Unexpected true atoms...

[EvanKomp]

I periodically get:

This is for pure unmotiffed generation of a binder eg.

"Zn_binding_no_motif": "inference.input_pdb=/projects/metalsitenn/RFdiffusion2/inputs/ZN_only.pdb inference.ligand=ZN contigmap.length=25-200 contigmap.contigs=[\\'25-200\\']",

Its always atoms associated with a phenylalanine. Pretty funky. Any wisdom appreciated.

[rclune]

Sorry, the code block under 'I periodically get:' is blank, can you clarify?

[EvanKomp]

Oops! What an idiot. Here it is, happens during metrics computation I've seen this 5-6 times and always on PHE:

Running step: metrics
Error executing job with overrides: ['sweep.benchmarks=Zn_binding_no_motif']
Traceback (most recent call last):
  File "/projects/metalsitenn/RFdiffusion2/rf_diffusion/benchmark/pipeline.py", line 158, in main
    jobid_add_metrics = add_metrics.main(conf.metrics)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/site-packages/hydra/main.py", line 79, in decorated_main
    return task_function(cfg_passthrough)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/projects/metalsitenn/RFdiffusion2/rf_diffusion/benchmark/add_metrics.py", line 118, in main
    af2_job, proc = slurm_tools.array_submit(job_fn, p = conf.slurm.p, gres=None if conf.slurm.p=='cpu' else conf.slurm.gres, log=conf.slurm.keep_logs, J=job_name, in_proc=conf.slurm.in_proc, mem=12)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/projects/metalsitenn/RFdiffusion2/rf_diffusion/benchmark/util/slurm_tools.py", line 70, in array_submit
    raise Exception(f'FAILED command: {job}. \n'
Exception: FAILED command: apptainer exec --env WANDB_MODE=offline /projects/metalsitenn/RFdiffusion2/rf_diffusion/exec/bakerlab_rf_diffusion_aa.sif python /projects/metalsitenn/RFdiffusion2/rf_diffusion/benchmark/per_sequence_metrics.py --metric chai1_pocket_aligned_ligand --outcsv /projects/metalsitenn/RFdiffusion2/pipeline_outputs/zs_binding_2025-11-13_17-21-14/metrics/per_sequence/chai1_pocket_aligned_ligand/csv.0 /projects/metalsitenn/RFdiffusion2/pipeline_outputs/zs_binding_2025-11-13_17-21-14/add_metrics.list.metrics_per_sequence_chai1_pocket_aligned_ligand.0
. 
stderr: /bin/sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
INFO:    squashfs image was compressed with lz4, if it failed to run, please contact image's author
INFO:    squashfs image was compressed with lz4, if it failed to run, please contact image's author
Matplotlib created a temporary cache directory at /tmp/scratch/11602748/matplotlib-onzlrlrg because the default path (/home/ekomp/.cache/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
/projects/metalsitenn/RFdiffusion2/rf2aa/model/Track_module.py:356: FutureWarning: `torch.cuda.amp.autocast(args...)` is deprecated. Please use `torch.amp.autocast('cuda', args...)` instead.
  @torch.cuda.amp.autocast(enabled=False)
/projects/metalsitenn/RFdiffusion2/rf2aa/model/Track_module.py:448: FutureWarning: `torch.cuda.amp.autocast(args...)` is deprecated. Please use `torch.amp.autocast('cuda', args...)` instead.
  @torch.cuda.amp.autocast(enabled=False)
ic| per_sequence_metrics.py:65 in main()- __name__: '__main__'
  0%|          | 0/200 [00:01<?, ?it/s]
Traceback (most recent call last):
  File "/projects/metalsitenn/RFdiffusion2/rf_diffusion/benchmark/per_sequence_metrics.py", line 1794, in <module>
    fire.Fire(main)
  File "/usr/lib/python3.11/site-packages/fire/core.py", line 143, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/site-packages/fire/core.py", line 477, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
                                ^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/site-packages/fire/core.py", line 693, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
                ^^^^^^^^^^^^^^^^^^^^^^
  File "/projects/metalsitenn/RFdiffusion2/rf_diffusion/benchmark/per_sequence_metrics.py", line 72, in main
    df = get_metrics(pdbs, metric_f)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/projects/metalsitenn/RFdiffusion2/rf_diffusion/benchmark/per_sequence_metrics.py", line 82, in get_metrics
    record = metric(pdb)
             ^^^^^^^^^^^
  File "/projects/metalsitenn/RFdiffusion2/rf_diffusion/benchmark/per_sequence_metrics.py", line 1371, in chai1_pocket_aligned_ligand
    pocket_metrics = get_pocket_aligned_ligand_rmsds(design_pdb, chai1_pdbs, aligned_pdb_dir=None)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/projects/metalsitenn/RFdiffusion2/rf_diffusion/benchmark/per_sequence_metrics.py", line 1257, in get_pocket_aligned_ligand_rmsds
    atoms_true, atoms_pred_stack, _, _ = correspond_chai_predictions(atoms_true, atoms_pred_stack)
                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/projects/metalsitenn/RFdiffusion2/rf_diffusion/benchmark/per_sequence_metrics.py", line 1209, in correspond_chai_predictions
    raise Exception('\n'.join(errors))
Exception: Unexpected true extra atoms: [Atom(np.array([-6.367,  4.528, -3.579], dtype=float32), chain_id="A", res_id=42, ins_code="", res_name="PHE", hetero=False, atom_name="N", element="N", b_factor=1.65, original_idx=291, res_name_occurance="PHE_0", res_name_occurance_atom_name="PHE_0_N"), Atom(np.array([-6.79 ,  3.65 , -4.663], dtype=float32), chain_id="A", res_id=42, ins_code="", res_name="PHE", hetero=False, atom_name="CA", element="C", b_factor=1.65, original_idx=292, res_name_occurance="PHE_0", res_name_occurance_atom_name="PHE_0_CA"), Atom(np.array([-8.075,  4.16 , -5.303], dtype=float32), chain_id="A", res_id=42, ins_code="", res_name="PHE", hetero=False, atom_name="C", element="C", b_factor=1.65, original_idx=293, res_name_occurance="PHE_0", res_name_occurance_atom_name="PHE_0_C"), Atom(np.array([-8.678,  3.474, -6.131], dtype=float32), chain_id="A", res_id=42, ins_code="", res_name="PHE", hetero=False, atom_name="O", element="O", b_factor=1.65, original_idx=294, res_name_occurance="PHE_0", res_name_occurance_atom_name="PHE_0_O"), Atom(np.array([-6.99 ,  2.22 , -4.151], dtype=float32), chain_id="A", res_id=42, ins_code="", res_name="PHE", hetero=False, atom_name="CB", element="C", b_factor=1.65, original_idx=295, res_name_occurance="PHE_0", res_name_occurance_atom_name="PHE_0_CB"), Atom(np.array([-5.711,  1.533, -3.753], dtype=float32), chain_id="A", res_id=42, ins_code="", res_name="PHE", hetero=False, atom_name="CG", element="C", b_factor=1.65, original_idx=296, res_name_occurance="PHE_0", res_name_occurance_atom_name="PHE_0_CG"), Atom(np.array([-4.544,  1.733, -4.479], dtype=float32), chain_id="A", res_id=42, ins_code="", res_name="PHE", hetero=False, atom_name="CD1", element="C", b_factor=0.41, original_idx=297, res_name_occurance="PHE_0", res_name_occurance_atom_name="PHE_0_CD1"), Atom(np.array([-5.678,  0.688, -2.652], dtype=float32), chain_id="A", res_id=42, ins_code="", res_name="PHE", hetero=False, atom_name="CD2", element="C", b_factor=0.41, original_idx=298, res_name_occurance="PHE_0", res_name_occurance_atom_name="PHE_0_CD2"), Atom(np.array([-3.359,  1.099, -4.112], dtype=float32), chain_id="A", res_id=42, ins_code="", res_name="PHE", hetero=False, atom_name="CE1", element="C", b_factor=0.41, original_idx=299, res_name_occurance="PHE_0", res_name_occurance_atom_name="PHE_0_CE1"), Atom(np.array([-4.497,  0.051, -2.279], dtype=float32), chain_id="A", res_id=42, ins_code="", res_name="PHE", hetero=False, atom_name="CE2", element="C", b_factor=0.41, original_idx=300, res_name_occurance="PHE_0", res_name_occurance_atom_name="PHE_0_CE2"), Atom(np.array([-3.339,  0.257, -3.012], dtype=float32), chain_id="A", res_id=42, ins_code="", res_name="PHE", hetero=False, atom_name="CZ", element="C", b_factor=0.41, original_idx=301, res_name_occurance="PHE_0", res_name_occurance_atom_name="PHE_0_CZ"), Atom(np.array([ 1.28 , -2.599,  8.614], dtype=float32), chain_id="A", res_id=73, ins_code="", res_name="LYS", hetero=False, atom_name="N", element="N", b_factor=1.57, original_idx=518, res_name_occurance="LYS_3", res_name_occurance_atom_name="LYS_3_N"), Atom(np.array([-0.16 , -2.42 ,  8.449], dtype=float32), chain_id="A", res_id=73, ins_code="", res_name="LYS", hetero=False, atom_name="CA", element="C", b_factor=1.57, original_idx=519, res_name_occurance="LYS_3", res_name_occurance_atom_name="LYS_3_CA"), Atom(np.array([-0.476, -1.656,  7.167], dtype=float32), chain_id="A", res_id=73, ins_code="", res_name="LYS", hetero=False, atom_name="C", element="C", b_factor=1.57, original_idx=520, res_name_occurance="LYS_3", res_name_occurance_atom_name="LYS_3_C"), Atom(np.array([ 0.086, -0.586,  6.921], dtype=float32), chain_id="A", res_id=73, ins_code="", res_name="LYS", hetero=False, atom_name="O", element="O", b_factor=1.57, original_idx=521, res_name_occurance="LYS_3", res_name_occurance_atom_name="LYS_3_O"), Atom(np.array([-0.752, -1.688,  9.654], dtype=float32), chain_id="A", res_id=73, ins_code="", res_name="LYS", hetero=False, atom_name="CB", element="C", b_factor=1.57, original_idx=522, res_name_occurance="LYS_3", res_name_occurance_atom_name="LYS_3_CB"), Atom(np.array([-2.249, -1.438,  9.553], dtype=float32), chain_id="A", res_id=73, ins_code="", res_name="LYS", hetero=False, atom_name="CG", element="C", b_factor=1.57, original_idx=523, res_name_occurance="LYS_3", res_name_occurance_atom_name="LYS_3_CG"), Atom(np.array([-2.778, -0.706, 10.78 ], dtype=float32), chain_id="A", res_id=73, ins_code="", res_name="LYS", hetero=False, atom_name="CD", element="C", b_factor=1.05, original_idx=524, res_name_occurance="LYS_3", res_name_occurance_atom_name="LYS_3_CD"), Atom(np.array([-4.29 , -0.536, 10.722], dtype=float32), chain_id="A", res_id=73, ins_code="", res_name="LYS", hetero=False, atom_name="CE", element="C", b_factor=0.81, original_idx=525, res_name_occurance="LYS_3", res_name_occurance_atom_name="LYS_3_CE"), Atom(np.array([-4.807,  0.234, 11.892], dtype=float32), chain_id="A", res_id=73, ins_code="", res_name="LYS", hetero=False, atom_name="NZ", element="N", b_factor=0.8, original_idx=526, res_name_occurance="LYS_3", res_name_occurance_atom_name="LYS_3_NZ"), Atom(np.array([-1.358, -2.182,  6.353], dtype=float32), chain_id="A", res_id=74, ins_code="", res_name="GLU", hetero=False, atom_name="N", element="N", b_factor=0.44, original_idx=527, res_name_occurance="GLU_8", res_name_occurance_atom_name="GLU_8_N"), Atom(np.array([-1.725, -1.548,  5.09 ], dtype=float32), chain_id="A", res_id=74, ins_code="", res_name="GLU", hetero=False, atom_name="CA", element="C", b_factor=0.44, original_idx=528, res_name_occurance="GLU_8", res_name_occurance_atom_name="GLU_8_CA"), Atom(np.array([-3.113, -0.919,  5.171], dtype=float32), chain_id="A", res_id=74, ins_code="", res_name="GLU", hetero=False, atom_name="C", element="C", b_factor=0.44, original_idx=529, res_name_occurance="GLU_8", res_name_occurance_atom_name="GLU_8_C"), Atom(np.array([-4.094, -1.604,  5.467], dtype=float32), chain_id="A", res_id=74, ins_code="", res_name="GLU", hetero=False, atom_name="O", element="O", b_factor=0.44, original_idx=530, res_name_occurance="GLU_8", res_name_occurance_atom_name="GLU_8_O"), Atom(np.array([-1.673, -2.561,  3.944], dtype=float32), chain_id="A", res_id=74, ins_code="", res_name="GLU", hetero=False, atom_name="CB", element="C", b_factor=0.44, original_idx=531, res_name_occurance="GLU_8", res_name_occurance_atom_name="GLU_8_CB"), Atom(np.array([-2.047, -1.977,  2.589], dtype=float32), chain_id="A", res_id=74, ins_code="", res_name="GLU", hetero=False, atom_name="CG", element="C", b_factor=0.44, original_idx=532, res_name_occurance="GLU_8", res_name_occurance_atom_name="GLU_8_CG"), Atom(np.array([-0.978, -1.064,  2.013], dtype=float32), chain_id="A", res_id=74, ins_code="", res_name="GLU", hetero=False, atom_name="CD", element="C", b_factor=0.49, original_idx=533, res_name_occurance="GLU_8", res_name_occurance_atom_name="GLU_8_CD"), Atom(np.array([-1.127, -0.608,  0.857], dtype=float32), chain_id="A", res_id=74, ins_code="", res_name="GLU", hetero=False, atom_name="OE1", element="O", b_factor=-0.18, original_idx=534, res_name_occurance="GLU_8", res_name_occurance_atom_name="GLU_8_OE1"), Atom(np.array([ 0.019, -0.802,  2.724], dtype=float32), chain_id="A", res_id=74, ins_code="", res_name="GLU", hetero=False, atom_name="OE2", element="O", b_factor=-0.18, original_idx=535, res_name_occurance="GLU_8", res_name_occurance_atom_name="GLU_8_OE2"), Atom(np.array([-5.859,  1.226,  2.866], dtype=float32), chain_id="A", res_id=76, ins_code="", res_name="PHE", hetero=False, atom_name="N", element="N", b_factor=1.78, original_idx=543, res_name_occurance="PHE_1", res_name_occurance_atom_name="PHE_1_N"), Atom(np.array([-6.261,  1.687,  1.542], dtype=float32), chain_id="A", res_id=76, ins_code="", res_name="PHE", hetero=False, atom_name="CA", element="C", b_factor=1.78, original_idx=544, res_name_occurance="PHE_1", res_name_occurance_atom_name="PHE_1_CA"), Atom(np.array([-7.334,  2.765,  1.646], dtype=float32), chain_id="A", res_id=76, ins_code="", res_name="PHE", hetero=False, atom_name="C", element="C", b_factor=1.78, original_idx=545, res_name_occurance="PHE_1", res_name_occurance_atom_name="PHE_1_C"), Atom(np.array([-8.378,  2.551,  2.265], dtype=float32), chain_id="A", res_id=76, ins_code="", res_name="PHE", hetero=False, atom_name="O", element="O", b_factor=1.78, original_idx=546, res_name_occurance="PHE_1", res_name_occurance_atom_name="PHE_1_O"), Atom(np.array([-6.773,  0.517,  0.696], dtype=float32), chain_id="A", res_id=76, ins_code="", res_name="PHE", hetero=False, atom_name="CB", element="C", b_factor=1.78, original_idx=547, res_name_occurance="PHE_1", res_name_occurance_atom_name="PHE_1_CB"), Atom(np.array([-5.678, -0.325,  0.098], dtype=float32), chain_id="A", res_id=76, ins_code="", res_name="PHE", hetero=False, atom_name="CG", element="C", b_factor=1.78, original_idx=548, res_name_occurance="PHE_1", res_name_occurance_atom_name="PHE_1_CG"), Atom(np.array([-4.371, -0.218,  0.557], dtype=float32), chain_id="A", res_id=76, ins_code="", res_name="PHE", hetero=False, atom_name="CD1", element="C", b_factor=1.12, original_idx=549, res_name_occurance="PHE_1", res_name_occurance_atom_name="PHE_1_CD1"), Atom(np.array([-5.956, -1.224, -0.923], dtype=float32), chain_id="A", res_id=76, ins_code="", res_name="PHE", hetero=False, atom_name="CD2", element="C", b_factor=1.12, original_idx=550, res_name_occurance="PHE_1", res_name_occurance_atom_name="PHE_1_CD2"), Atom(np.array([-3.355, -0.995,  0.005], dtype=float32), chain_id="A", res_id=76, ins_code="", res_name="PHE", hetero=False, atom_name="CE1", element="C", b_factor=1.12, original_idx=551, res_name_occurance="PHE_1", res_name_occurance_atom_name="PHE_1_CE1"), Atom(np.array([-4.947, -2.004, -1.479], dtype=float32), chain_id="A", res_id=76, ins_code="", res_name="PHE", hetero=False, atom_name="CE2", element="C", b_factor=1.12, original_idx=552, res_name_occurance="PHE_1", res_name_occurance_atom_name="PHE_1_CE2"), Atom(np.array([-3.647, -1.888, -1.014], dtype=float32), chain_id="A", res_id=76, ins_code="", res_name="PHE", hetero=False, atom_name="CZ", element="C", b_factor=1.12, original_idx=553, res_name_occurance="PHE_1", res_name_occurance_atom_name="PHE_1_CZ"), Atom(np.array([-17.595,   3.037,  -2.049], dtype=float32), chain_id="A", res_id=81, ins_code="", res_name="GLU", hetero=False, atom_name="N", element="N", b_factor=0.95, original_idx=586, res_name_occurance="GLU_9", res_name_occurance_atom_name="GLU_9_N"), Atom(np.array([-17.916,   2.027,  -1.045], dtype=float32), chain_id="A", res_id=81, ins_code="", res_name="GLU", hetero=False, atom_name="CA", element="C", b_factor=0.95, original_idx=587, res_name_occurance="GLU_9", res_name_occurance_atom_name="GLU_9_CA"), Atom(np.array([-17.746,   0.618,  -1.606], dtype=float32), chain_id="A", res_id=81, ins_code="", res_name="GLU", hetero=False, atom_name="C", element="C", b_factor=0.95, original_idx=588, res_name_occurance="GLU_9", res_name_occurance_atom_name="GLU_9_C"), Atom(np.array([-17.264,  -0.279,  -0.91 ], dtype=float32), chain_id="A", res_id=81, ins_code="", res_name="GLU", hetero=False, atom_name="O", element="O", b_factor=0.95, original_idx=589, res_name_occurance="GLU_9", res_name_occurance_atom_name="GLU_9_O"), Atom(np.array([-19.344,   2.218,  -0.527], dtype=float32), chain_id="A", res_id=81, ins_code="", res_name="GLU", hetero=False, atom_name="CB", element="C", b_factor=0.95, original_idx=590, res_name_occurance="GLU_9", res_name_occurance_atom_name="GLU_9_CB"), Atom(np.array([-19.516,   3.437,   0.368], dtype=float32), chain_id="A", res_id=81, ins_code="", res_name="GLU", hetero=False, atom_name="CG", element="C", b_factor=0.95, original_idx=591, res_name_occurance="GLU_9", res_name_occurance_atom_name="GLU_9_CG"), Atom(np.array([-20.941,   3.622,   0.862], dtype=float32), chain_id="A", res_id=81, ins_code="", res_name="GLU", hetero=False, atom_name="CD", element="C", b_factor=0.5, original_idx=592, res_name_occurance="GLU_9", res_name_occurance_atom_name="GLU_9_CD"), Atom(np.array([-21.205,   4.595,   1.605], dtype=float32), chain_id="A", res_id=81, ins_code="", res_name="GLU", hetero=False, atom_name="OE1", element="O", b_factor=-0.35, original_idx=593, res_name_occurance="GLU_9", res_name_occurance_atom_name="GLU_9_OE1"), Atom(np.array([-21.802,   2.788,   0.504], dtype=float32), chain_id="A", res_id=81, ins_code="", res_name="GLU", hetero=False, atom_name="OE2", element="O", b_factor=-0.35, original_idx=594, res_name_occurance="GLU_9", res_name_occurance_atom_name="GLU_9_OE2"), Atom(np.array([-18.147,   0.43 ,  -2.868], dtype=float32), chain_id="A", res_id=82, ins_code="", res_name="GLU", hetero=False, atom_name="N", element="N", b_factor=0.18, original_idx=595, res_name_occurance="GLU_10", res_name_occurance_atom_name="GLU_10_N"), Atom(np.array([-17.992,  -0.865,  -3.525], dtype=float32), chain_id="A", res_id=82, ins_code="", res_name="GLU", hetero=False, atom_name="CA", element="C", b_factor=0.18, original_idx=596, res_name_occurance="GLU_10", res_name_occurance_atom_name="GLU_10_CA"), Atom(np.array([-16.521,  -1.259,  -3.629], dtype=float32), chain_id="A", res_id=82, ins_code="", res_name="GLU", hetero=False, atom_name="C", element="C", b_factor=0.18, original_idx=597, res_name_occurance="GLU_10", res_name_occurance_atom_name="GLU_10_C"), Atom(np.array([-16.157,  -2.401,  -3.343], dtype=float32), chain_id="A", res_id=82, ins_code="", res_name="GLU", hetero=False, atom_name="O", element="O", b_factor=0.18, original_idx=598, res_name_occurance="GLU_10", res_name_occurance_atom_name="GLU_10_O"), Atom(np.array([-18.63 ,  -0.842,  -4.916], dtype=float32), chain_id="A", res_id=82, ins_code="", res_name="GLU", hetero=False, atom_name="CB", element="C", b_factor=0.18, original_idx=599, res_name_occurance="GLU_10", res_name_occurance_atom_name="GLU_10_CB"), Atom(np.array([-18.74 ,  -2.214,  -5.565], dtype=float32), chain_id="A", res_id=82, ins_code="", res_name="GLU", hetero=False, atom_name="CG", element="C", b_factor=0.18, original_idx=600, res_name_occurance="GLU_10", res_name_occurance_atom_name="GLU_10_CG"), Atom(np.array([-19.441,  -2.186,  -6.914], dtype=float32), chain_id="A", res_id=82, ins_code="", res_name="GLU", hetero=False, atom_name="CD", element="C", b_factor=0.44, original_idx=601, res_name_occurance="GLU_10", res_name_occurance_atom_name="GLU_10_CD"), Atom(np.array([-19.626,  -3.263,  -7.525], dtype=float32), chain_id="A", res_id=82, ins_code="", res_name="GLU", hetero=False, atom_name="OE1", element="O", b_factor=-0.36, original_idx=602, res_name_occurance="GLU_10", res_name_occurance_atom_name="GLU_10_OE1"), Atom(np.array([-19.806,  -1.077,  -7.365], dtype=float32), chain_id="A", res_id=82, ins_code="", res_name="GLU", hetero=False, atom_name="OE2", element="O", b_factor=-0.36, original_idx=603, res_name_occurance="GLU_10", res_name_occurance_atom_name="GLU_10_OE2"), Atom(np.array([-6.973, -2.484,  6.585], dtype=float32), chain_id="A", res_id=94, ins_code="", res_name="GLU", hetero=False, atom_name="N", element="N", b_factor=1.31, original_idx=677, res_name_occurance="GLU_11", res_name_occurance_atom_name="GLU_11_N"), Atom(np.array([-7.917, -1.391,  6.797], dtype=float32), chain_id="A", res_id=94, ins_code="", res_name="GLU", hetero=False, atom_name="CA", element="C", b_factor=1.31, original_idx=678, res_name_occurance="GLU_11", res_name_occurance_atom_name="GLU_11_CA"), Atom(np.array([-8.283, -0.714,  5.479], dtype=float32), chain_id="A", res_id=94, ins_code="", res_name="GLU", hetero=False, atom_name="C", element="C", b_factor=1.31, original_idx=679, res_name_occurance="GLU_11", res_name_occurance_atom_name="GLU_11_C"), Atom(np.array([-7.41 , -0.442,  4.652], dtype=float32), chain_id="A", res_id=94, ins_code="", res_name="GLU", hetero=False, atom_name="O", element="O", b_factor=1.31, original_idx=680, res_name_occurance="GLU_11", res_name_occurance_atom_name="GLU_11_O"), Atom(np.array([-7.339, -0.364,  7.774], dtype=float32), chain_id="A", res_id=94, ins_code="", res_name="GLU", hetero=False, atom_name="CB", element="C", b_factor=1.31, original_idx=681, res_name_occurance="GLU_11", res_name_occurance_atom_name="GLU_11_CB"), Atom(np.array([-8.312,  0.746,  8.146], dtype=float32), chain_id="A", res_id=94, ins_code="", res_name="GLU", hetero=False, atom_name="CG", element="C", b_factor=1.31, original_idx=682, res_name_occurance="GLU_11", res_name_occurance_atom_name="GLU_11_CG"), Atom(np.array([-7.748,  1.72 ,  9.168], dtype=float32), chain_id="A", res_id=94, ins_code="", res_name="GLU", hetero=False, atom_name="CD", element="C", b_factor=1.37, original_idx=683, res_name_occurance="GLU_11", res_name_occurance_atom_name="GLU_11_CD"), Atom(np.array([-8.372,  2.78 ,  9.404], dtype=float32), chain_id="A", res_id=94, ins_code="", res_name="GLU", hetero=False, atom_name="OE1", element="O", b_factor=0.46, original_idx=684, res_name_occurance="GLU_11", res_name_occurance_atom_name="GLU_11_OE1"), Atom(np.array([-6.675,  1.422,  9.737], dtype=float32), chain_id="A", res_id=94, ins_code="", res_name="GLU", hetero=False, atom_name="OE2", element="O", b_factor=0.46, original_idx=685, res_name_occurance="GLU_11", res_name_occurance_atom_name="GLU_11_OE2"), Atom(np.array([-10.394,   2.763,   4.236], dtype=float32), chain_id="A", res_id=96, ins_code="", res_name="VAL", hetero=False, atom_name="N", element="N", b_factor=2.0, original_idx=693, res_name_occurance="VAL_15", res_name_occurance_atom_name="VAL_15_N"), Atom(np.array([-11.022,   3.985,   4.728], dtype=float32), chain_id="A", res_id=96, ins_code="", res_name="VAL", hetero=False, atom_name="CA", element="C", b_factor=2.0, original_idx=694, res_name_occurance="VAL_15", res_name_occurance_atom_name="VAL_15_CA"), Atom(np.array([-11.598,   4.778,   3.557], dtype=float32), chain_id="A", res_id=96, ins_code="", res_name="VAL", hetero=False, atom_name="C", element="C", b_factor=2.0, original_idx=695, res_name_occurance="VAL_15", res_name_occurance_atom_name="VAL_15_C"), Atom(np.array([-10.945,   4.93 ,   2.521], dtype=float32), chain_id="A", res_id=96, ins_code="", res_name="VAL", hetero=False, atom_name="O", element="O", b_factor=2.0, original_idx=696, res_name_occurance="VAL_15", res_name_occurance_atom_name="VAL_15_O"), Atom(np.array([-10.023,   4.856,   5.522], dtype=float32), chain_id="A", res_id=96, ins_code="", res_name="VAL", hetero=False, atom_name="CB", element="C", b_factor=2.0, original_idx=697, res_name_occurance="VAL_15", res_name_occurance_atom_name="VAL_15_CB"), Atom(np.array([-10.659,   6.191,   5.908], dtype=float32), chain_id="A", res_id=96, ins_code="", res_name="VAL", hetero=False, atom_name="CG1", element="C", b_factor=2.0, original_idx=698, res_name_occurance="VAL_15", res_name_occurance_atom_name="VAL_15_CG1"), Atom(np.array([-9.538,  4.113,  6.765], dtype=float32), chain_id="A", res_id=96, ins_code="", res_name="VAL", hetero=False, atom_name="CG2", element="C", b_factor=2.0, original_idx=699, res_name_occurance="VAL_15", res_name_occurance_atom_name="VAL_15_CG2"), Atom(np.array([-12.809,   5.283,   3.725], dtype=float32), chain_id="A", res_id=97, ins_code="", res_name="LEU", hetero=False, atom_name="N", element="N", b_factor=1.51, original_idx=700, res_name_occurance="LEU_8", res_name_occurance_atom_name="LEU_8_N"), Atom(np.array([-13.378,   6.218,   2.761], dtype=float32), chain_id="A", res_id=97, ins_code="", res_name="LEU", hetero=False, atom_name="CA", element="C", b_factor=1.51, original_idx=701, res_name_occurance="LEU_8", res_name_occurance_atom_name="LEU_8_CA"), Atom(np.array([-12.842,   7.628,   2.989], dtype=float32), chain_id="A", res_id=97, ins_code="", res_name="LEU", hetero=False, atom_name="C", element="C", b_factor=1.51, original_idx=702, res_name_occurance="LEU_8", res_name_occurance_atom_name="LEU_8_C"), Atom(np.array([-13.199,   8.28 ,   3.973], dtype=float32), chain_id="A", res_id=97, ins_code="", res_name="LEU", hetero=False, atom_name="O", element="O", b_factor=1.51, original_idx=703, res_name_occurance="LEU_8", res_name_occurance_atom_name="LEU_8_O"), Atom(np.array([-14.906,   6.219,   2.853], dtype=float32), chain_id="A", res_id=97, ins_code="", res_name="LEU", hetero=False, atom_name="CB", element="C", b_factor=1.51, original_idx=704, res_name_occurance="LEU_8", res_name_occurance_atom_name="LEU_8_CB"), Atom(np.array([-15.608,   4.911,   2.485], dtype=float32), chain_id="A", res_id=97, ins_code="", res_name="LEU", hetero=False, atom_name="CG", element="C", b_factor=1.51, original_idx=705, res_name_occurance="LEU_8", res_name_occurance_atom_name="LEU_8_CG"), Atom(np.array([-17.115,   5.044,   2.684], dtype=float32), chain_id="A", res_id=97, ins_code="", res_name="LEU", hetero=False, atom_name="CD1", element="C", b_factor=1.12, original_idx=706, res_name_occurance="LEU_8", res_name_occurance_atom_name="LEU_8_CD1"), Atom(np.array([-15.286,   4.516,   1.048], dtype=float32), chain_id="A", res_id=97, ins_code="", res_name="LEU", hetero=False, atom_name="CD2", element="C", b_factor=1.12, original_idx=707, res_name_occurance="LEU_8", res_name_occurance_atom_name="LEU_8_CD2"), Atom(np.array([-2.593, 11.627, -1.628], dtype=float32), chain_id="A", res_id=103, ins_code="", res_name="GLU", hetero=False, atom_name="N", element="N", b_factor=0.97, original_idx=753, res_name_occurance="GLU_12", res_name_occurance_atom_name="GLU_12_N"), Atom(np.array([-1.195, 11.327, -1.333], dtype=float32), chain_id="A", res_id=103, ins_code="", res_name="GLU", hetero=False, atom_name="CA", element="C", b_factor=0.97, original_idx=754, res_name_occurance="GLU_12", res_name_occurance_atom_name="GLU_12_CA"), Atom(np.array([-1.041,  9.918, -0.768], dtype=float32), chain_id="A", res_id=103, ins_code="", res_name="GLU", hetero=False, atom_name="C", element="C", b_factor=0.97, original_idx=755, res_name_occurance="GLU_12", res_name_occurance_atom_name="GLU_12_C"), Atom(np.array([-1.853,  9.479,  0.049], dtype=float32), chain_id="A", res_id=103, ins_code="", res_name="GLU", hetero=False, atom_name="O", element="O", b_factor=0.97, original_idx=756, res_name_occurance="GLU_12", res_name_occurance_atom_name="GLU_12_O"), Atom(np.array([-0.62 , 12.353, -0.353], dtype=float32), chain_id="A", res_id=103, ins_code="", res_name="GLU", hetero=False, atom_name="CB", element="C", b_factor=0.97, original_idx=757, res_name_occurance="GLU_12", res_name_occurance_atom_name="GLU_12_CB"), Atom(np.array([-0.536, 13.763, -0.917], dtype=float32), chain_id="A", res_id=103, ins_code="", res_name="GLU", hetero=False, atom_name="CG", element="C", b_factor=0.97, original_idx=758, res_name_occurance="GLU_12", res_name_occurance_atom_name="GLU_12_CG"), Atom(np.array([ 0.139, 14.747,  0.025], dtype=float32), chain_id="A", res_id=103, ins_code="", res_name="GLU", hetero=False, atom_name="CD", element="C", b_factor=0.72, original_idx=759, res_name_occurance="GLU_12", res_name_occurance_atom_name="GLU_12_CD"), Atom(np.array([ 0.59 , 15.819, -0.438], dtype=float32), chain_id="A", res_id=103, ins_code="", res_name="GLU", hetero=False, atom_name="OE1", element="O", b_factor=-0.14, original_idx=760, res_name_occurance="GLU_12", res_name_occurance_atom_name="GLU_12_OE1"), Atom(np.array([ 0.218, 14.443,  1.236], dtype=float32), chain_id="A", res_id=103, ins_code="", res_name="GLU", hetero=False, atom_name="OE2", element="O", b_factor=-0.14, original_idx=761, res_name_occurance="GLU_12", res_name_occurance_atom_name="GLU_12_OE2"), Atom(np.array([-0.013,  9.187, -1.178], dtype=float32), chain_id="A", res_id=104, ins_code="", res_name="ASP", hetero=False, atom_name="N", element="N", b_factor=1.82, original_idx=762, res_name_occurance="ASP_7", res_name_occurance_atom_name="ASP_7_N"), Atom(np.array([ 0.427,  8.022, -0.417], dtype=float32), chain_id="A", res_id=104, ins_code="", res_name="ASP", hetero=False, atom_name="CA", element="C", b_factor=1.82, original_idx=763, res_name_occurance="ASP_7", res_name_occurance_atom_name="ASP_7_CA"), Atom(np.array([1.291, 8.437, 0.772], dtype=float32), chain_id="A", res_id=104, ins_code="", res_name="ASP", hetero=False, atom_name="C", element="C", b_factor=1.82, original_idx=764, res_name_occurance="ASP_7", res_name_occurance_atom_name="ASP_7_C"), Atom(np.array([1.91 , 9.503, 0.754], dtype=float32), chain_id="A", res_id=104, ins_code="", res_name="ASP", hetero=False, atom_name="O", element="O", b_factor=1.82, original_idx=765, res_name_occurance="ASP_7", res_name_occurance_atom_name="ASP_7_O"), Atom(np.array([ 1.199,  7.054, -1.316], dtype=float32), chain_id="A", res_id=104, ins_code="", res_name="ASP", hetero=False, atom_name="CB", element="C", b_factor=1.82, original_idx=766, res_name_occurance="ASP_7", res_name_occurance_atom_name="ASP_7_CB"), Atom(np.array([ 0.328,  6.411, -2.381], dtype=float32), chain_id="A", res_id=104, ins_code="", res_name="ASP", hetero=False, atom_name="CG", element="C", b_factor=1.82, original_idx=767, res_name_occurance="ASP_7", res_name_occurance_atom_name="ASP_7_CG"), Atom(np.array([-0.836,  6.063, -2.088], dtype=float32), chain_id="A", res_id=104, ins_code="", res_name="ASP", hetero=False, atom_name="OD1", element="O", b_factor=1.36, original_idx=768, res_name_occurance="ASP_7", res_name_occurance_atom_name="ASP_7_OD1"), Atom(np.array([ 0.811,  6.249, -3.522], dtype=float32), chain_id="A", res_id=104, ins_code="", res_name="ASP", hetero=False, atom_name="OD2", element="O", b_factor=1.36, original_idx=769, res_name_occurance="ASP_7", res_name_occurance_atom_name="ASP_7_OD2"), Atom(np.array([ 7.703,  3.612, 12.922], dtype=float32), chain_id="A", res_id=109, ins_code="", res_name="TYR", hetero=False, atom_name="N", element="N", b_factor=1.74, original_idx=792, res_name_occurance="TYR_1", res_name_occurance_atom_name="TYR_1_N"), Atom(np.array([ 7.981,  3.69 , 14.352], dtype=float32), chain_id="A", res_id=109, ins_code="", res_name="TYR", hetero=False, atom_name="CA", element="C", b_factor=1.74, original_idx=793, res_name_occurance="TYR_1", res_name_occurance_atom_name="TYR_1_CA"), Atom(np.array([ 9.297,  3.001, 14.69 ], dtype=float32), chain_id="A", res_id=109, ins_code="", res_name="TYR", hetero=False, atom_name="C", element="C", b_factor=1.74, original_idx=794, res_name_occurance="TYR_1", res_name_occurance_atom_name="TYR_1_C"), Atom(np.array([ 9.521,  1.851, 14.304], dtype=float32), chain_id="A", res_id=109, ins_code="", res_name="TYR", hetero=False, atom_name="O", element="O", b_factor=1.74, original_idx=795, res_name_occurance="TYR_1", res_name_occurance_atom_name="TYR_1_O"), Atom(np.array([ 6.84 ,  3.06 , 15.156], dtype=float32), chain_id="A", res_id=109, ins_code="", res_name="TYR", hetero=False, atom_name="CB", element="C", b_factor=1.74, original_idx=796, res_name_occurance="TYR_1", res_name_occurance_atom_name="TYR_1_CB"), Atom(np.array([ 5.503,  3.725, 14.937], dtype=float32), chain_id="A", res_id=109, ins_code="", res_name="TYR", hetero=False, atom_name="CG", element="C", b_factor=1.74, original_idx=797, res_name_occurance="TYR_1", res_name_occurance_atom_name="TYR_1_CG"), Atom(np.array([ 5.014,  4.665, 15.841], dtype=float32), chain_id="A", res_id=109, ins_code="", res_name="TYR", hetero=False, atom_name="CD1", element="C", b_factor=1.48, original_idx=798, res_name_occurance="TYR_1", res_name_occurance_atom_name="TYR_1_CD1"), Atom(np.array([ 4.726,  3.413, 13.826], dtype=float32), chain_id="A", res_id=109, ins_code="", res_name="TYR", hetero=False, atom_name="CD2", element="C", b_factor=1.48, original_idx=799, res_name_occurance="TYR_1", res_name_occurance_atom_name="TYR_1_CD2"), Atom(np.array([ 3.781,  5.279, 15.643], dtype=float32), chain_id="A", res_id=109, ins_code="", res_name="TYR", hetero=False, atom_name="CE1", element="C", b_factor=1.48, original_idx=800, res_name_occurance="TYR_1", res_name_occurance_atom_name="TYR_1_CE1"), Atom(np.array([ 3.492,  4.021, 13.619], dtype=float32), chain_id="A", res_id=109, ins_code="", res_name="TYR", hetero=False, atom_name="CE2", element="C", b_factor=1.48, original_idx=801, res_name_occurance="TYR_1", res_name_occurance_atom_name="TYR_1_CE2"), Atom(np.array([ 3.029,  4.951, 14.531], dtype=float32), chain_id="A", res_id=109, ins_code="", res_name="TYR", hetero=False, atom_name="CZ", element="C", b_factor=1.48, original_idx=802, res_name_occurance="TYR_1", res_name_occurance_atom_name="TYR_1_CZ"), Atom(np.array([ 1.808,  5.556, 14.331], dtype=float32), chain_id="A", res_id=109, ins_code="", res_name="TYR", hetero=False, atom_name="OH", element="O", b_factor=1.48, original_idx=803, res_name_occurance="TYR_1", res_name_occurance_atom_name="TYR_1_OH"), Atom(np.array([12.371,  2.553, 17.966], dtype=float32), chain_id="A", res_id=111, ins_code="", res_name="GLU", hetero=False, atom_name="N", element="N", b_factor=-0.08, original_idx=808, res_name_occurance="GLU_13", res_name_occurance_atom_name="GLU_13_N"), Atom(np.array([12.659,  2.723, 19.387], dtype=float32), chain_id="A", res_id=111, ins_code="", res_name="GLU", hetero=False, atom_name="CA", element="C", b_factor=-0.08, original_idx=809, res_name_occurance="GLU_13", res_name_occurance_atom_name="GLU_13_CA"), Atom(np.array([14.108,  3.146, 19.609], dtype=float32), chain_id="A", res_id=111, ins_code="", res_name="GLU", hetero=False, atom_name="C", element="C", b_factor=-0.08, original_idx=810, res_name_occurance="GLU_13", res_name_occurance_atom_name="GLU_13_C"), Atom(np.array([15.026,  2.571, 19.02 ], dtype=float32), chain_id="A", res_id=111, ins_code="", res_name="GLU", hetero=False, atom_name="O", element="O", b_factor=-0.08, original_idx=811, res_name_occurance="GLU_13", res_name_occurance_atom_name="GLU_13_O"), Atom(np.array([12.364,  1.431, 20.154], dtype=float32), chain_id="A", res_id=111, ins_code="", res_name="GLU", hetero=False, atom_name="CB", element="C", b_factor=-0.08, original_idx=812, res_name_occurance="GLU_13", res_name_occurance_atom_name="GLU_13_CB"), Atom(np.array([10.88 ,  1.12 , 20.286], dtype=float32), chain_id="A", res_id=111, ins_code="", res_name="GLU", hetero=False, atom_name="CG", element="C", b_factor=-0.08, original_idx=813, res_name_occurance="GLU_13", res_name_occurance_atom_name="GLU_13_CG"), Atom(np.array([10.606, -0.216, 20.959], dtype=float32), chain_id="A", res_id=111, ins_code="", res_name="GLU", hetero=False, atom_name="CD", element="C", b_factor=0.09, original_idx=814, res_name_occurance="GLU_13", res_name_occurance_atom_name="GLU_13_CD"), Atom(np.array([ 9.421, -0.6  , 21.083], dtype=float32), chain_id="A", res_id=111, ins_code="", res_name="GLU", hetero=False, atom_name="OE1", element="O", b_factor=-0.3, original_idx=815, res_name_occurance="GLU_13", res_name_occurance_atom_name="GLU_13_OE1"), Atom(np.array([11.583, -0.882, 21.366], dtype=float32), chain_id="A", res_id=111, ins_code="", res_name="GLU", hetero=False, atom_name="OE2", element="O", b_factor=-0.3, original_idx=816, res_name_occurance="GLU_13", res_name_occurance_atom_name="GLU_13_OE2")]


Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.```

[rclune]

This exception is coming from rf_diffusion/benchmark/per_sequence_metrics.py, as far as I can tell. It is supposed to record any unexpected hetero atoms. What is in your input file, is it just a Zn ion? Are the residue IDs it's returning at the end from the designed protein or fro your input file?

[EvanKomp]

Its just a Zn ion and an glycine, as I was observing errors when trying to define contigs for files without amino acids. Shown below. For the second part of your question I don't think its from the PDB file since its a PHE and I am defining 1-150 residues to be randomly generated, but I'm a little fuzzy on how that all works tbh. Thanks for your time.

HEADER    NICKEL ION FOR BINDER DESIGN
ATOM      1  N   GLY A   1       5.000   0.000   0.000  1.00 20.00           N  
ATOM      2  CA  GLY A   1       3.500   0.000   0.000  1.00 20.00           C  
ATOM      3  C   GLY A   1       3.000   1.400   0.000  1.00 20.00           C  
ATOM      4  O   GLY A   1       3.700   2.400   0.000  1.00 20.00           O  
HETATM    5 ORI  ORI A 200       0.000   0.000   0.000  1.00 20.00          OR  
HETATM    6 ZN   ZN A 201       0.000   0.000   0.000  1.00 20.00          ZN  
END

Thanks for your time!

[rclune]

Can you provide more information how you are running RFdiffusion2? Are you using the run_inference.py script or the pipeline.py file? Did you have to change anything to get RFdiffusion2 to recognize ZN as a ligand?

[EvanKomp]

pipeline.py through the container, with the following cofing:

defaults:
  - enzyme_bench_n41
  - _self_

in_proc: True
sweep:
  retries: 2
  command_args: >
    --config-name=aa
    inference.deterministic=False
    inference.ckpt_path=REPO_ROOT/rf_diffusion/model_weights/RFD_173.pt
    inference.seed_offset=43
  benchmarks: "Zn_binding_no_motif"
  
  num_per_condition: 100
  num_per_job: 100
  benchmark_json: working_config.json 

mpnn:
  num_seq_per_target: 1

stop_step: end
outdir: ${hydra:runtime.cwd}/pipeline_outputs/zs_binding_${now:%Y-%m-%d}_${now:%H-%M-%S}

The spec for that benchmark is :

"Zn_binding_no_motif": "inference.input_pdb=/projects/metalsitenn/RFdiffusion2/inputs/Zn_only.pdb inference.ligand=ZN contigmap.length=25-200 contigmap.contigs=[\\'25-200\\']"

I think it is recognizing ZN as is - when I try with more niche metals it throws some funky errors which makes me think those atoms are not in the token vocab (While Zn is?)

Appreciation

[rclune]

I'm still in the process of recreating your error, but I'm wondering if the issue is that the way they were calculating metrics for their benchmark for RFD2 won't work with what you are trying to do.

If you look at rf_diffusion/benchmark/per_sequence_metrics.py, there is a function correspond_chai_predictions which is where this error is coming from. The function compares the predicted structure predicted by Chai1 to your input structure. The function is supposed to throw an error when there are atoms in the input structure that the model failed to predict but should not be missing. It's possible this function was not meant to work well with this type of input, since you are not trying to have Chai1 return something resembling your input structure.

Is there a reason you need the metrics calculated for what you are dong?

[EvanKomp]

@rclune
Good question. It is my understanding that the best performance / highest hit rates have come from extensive filtering based on inverse folding, designability, recovery of the inout motif as predicted by protein-ligand structure predictions. Eg. Just taking generative model outputs and testing them in the lab has extremely low hit rate.

I am basically trying to use the model to get an idea of the modes of metal binding for different metals. For this task it feels necessary to at least make sure that the designed and inverse folded sequence would achieve the target fold (design-ability?) Maybe I should look to disable certain metrics but based on my read this is pretty foundational error (eg. the chai predictions that are actually used to compute basically every metric cannot be loaded). Thoughts?

Congrats on the paper!