Refinement from mmCIF format

[noi-irantzu]

I am running the following command, using the provided docker image rosettacommons/rosetta:serial-405:

relax.default.linuxgccrelease -in:file:s 1mhp.cif -ex1 -ex2 -use_input_sc -relax:fast -relax:constrain_relax_to_start_coords

Giving as input a .cif file downloaded from PDB: https://www.rcsb.org/structure/1MHP

I get the following error:

...
protocols.jd2.PDBJobInputter: filling pose from PDB 1mhp.cif
core.import_pose.import_pose: File '1mhp.cif' automatically determined to be of type mmCIF from contents.
core.io.mmcif.cif_reader: [ WARNING ] atom_site table apparently not present in mmCIF file - Structure will not have coordinates!
core.io.mmcif.cif_reader: [ WARNING ]  Tables present: entry audit_conform database_2 pdbx_audit_revision_history pdbx_audit_revision_details pdbx_audit_revision_group pdbx_audit_revision_category pdbx_audit_revision_item pdbx_database_status audit_author citation citation_author entity entity_name_com entity_poly pdbx_entity_nonpoly entity_poly_seq entity_src_gen chem_comp pdbx_poly_seq_scheme pdbx_nonpoly_scheme pdbx_unobs_or_zero_occ_atoms software cell symmetry exptl exptl_crystal exptl_crystal_grow diffrn diffrn_detector diffrn_radiation diffrn_radiation_wavelength diffrn_source reflns reflns_shell refine refine_hist refine_ls_restr database_PDB_matrix struct struct_keywords struct_asym struct_ref struct_ref_seq struct_ref_seq_dif pdbx_struct_assembly pdbx_struct_assembly_prop pdbx_struct_assembly_gen pdbx_struct_oper_list struct_biol struct_conf struct_conf_type struct_conn struct_conn_type pdbx_struct_conn_angle pdbx_modification_feature struct_mon_prot_cis struct_sheet struct_sheet_order struct_sheet_range pdbx_struct_sheet_hbond struct_site struct_site_gen pdbx_entry_details pdbx_validate_torsion pdbx_database_remark pdbx_unobs_or_zero_occ_residues chem_comp_atom chem_comp_bond atom_sites atom_type
core.io.mmcif.cif_reader: [ WARNING ]  Note that the final table in the cif file may not be recognized - adding a dummy entry (like `_citation.title  ""`) to the end of the file may help.
protocols.relax.FastRelax: [ WARNING ] Pose has no residues. Doing a FastRelax would be pointless. Skipping.

The table atom_site is present, but as suggested by the error message, I edit the cif file and I append this dummy line in the end of the file _citation.title "".

Now I rerun the command with the new file, and I get the following error ERROR: Unrecognized residue: .:

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C  C in residue 0 P.  Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C  C in residue 0 P.  Pass flag -ignore_zero_occupancy false to change this behavior
basic.io.database: [ WARNING ] Unable to locate database file chemical/pdb_components/components...cif
basic.io.database: [ WARNING ] Unable to locate database file chemical/pdb_components/components...cif.gz
core.chemical.GlobalResidueTypeSet: [ WARNING ] Could not find: '.' in pdb components files! Skipping residue...

ERROR: Unrecognized residue:   .
ERROR:: Exit from: src/core/io/pose_from_sfr/PoseFromSFRBuilder.cc line: 1821
Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job '1mhp_mod_0001'
Error: [ ERROR ] Treating failure as bad input; canceling similar jobs

[ ERROR ]: Caught exception:


File: src/core/io/pose_from_sfr/PoseFromSFRBuilder.cc:1821
[ ERROR ] UtilityExitException
ERROR: Unrecognized residue:   .


 ------------------------ Begin developer's backtrace -------------------------
BACKTRACE:
/usr/local/bin/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7fbca8f537ea]
/usr/local/bin/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x103) [0x7fbca8f8caa3]
/usr/local/bin/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7fbca8f58863]
/usr/local/bin/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7fbca8f5847b]
/usr/local/bin/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, utility::vector1<std::shared_ptr<core::chemical::ResidueType const>, std::allocator<std::shared_ptr<core::chemical::ResidueType const> > > const&)+0x159) [0x7fbc9e8807e9]
/usr/local/bin/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool&)+0x1c7) [0x7fbc9e894847]
/usr/local/bin/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types()+0x279) [0x7fbc9e895b19]
/usr/local/bin/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose(core::io::StructFileRep const&, core::pose::Pose&)+0x14d) [0x7fbc9e89ce9d]
/usr/local/bin/libcore.6.so(core::import_pose::build_pose_as_is(std::shared_ptr<core::io::StructFileRep>, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&)+0xf1) [0x7fbca14d0051]
/usr/local/bin/libcore.6.so(core::import_pose::build_pose(std::shared_ptr<core::io::StructFileRep>, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&)+0x8c) [0x7fbca14d149c]
/usr/local/bin/libcore.6.so(core::import_pose::pose_from_file(core::pose::Pose&, core::chemical::ResidueTypeSet const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x877) [0x7fbca14d3ac7]
/usr/local/bin/libcore.6.so(core::import_pose::pose_from_file(core::pose::Pose&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x11d) [0x7fbca14d986d]
/usr/local/bin/libcore.6.so(core::import_pose::pose_from_file(core::pose::Pose&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, core::import_pose::FileType)+0x50) [0x7fbca14d9a70]
/usr/local/bin/libprotocols.1.so(protocols::jd2::PDBJobInputter::pose_from_job(core::pose::Pose&, std::shared_ptr<protocols::jd2::Job>)+0x6a2) [0x7fbca9dc6b22]
/usr/local/bin/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0x2104) [0x7fbca9d91134]
/usr/local/bin/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7fbca9d92a48]
/usr/local/bin/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x57) [0x7fbca9d79de7]
/usr/local/bin/libprotocols.4.so(protocols::relax::Relax_main(bool)+0x11c3) [0x7fbcaad69083]
relax.default.linuxgccrelease(+0x12ce) [0x55f5fa5d22ce]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7fbca89d3083]
relax.default.linuxgccrelease(+0x136e) [0x55f5fa5d236e]
 ------------------------- End developer's backtrace --------------------------


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


protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: 1mhp_mod_0001
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 0 seconds

---------------------------------------------------------------
[ ERROR ]: Error(s) were encountered when running jobs.
1 jobs failed;
Check the output further up for additional error messages.
---------------------------------------------------------------

An additional question, is the option of outputting a .cif file available? I see cif_writer in github but not sure what is the command line option that outputs a cif file.

Any help is appreciated!
Thank you,

[roccomoretti]

The option to output mmCIF files is -out:mmCIF -- just add that to the command line and Rosetta should output mmCIF files instead of PDB files. (There's also an -out:mmCIF_gz flag you can add to the -out:mmCIF one to get compressed outputs to save disk space -- Rosetta should be able to automatically read gz compressed inputs.)

Regarding your other issues, there was a recent change in how Rosetta reads mmCIF files, allowing for more robust reading. (Most notably, the ignoring of the atom_site_table if it's the last entry in the file is no longer an issue.) -- That should be available with the most recent development version built from the GitHub checkout. It should also address the Unrecognized residue: . error as well.

[noi-irantzu]

Thank you for the fast answer!
The version of rosetta I am using is the version provided in the docker image tag rosettacommons/rosetta:serial-405, which as far as I can see it was updated only 6 days ago. Do you know when a new docker image will be available with the fix you mentioned?

About the "most recent development version built from the GitHub checkout", I don't find any dev/development branch in github, should I clone main branch?

[roccomoretti]

So that docker container build just missed the mmCIF updates. I'm not sure how frequently we're updating the Docker container builds (having officially supported docker containers is something that we've just started recently).

For the GitHub checkout, by "the most recent development version", I do indeed mean the main branch. ("development" here is simply to contrast to the official releases, which sometimes can lag behind).

[noi-irantzu]

I see, thank you for the clarification, it helps a lot!
One last question, when I install pyrosetta using:

pip install pyrosetta-installer
python -c 'import pyrosetta_installer; pyrosetta_installer.install_pyrosetta()'

Instead of the docker image listed above, I ended up in the same issue about the mmCIF.
Do you know if this installation is updated frequently so that it installs the latest updates?

Thank you again,

[roccomoretti]

I believe that the PyRosetta installer should nominally be updated weekly, but sometimes it can go several weeks between updates, if the releases don't match quality control.

The most recent PyRosetta release at the moment does happen to be the same version as the docker container.

[noi-irantzu]

I see. Hopefully they will be updated soon 🤞.
Thank you for the quick and clear answers.