Convert coarse-grained protein structure to all-atom model
A demo web page is available for conversions of CG model to all-atom structure via Huggingface space.
A Google Colab notebook is available for tasks:
- Task 1: Conversion of an all-atom structure to a CG model using convert_all2cg
- Task 2: Conversion of a CG model to an all-atom structure using convert_cg2all
- Task 3: Conversion of a CG simulation trajectory to an atomistic simulation trajectory using convert_cg2all
A Google Colab notebook is available for local optimization of a protein model structure against a cryo-EM density map using cryo_em_minimizer.py
These steps will install Python libraries including cg2all (this repository), a modified MDTraj, a modified SE3Transformer, and other dependent libraries. The installation steps also place executables convert_cg2all and convert_all2cg in your python binary directory.
This package is tested on Linux (CentOS) and MacOS (Apple Silicon, M1).
pip install git+http://github.com/huhlim/cg2all# This is an example with cudatoolkit=11.3.
# Set a proper cudatoolkit version that is compatible with your CUDA drivier and DGL library.
# dgl>=1.1 occassionally raises some errors, so please use dgl<=1.0.
conda create --name cg2all pip cudatoolkit=11.3 dgl=1.0 -c dglteam/label/cu113- Activate the environment
conda activate cg2all- Install this package
pip install git+http://github.com/huhlim/cg2allYou need additional python package, mrcfile to deal with cryo-EM density map.
pip install mrcfileconvert a coarse-grained protein structure to all-atom model
usage: convert_cg2all [-h] -p IN_PDB_FN [-d IN_DCD_FN] -o OUT_FN [-opdb OUTPDB_FN]
[--cg {supported_cg_models}] [--chain-break-cutoff CHAIN_BREAK_CUTOFF] [-a]
[--fix] [--ckpt CKPT_FN] [--time TIME_JSON] [--device DEVICE] [--batch BATCH_SIZE] [--proc N_PROC]
options:
-h, --help show this help message and exit
-p IN_PDB_FN, --pdb IN_PDB_FN
-d IN_DCD_FN, --dcd IN_DCD_FN
-o OUT_FN, --out OUT_FN, --output OUT_FN
-opdb OUTPDB_FN
--cg {supported_cg_models}
--chain-break-cutoff CHAIN_BREAK_CUTOFF
-a, --all, --is_all
--fix, --fix_atom
--standard-name
--ckpt CKPT_FN
--time TIME_JSON
--device DEVICE
--batch BATCH_SIZE
--proc N_PROC- -p/--pdb: Input PDB file (mandatory).
- -d/--dcd: Input DCD file (optional). If a DCD file is given, the input PDB file will be used to define its topology.
- -o/--out/--output: Output PDB or DCD file (mandatory). If a DCD file is given, it will be a DCD file. Otherwise, a PDB file will be created.
- -opdb: If a DCD file is given, it will write the last snapshot as a PDB file. (optional)
- --cg: Coarse-grained representation to use (optional, default=CalphaBasedModel).
- CalphaBasedModel: CA-trace (atom names should be "CA")
- ResidueBasedModel: Residue center-of-mass (atom names should be "CA")
- SidechainModel: Sidechain center-of-mass (atom names should be "SC")
- CalphaCMModel: CA-trace + Residue center-of-mass (atom names should be "CA" and "CM")
- CalphaSCModel: CA-trace + Sidechain center-of-mass (atom names should be "CA" and "SC")
- BackboneModel: Model only with backbone atoms (N, CA, C)
- MainchainModel: Model only with mainchain atoms (N, CA, C, O)
- Martini: Martini model
- Martini3: Martini3 model
- PRIMO: PRIMO model
- --chain-break-cutoff: The CA-CA distance cutoff that determines chain breaks. (default=10 Angstroms)
- --fix/--fix_atom: preserve coordinates in the input CG model. For example, CA coordinates in a CA-trace model will be kept in its cg2all output model.
- --standard-name: output atom names follow the IUPAC nomenclature. (default=False; output atom names will use CHARMM atom names)
- --ckpt: Input PyTorch ckpt file (optional). If a ckpt file is given, it will override "--cg" option.
- --time: Output JSON file for recording timing. (optional)
- --device: Specify a device to run the model. (optional) You can choose "cpu" or "cuda", or the script will detect one automatically.
"cpu" is usually faster than "cuda" unless the input/output system is really big or you provided a DCD file with many frames because it takes a lot for loading a model ckpt file on a GPU. - --batch: the number of frames to be dealt at a time. (optional, default=1)
- --proc: Specify the number of threads for loading input data. It is only used for dealing with a DCD file. (optional, default=OMP_NUM_THREADS or 1)
Conversion of a PDB file
convert_cg2all -p tests/1ab1_A.calpha.pdb -o tests/1ab1_A.calpha.all.pdb --cg CalphaBasedModelConversion of a DCD trajectory file
convert_cg2all -p tests/1jni.calpha.pdb -d tests/1jni.calpha.dcd -o tests/1jni.calpha.all.dcd --cg CalphaBasedModelConversion of a PDB file using a ckpt file
convert_cg2all -p tests/1ab1_A.calpha.pdb -o tests/1ab1_A.calpha.all.pdb --ckpt CalphaBasedModel-104.ckptconvert an all-atom protein structure to coarse-grained model
usage: convert_all2cg [-h] -p IN_PDB_FN [-d IN_DCD_FN] -o OUT_FN [--cg {supported_cg_models}]
options:
-h, --help show this help message and exit
-p IN_PDB_FN, --pdb IN_PDB_FN
-d IN_DCD_FN, --dcd IN_DCD_FN
-o OUT_FN, --out OUT_FN, --output OUT_FN
--cg- -p/--pdb: Input PDB file (mandatory).
- -d/--dcd: Input DCD file (optional). If a DCD file is given, the input PDB file will be used to define its topology.
- -o/--out/--output: Output PDB or DCD file (mandatory). If a DCD file is given, it will be a DCD file. Otherwise, a PDB file will be created.
- --cg: Coarse-grained representation to use (optional, default=CalphaBasedModel).
- CalphaBasedModel: CA-trace (atom names should be "CA")
- ResidueBasedModel: Residue center-of-mass (atom names should be "CA")
- SidechainModel: Sidechain center-of-mass (atom names should be "SC")
- CalphaCMModel: CA-trace + Residue center-of-mass (atom names should be "CA" and "CM")
- CalphaSCModel: CA-trace + Sidechain center-of-mass (atom names should be "CA" and "SC")
- BackboneModel: Model only with backbone atoms (N, CA, C)
- MainchainModel: Model only with mainchain atoms (N, CA, C, O)
- Martini: Martini model
- Martini3: Martini3 model
- PRIMO: PRIMO model
convert_all2cg -p tests/1ab1_A.pdb -o tests/1ab1_A.calpha.pdb --cg CalphaBasedModelLocal optimization of protein model structure against given electron density map. This script is a proof-of-concept that utilizes cg2all network to optimize at CA-level resolution with objective functions in both atomistic and CA-level resolutions. It is highly recommended to use cuda environment.
usage: cryo_em_minimizer [-h] -p IN_PDB_FN -m IN_MAP_FN -o OUT_DIR [-a]
[-n N_STEP] [--freq OUTPUT_FREQ]
[--chain-break-cutoff CHAIN_BREAK_CUTOFF]
[--restraint RESTRAINT]
[--cg {CalphaBasedModel,CA,ca,ResidueBasedModel,RES,res}]
[--standard-name] [--uniform_restraint]
[--nonuniform_restraint] [--segment SEGMENT_S]
options:
-h, --help show this help message and exit
-p IN_PDB_FN, --pdb IN_PDB_FN
-m IN_MAP_FN, --map IN_MAP_FN
-o OUT_DIR, --out OUT_DIR, --output OUT_DIR
-a, --all, --is_all
-n N_STEP, --step N_STEP
--freq OUTPUT_FREQ, --output_freq OUTPUT_FREQ
--chain-break-cutoff CHAIN_BREAK_CUTOFF
--restraint RESTRAINT
--cg {CalphaBasedModel,CA,ca,ResidueBasedModel,RES,res}
--standard-name
--uniform_restraint
--nonuniform_restraint
--segment SEGMENT_S- -p/--pdb: Input PDB file (mandatory).
- -m/--map: Input electron density map file in the MRC or CCP4 format (mandatory).
- -o/--out/--output: Output directory to save optimized structures (mandatory).
- -a/--all/--is_all: Whether the input PDB file is atomistic structure or not. (optional, default=False)
- -n/--step: The number of minimization steps. (optional, default=1000)
- --freq/--output_freq: The interval between saving intermediate outputs. (optional, default=100)
- --chain-break-cutoff: The CA-CA distance cutoff that determines chain breaks. (default=10 Angstroms)
- --restraint: The weight of distance restraints. (optional, default=100.0)
- --cg: Coarse-grained representation to use (default=ResidueBasedModel)
- --standard-name: output atom names follow the IUPAC nomenclature. (default=False; output atom names will use CHARMM atom names)
- --uniform_restraint/--nonuniform_restraint: Whether to use uniform restraints. (default=True) If it is set to False, the restraint weights will be dependent on the pLDDT values recorded in the PDB file's B-factor columns.
- --segment: The segmentation method for applying rigid-body operations. (default=None)
- None: Input structure is not segmented, so the same rigid-body operations are applied to the whole structure.
- chain: Input structure is segmented based on chain IDs. Rigid-body operations are independently applied to each chain.
- segment: Similar to "chain" option, but the structure is segmented based on peptide bond connectivities.
- 0-99,100-199: Explicit segmentation based on the 0-index based residue numbers.
./cg2all/script/cryo_em_minimizer.py -p tests/3isr.af2.pdb -m tests/3isr_5.mrc -o 3isr_5+3isr.af2 --allThe training/validation/test sets are available at zenodo.
Lim Heo & Michael Feig, "One particle per residue is sufficient to describe all-atom protein structures", bioRxiv (2023). Link
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent