f23 in _PyFunction_Vectorcall ()
#20 0x0000000000553b10 in ?? ()
#21 0x0000000000583dc1 in PyObject_CallMethodObjArgs ()
#22 0x0000000000583860 in PyImport_ImportModuleLevelObject ()
#23 0x0000000000598d96 in ?? ()
#24 0x000000000054adab in ?? ()
#25 0x00000000005458d7 in _PyEval_EvalFrameDefault ()
#26 0x0000000000565f23 in _PyFunction_Vectorcall ()
#27 0x0000000000553b10 in ?? ()
#28 0x0000000000583dc1 in PyObject_CallMethodObjArgs ()
#29 0x0000000000583860 in PyImport_ImportModuleLevelObject ()
#30 0x00000000005428f7 in _PyEval_EvalFrameDefault ()
#31 0x0000000000613134 in ?? ()
#32 0x0000000000612797 in PyEval_EvalCode ()
#33 0x00000000006335ab in ?? ()
#34 0x000000000062f7f4 in ?? ()
#35 0x0000000000643e95 in ?? ()
#36 0x0000000000643504 in _PyRun_SimpleFileObject ()
#37 0x0000000000643317 in _PyRun_AnyFileObject ()
#38 0x000000000063dea9 in Py_RunMain ()
#39 0x0000000000603b0d in Py_BytesMain ()
#40 0x00007ffff7c29d90 in __libc_start_call_main (main=main@entry=0x603a60, argc=argc@entry=2, argv=argv@entry=0x7fffffffdde8) at ../sysdeps/nptl/libc_start_call_main.h:58
#41 0x00007ffff7c29e40 in __libc_start_main_impl (main=0x603a60, argc=2, argv=0x7fffffffdde8, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffddd8) at ../csu/libc-start.c:392
#42 0x0000000000603995 in _start ()

Any Idea why this is happening in general with Tensorflow? Are those two modules trying to get access to the memory at the same time or something?

Category:

PyRosetta

Forums:

PyRosetta - Build/Install

Post Situation:

Unsolved

Error concerning PhenixInterface upon running rosetta.run_tests

vcalderone — Sat, 15 Jun 2024 15:02:30 +0000

I have successully compiled rosetta 2019.47.61047_bundle using 'rosetta.build_phenix_interface' command on a fedora 40 pc with gcc-12.3.0.

When I run 'rosetta.run_tests' I get the following error that apparently concerns PhenixInterface.

The same error occurs even with the most recent rosetta version on the website.

Any hint?

##############################################################################################################
#
# Rosetta crash log.
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2019.47+release.3d995b1
[COMMIT_DATE]: 2019-11-23T16:25:53.340829
[APPLICATION]: /usr/local/rosetta_src_2019.47.61047_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease
[MODE]: Release
[EXTRAS]: python
[OS]: GNU/Linux
[COMPILER]: GCC version "12.3.0"
[STDLIB]: libstdc++ version 20230508
[START_OPTIONS]
-in:file:s=1yjp_rosetta_in.pdb -out:nstruct=1 -out:suffix=_1 -run:preserve_header -parser:protocol=/usr/local/rosetta_src_2019.47.61047_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml -parser:script_vars=symmdef=1yjp_rosetta.symm bfactstrat=individual map_type=Auto -cryst:mtzfile=1yjp_rosetta_data.mtz -cryst:crystal_refine

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libcore.6.so(backtrace_string(int)+0x37) [0x148676316b87]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libutility.so(utility::excn::Exception::Exception(char const*, int, std::string const&)+0x7b) [0x148670e98cdb]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::string const&)+0xa2) [0x148670f4c9a2]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libutility.so(utility::exit(char const*, int, std::string const&, int)+0x34) [0x148670f4c564]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libcore.3.so(core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)+0x2003) [0x1486743bf1b3]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.4.so(protocols::cryst::FitBfactorsMover::apply(core::pose::Pose&)+0xa1) [0x14867980e381]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const&)+0x26e) [0x148676d8149e]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/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) [0x148676d82b5b]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x1a6) [0x148676d83496]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const&)+0x26e) [0x148676d8149e]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/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) [0x148676d82b5b]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x1a6) [0x148676d83496]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/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)+0xd39) [0x148676f02c89]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x18b) [0x148676f0486b]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x49) [0x148676eec099]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease() [0x4025ed]
/lib64/libc.so.6(+0x2a088) [0x14867063d088]
/lib64/libc.so.6(__libc_start_main+0x8b) [0x14867063d14b]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease() [0x4028a5]

[END_BACKTRACE]

[FILE]: src/core/scoring/cryst/PhenixInterface.cc
[LINE]: 257
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: importing phenix.refine failed

[END_MESSAGE]
[END_CRASH_REPORT]

##############################################################################################################
#
# Rosetta crash log.
#

[END_OPTIONS]

[END_BACKTRACE]

[FILE]: src/protocols/jd2/JobDistributor.cc
[LINE]: 329
[START_MESSAGE]
1 jobs failed; check output for error messages

[END_MESSAGE]
[END_CRASH_REPORT]

Category:

Compilation

Forums:

Rosetta 3 - Build/Install

Post Situation:

Unsolved

Verification of Academic Email

jade — Thu, 06 Jun 2024 12:23:56 +0000

Hello,

I am a student at the French School EBI and would to use ROSIE for acedemic purposes. I would like to confirm that my email address is an academic email. Could you please verify it?

Thank you!

Category:

Docking

Forums:

ROSIE - General

Post Situation:

Unsolved

energy_based_clustering and silentfile option

weiw26 — Wed, 05 Jun 2024 23:28:59 +0000

I want to use energy_based_clustering to cluster structures from a silentfile. I run `source/bin/energy_based_clustering.linuxgccrelease @cluster_flag`.

Here cluster_flag is:

-in:file:silent ../global_output/decoys_P_renumbered_0001_traj.out
-in:file:fullatom
-cluster:energy_based_clustering:limit_structures_per_cluster 0
-cluster:energy_based_clustering:cluster_radius 2.0
-cluster:energy_based_clustering:cluster_by bb_cartesian
-cluster:energy_based_clustering:alternative_score_file input_score.txt
-cluster:energy_based_clustering:silent_output

-----------------------------------------------------------------------------

input_score.txt is the score file I prepared:

$ head input_score.txt

P_renumbered_0001_003_00000001 -5825.852
P_renumbered_0001_002_00000001 1107.339
P_renumbered_0001_001_00000001 8082.621
P_renumbered_0001_003_00000002 -5853.732
P_renumbered_0001_001_00000002 8072.546
P_renumbered_0001_002_00000002 1101.128
P_renumbered_0001_003_00000003 -5841.483

...

-----------------------------------------------------------------------------

When I run the clustering, I receive error message:

[FILE]: src/protocols/energy_based_clustering/EnergyBasedClusteringProtocol.cc
[LINE]: 1670
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to assign loaded score to pose 'P_renumbered_0001_001_00000001_../global_output/decoys_P_renumbered_0001_traj.out'. Please check your score file.

-----------------------------------------------------------------------------

I would like to get help on how to solve this error. Thanks

Category:

Scoring

Forums:

Rosetta 3 - General

Post Situation:

Unsolved

Serialization for Python 3.5

Getmo — Fri, 31 May 2024 19:36:43 +0000

I am working with a GitHub repo (Link) that creates a pipeline for the Rocklin et al. 2017, Science metrics. The provided environment yml file specifies python 3.5 while the code imports pyrosetta.distributed libraries. I've looked through the archive release versions of PyRosetta but did not see a serialization/distributed build for Python 3.5. I've tried running the code with the available 3.5 build but get the following error code:

"CRITICAL:root:Exception while running score_designs.score_pdb_file: __cereal_getstate__ requires pyrosetta '--serialization' build."

Is there an internal or old version of PyRosetta that supports serialization for Python 3.5?

Category:

PyRosetta

Forums:

PyRosetta - Build/Install

Post Situation:

Unsolved

Abnormal output of ScoreCutoffFilter

DivingWhale — Fri, 31 May 2024 01:46:14 +0000

Hi everyone!

The output of `ScoreCuoffFilter` looks like this:
ResResE Res1 Res2 fa_atr fa_rep fa_sol fa_intra_r fa_intra_s lk_ball_wt fa_elec pro_close hbond_sr_b hbond_lr_b hbond_bb_s hbond_sc dslf_fa13 omega fa_dun p_aa_pp yhh_planar ref rama_prepr total
ResResE 83_6531 72_6532 -1.663 0.129 1.501 0.000 0.000 -0.424 0.258 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.198
....

The filed of Res1 or Res2 looks strange. In older version, this field will have the one-letter amino acid name, chain ID, and residue index. Why are name and chain ID replaced by numbers? Is there any update on this filter or it's replaced by other filter? I can't find documentation.

Rosetta version: rosetta.binary.linux.release-371

XML file:
<ROSETTASCRIPTS>
<SCOREFXNS>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Neighborhood name="nbrhood" resnums="35A-290A"/>
<Not name="others" selector="nbrhood" />
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<OperateOnResidueSubset name="turn_off_others" selector="others">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
<RestrictToRepacking name="rtrp"/>
</TASKOPERATIONS>
<FILTERS>
<ScoreCutoffFilter name="scofilter" report_residue_pair_energies="1" cutoff="5000000.0" />
</FILTERS>
<SIMPLE_METRICS>
</SIMPLE_METRICS>

Could you please help me with this?

Category:

Scoring

Forums:

Rosetta 3 - Applications

Post Situation:

Unsolved

Error about using BuildDeNovoBackboneMover

ng98 — Wed, 29 May 2024 08:47:05 +0000

Hi! I am sorry for asking about the segementation fault problems because this be caused by many things. It is the first time I wrote a Rosetta scripts and I really stuck on the script.

I tried to use BuildDeNovoBackboneMover to generate backbones based on the antibody structure I got, I wrote the xml file but it shows:

[FILE]: SIGSEGV
[LINE]: 11
[START_MESSAGE]

Segmentation Fault

[END_MESSAGE]
[END_CRASH_REPORT]

This is my XML file:

<ROSETTASCRIPTS>
        <SCOREFXNS>
                <ScoreFunction name="sfxn_16" weights="beta_nov16"/>
                <ScoreFunction name="sfxn" weights="beta_nov16"/>
        </SCOREFXNS>
        <RESIDUE_SELECTORS>
                <AntibodyRegion name="Abselect" region="cdr_region" cdr_definition="Chothia"/>
        </RESIDUE_SELECTORS>
        <TASKOPERATIONS>
                <AddCDRProfileSetsOperation name="AddCDRs" cdrs="all cdrs" include_native_restype="true" picking_rounds="3"/>
        </TASKOPERATIONS>
        <FILTERS>
                <ScoreType name="score_filter" score_type="sfxn_16" threshold="0" confidence="0"/>
                <ResidueCount name="res_count_all" max_residue_count="9999" confidence="0"/>
        </FILTERS>
        <MOVERS>
                <BuildDeNovoBackboneMover name="dn_backbone" dump_pdbs="false" >
                        <BlueprintArchitect name="bp_arch" blueprint="template1.bp"/>
                        <RemodelLoopMoverPoseFolder scorefxn="sfxn_16"/>
                </BuildDeNovoBackboneMover>
        </MOVERS>
        <APPLY_TO_POSE>
        </APPLY_TO_POSE>
        <PROTOCOLS>
                <Add mover="dn_backbone"/>
        </PROTOCOLS>
        <OUTPUT />
          
         
</ROSETTASCRIPTS>

My input is :rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease -parser:protocol blueprint_build.xml -corrections::beta_nov16 -s model-0.relaxed_0003.pdb -out:prefix test_

The model-0.relaxed_0003.pdb file is attached, I think it is because my input pdb or the blueprint file? But I do not know how to modify it based on my purpose. Could anyone please help me solve the problem? Thank you!

Attachment	Size
This is blueprint file.	1.16 KB
model-0.relaxed_0003.pdb	308.96 KB

Category:

Design

Post Situation:

Unsolved

Forums:

Rosetta 3 - General