RosettaCommons - Structure prediction

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Post Situation:

Is Biopython required to run pdb_renumber.py?

ljjjxay — Thu, 23 Nov 2023 04:00:10 +0000

Hi,

When I ran "pdb_renumber.py", I got the " ERROR: This script requires that Biopython (http://biopython.org) is installed." Acutally I installed Biopython. Is there any suggestion.

Thanks

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Post Situation:

FARFAR2 error: [ERROR: Not complementary at positions]

Eden — Sat, 18 Nov 2023 10:39:59 +0000

Any help with the following error from the rna_denovo function? Thank you

ERROR: Not complementary at positions g 4 and a 21
ERROR:: Exit from: src/core/pose/rna/RNA_SecStruct.cc line: 284

[ ERROR ]: Caught exception:

File: src/core/pose/rna/RNA_SecStruct.cc:284
[ ERROR ] UtilityExitException
ERROR: Not complementary at positions g 4 and a 21

====

my fasta file:

cgcgaauuagcgcgcgaauuagcg

the secondary structure file:

(((((((..((..))..)))))))

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Rosetta 3 - General

Post Situation:

'Use_filters true' option - failure of AbInitio Relax application

Corvin — Wed, 08 Nov 2023 14:34:13 +0000

Dear Rosetta community,

I would kindly ask you about possible reasons of AbInitio Relax failure after application of all filters.

It was decided to do an extensive run of AbRelax application with 'use_filters true' option to generate 1000 constructs (nstruct) in hope, that some of them will pass all filters and will have a nature-like fold structure.

I noticed, that when all 3 filters are applied during the construct trial, the AbRelax application fails with such an error:

Finished Abinitio

protocols.simple_filters.AbinitioBaseFilter: {0} apply filter: RGFilter
protocols.simple_filters.AbinitioBaseFilter: {0} apply filter: Contact-Order Filter
protocols.simple_filters.AbinitioBaseFilter: {0} apply filter: SheetFilter

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

terminate called after throwing an instance of 'std::out_of_range'
what(): map::at

If only 1 filter is used (namely, "RGFilter"), then everything is OK.

Would anyone be kind to tell me the possible reason of such a fail and how to solve this issue, please?

In addition, I tracked down the negative correlation between the 'kill_hairpin_frequency' and appearance rates of such all-3-filters application.
I.e., the higher 'kill_hairpin_frequency' value, the more constructs AbRelax tends to produce before the usage of all-3-filters to the generated construct and consequent failure.
I hope, that these extra details may shed some light on this problem.

I will be sincerely grateful for your response, and I am looking forward to it.

Best regards,
Corvin.

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Post Situation:

Predicting conformations of mutated residues

Delfosse57 — Tue, 22 Aug 2023 19:26:59 +0000

Hi all,

I am attempting to predict the conformations of an enzyme after a single mutation. I have been using pymol to place the mutation into the protein and then I use the rosetta relax application to optimize the structure. Is this a valid way of performing this technique? Or should I be using rosetta scripts and repack the sidechains instead. I am worried that the relax protocol may not be able to optimize the residue if pymol puts it in a conformation that is far away from the optimal conformation.

Thank you!

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Rosetta 3 - General

Post Situation:

ValueError("Path %s does not exist!" % path_name) for rna_helix.py

kameisel — Wed, 16 Aug 2023 07:39:57 +0000

Hi everyone,

I want to model helices with rna_helix.py but I get an error that rna_helix.linuxgccrelease isn't in the path where python script is looking for it:

File "/home/software/rosetta_bin_linux_2021.16.61629_bundle/main/tools/rna_tools/bin/rna_helix.py", line 27, in <module>

cmdline = rosetta_exe('rna_helix', rosetta_folder=args.rosetta_folder, extension=args.extension)

File "/home/software/rosetta_bin_linux_2021.16.61629_bundle/main/tools/rna_tools/bin/rosetta_exe.py", line 35, in rosetta_exe

check_path_exist(exe_path)

File "/home/software/rosetta_bin_linux_2021.16.61629_bundle/main/tools/rna_tools/bin/rosetta_exe.py", line 55, in check_path_exist

raise ValueError("Path %s does not exist!" % path_name)

ValueError: Path /home/software/rosetta_bin_linux_2021.16.61629_bundle/main/rna_helix.macosclangrelease

This ValueError regarding a MacOS version is due to the following line from rosetta_exe.py but also appears for the Linux Version by deleting the MacOS extensions:

name_extensions = ['', ".linuxgccrelease", ".linuxclangrelease", ".macosgccrelease", ".macosclangrelease"]

I found that rna_helix.linuxgccrelease is located in Path /home/software/rosetta_bin_linux_2021.16.61629_bundle/main/source/bin

when it should be in /home/software/rosetta_bin_linux_2021.16.61629_bundle/main

By using rna_helix.linuxgccrelease instead of rna_helix.py in bash it works and models a helix.

By running python rna_helix.py in bash I get:

File "/home/software/rosetta_bin_linux_2021.16.61629_bundle/main/tools/rna_tools/sym_link.py", line 22, in <module>

os.remove(f)

PermissionError: [Errno 13] Permission denied: './bin/rsync_from_cluster.py'

Feels like there's a problem with pathes in python script rosetta_exe.py and/or in the symbolic links in sym_link.py

Hopefully I was able to explain everything traceably and you can shed some light on this situation. Big thanks in advance!

Kind regards

Katherina

Category:

Nucleic Acids

Forums:

Post Situation:

Antibody Structure Prediction - Error on antibody_H3 step: "Option matching -antibody:remodel not found in command line"

ramon-arg — Tue, 25 Jul 2023 00:56:29 +0000

I'm trying to predict the structure of an antibody by following this Rosetta Antibody Modelling tutorial: https://meilerlab.org/wp-content/uploads/2022/02/RosettaAntibody_tutorial.pdf

At the 5th step, during the refinement of the model, I find the following error:

[ ERROR ]: Caught exception:


File: src/utility/options/OptionCollection.cc:1467
Option matching -antibody:remodel not found in command line top-level context
Did you mean:
         -loops:remodel
         -remodel

This is the command line I'm using:

/home/user/Rosetta/main/source/bin/antibody_H3.linuxclangrelease @abH3.flags -s ./model-0.relaxed.pdb -nstruct 1 -auto_generate_h3_kink_constraint -h3_loop_csts_hr -out:file:sc
orefile H3_modeling_scores.fasc -out:path:pdb .

Any kind of help would be very appreciated! I will be attaching the crash log for this error on the post.

Attachment	Size
ROSETTA_CRASH.log	43.73 KB

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Post Situation:

Forums:

rosetta_cm - ERROR: Assertion `tlen < slen` failed on File: src/core/fragment/util.cc:177

ramon-arg — Fri, 14 Jul 2023 01:41:16 +0000

I'm following this tutorial to run a protein structure prediction: https://new.rosettacommons.org/demos/latest/tutorials/rosetta_cm/rosetta_cm_tutorial

I was able to model one protein sequence successfully following those steps, but trying for different ones I've been getting this same error:

ERROR: Assertion `tlen < slen` failed.
ERROR:: Exit from: src/core/fragment/util.cc line: 177
protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing protocol:

File: src/core/fragment/util.cc:177
[ ERROR ] UtilityExitException
ERROR: Assertion `tlen < slen` failed.


protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job S_0001

[ ERROR ]: Caught exception:


File: src/core/fragment/util.cc:177
[ ERROR ] UtilityExitException
ERROR: Assertion `tlen < slen` failed.

It repeats other 2 times for each job (S_0002 and S_0003). I checked to see if the files were appropriately edited with the right pdb/fasta/grinshin/frags files, and couldn't find any problems.

I will be attaching the crash log to this post. Any help would be much appreciated!

Attachment	Size
ROSETTA_CRASH.log	56.81 KB

Category:

Post Situation:

Solved

Forums:

fragment_picker:[ ERROR ] UtilityExitException ERROR: can't open file: $ROSETTA/tools/fragment_tools/vall.jul19.2011.gz

yueyuedake — Wed, 12 Jul 2023 10:36:48 +0000

Hi,

When I run fragment_picker, it gives the message:

ERROR: can't open file: $ROSETTA/tools/fragment_tools/vall.jul19.2011.gz
ERROR:: Exit from: src/protocols/frag_picker/VallProvider.cc line: 17

the detail message as follows:

[START_BACKTRACE]: RAW_LIBC
/home/adminroot/rosetta.source.release-351/main/source/build/src/release/linux/5.19/64/x86/gcc/11/mpi/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f5cac7aa59a]
/home/adminroot/rosetta.source.release-351/main/source/build/src/release/linux/5.19/64/x86/gcc/11/mpi/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f5cac7e9890]
/home/adminroot/rosetta.source.release-351/main/source/build/src/release/linux/5.19/64/x86/gcc/11/mpi/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f5cac7af823]
/home/adminroot/rosetta.source.release-351/main/source/build/src/release/linux/5.19/64/x86/gcc/11/mpi/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f5cac7af46b]
/home/adminroot/rosetta.source.release-351/main/source/build/src/release/linux/5.19/64/x86/gcc/11/mpi/libprotocols.4.so(protocols::frag_picker::VallProvider::vallChunksFromLibrary(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, unsigned long)+0x2e51) [0x7f5cada59ad1]
/home/adminroot/rosetta.source.release-351/main/source/build/src/release/linux/5.19/64/x86/gcc/11/mpi/libprotocols.4.so(protocols::frag_picker::VallProvider::vallChunksFromLibraries(utility::vector1<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)+0xe3) [0x7f5cada59e13]
/home/adminroot/rosetta.source.release-351/main/source/build/src/release/linux/5.19/64/x86/gcc/11/mpi/libprotocols.4.so(protocols::frag_picker::FragmentPicker::parse_command_line()+0x11eb) [0x7f5cad9f885b]
fragment_picker.mpi.linuxgccrelease(+0xa32a) [0x55bd5790132a]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5cabe29d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f5cabe29e40]
fragment_picker.mpi.linuxgccrelease(+0xba65) [0x55bd57902a65]

Ubuntu=22.04

python=2.7/3.10

version=rosetta.source_release_351/rosetta_src_2018.09.60072_bundle

gcc=5/11

I have tried many combinations of the above and will all give the same error. I don't know how to solve it.

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