This tool provides information about a protein pdb file on its structure, along with applied transformations and issues flagged in the run.log produced by MCCE's step1.py.
This information is saved into a file named ProtInfo.md.
- See sample markdown reports
Command line interface for the MCCE ProtInfo tool, which gathers:
* Info about the input protein from Bio.PDB parser.
* Info from MCCE step1 run.log & debug.log when step1 can be run.
This is the 'main' module for the cli, which calls the function
that outputs a single protein report: `get_single_pdb_report(args)`.
Options:
1. pdb (required): a pdb file name or pdbid.
2. --fetch (False if not used): If 'pdb' is a pdbid and flag is used,
the biological assembly is downloaded from rcsb.org.
Step1 options:
--wet (False): Keep water molecules.
--noter (False): Do not label terminal residues (for making ftpl).
-d (4.0): Protein dielectric constant for delphi.
-u (''): User selected, comma-separated KEY=var pairs from run.prm; e.g.:
-u HOME_MCCE=/path/to/mcce_home,EXTRA=./extra.tpl.
-e (mcce): mcce executable location.
-h, --help Show this help message and exit.
--fetch Download the biological assembly of given pdb (if not a file).
Usage:
>ProtInfo 1fat --fetch
>ProtInfo 1fat.pdb --noter
Info recorded in the final report:
- Number of models
- Number of chains
- Breaks in chains
- Number of residues
- Unknown residues
- Residues with multiple alternate locations:
- MCCE can only handle a single location and only considers the 'A' location (which may cause problems)
- Number of water molecules
- Number and identity of cofactors
After running MCCE's step1.py, the run.log provides information about errors and repairs applied.
Info recorded in the final report:
- Terminal residues
- Waters: count and buried list
- Buried Cofactors:
- Water: buried list & count
- Other: buried list & count
- Missing topology
- TODO: Which repairs were applied :: Need more info.
- Fatal errors
- Waters: 15: A 305, A 306, A 307, A 308, B 301, B 302, B 303, C 313, C 314, C 315, C 316, D 309, D 310, D 311, D 312
- Heteros: 8: A MN 254, A CA 255, B MN 254, B CA 255, C MN 254, C CA 255, D MN 254, D CA 255
Chain discontinuity: A (7975, 8039); B (7991, 8043); C (8007, 8047); D (8023, 8051);
"CA CA A 255" to "CA _CA A 255" "CA CA B 255" to "CA _CA B 255" "CA CA C 255" to "CA _CA C 255" "CA CA D 255" to "CA _CA D 255" "MN MN A 254" to "MN _MN A 254" "MN MN B 254" to "MN _MN B 254" "MN MN C 254" to "MN _MN C 254" "MN MN D 254" to "MN _MN D 254"
NTR: "SER A 1", "ASN A 38", "SER B 1", "SER C 1", "ASN C 38", "SER D 1", "ASN D 38" CTR: "ASN A 36", "SER A 233", "SER B 233", "ASN C 36", "SER C 233", "LEU D 35", "SER D 233"
- Generic topology file created for: NAG: https://pubchem.ncbi.nlm.nih.gov/#query=NAG&tab=substance; _MN: https://pubchem.ncbi.nlm.nih.gov/#query=MN&tab=substance; _CA: https://pubchem.ncbi.nlm.nih.gov/#query=CA&tab=substance;
OXT of conf CTR01 in "CTR A 36". OXT of conf CTR01 in "CTR A 233". OXT of conf CTR01 in "CTR B 233". OXT of conf CTR01 in "CTR C 36". OXT of conf CTR01 in "CTR C 233". OXT of conf CTR01 in "CTR D 35". OXT of conf CTR01 in "CTR D 233".
Clashes found
d= 1.53: " CA NTR A 1" to " CB SER A 1" d= 1.45: " ND2 ASN A 12" to " C1 NAG A 253" d= 1.53: " CA NTR A 38" to " CB ASN A 38" d= 1.52: " CA NTR B 1" to " CB SER B 1" d= 1.48: " ND2 ASN B 12" to " C1 NAG B 253" d= 1.53: " CA NTR C 1" to " CB SER C 1" d= 1.45: " ND2 ASN C 12" to " C1 NAG C 253" d= 1.52: " CA NTR C 38" to " CB ASN C 38" d= 1.87: " OD1 ASN C 128" to "CA _CA C 255" d= 1.82: " NE2 HIS C 137" to "MN _MN C 254" d= 1.54: " CA NTR D 1" to " CB SER D 1" d= 1.43: " ND2 ASN D 12" to " C1 NAG D 253" d= 1.55: " CA NTR D 38" to " CB ASN D 38"1aig :: Photosynthetic Reaction Center From Rhodobacter Sphaeroides In The D+Qb-Charge Separated State
- Waters: 16: L 289, L 290, L 292, L 295, L 297, L 298, L 300, L 301, L 304, L 305, M 313, M 314, M 315, M 322, M 327, H 272
- Heteros: 1: M FE2 308
Chain discontinuity: L (6949, 7470); M (7274, 7489); H (7510);
NTR: "ALA L 1", "TYR M 3", "ASP H 11" CTR: "GLY L 281", "HIS M 301", "GLU H 258"
- Generic topology file created for: BPH: https://pubchem.ncbi.nlm.nih.gov/#query=BPH&tab=substance; U10: https://pubchem.ncbi.nlm.nih.gov/#query=U10&tab=substance;
- Unloadable topology: Atoms of residue BCL (L 282, L 283, M 309, M 310), do not match the topology conformer BCL-1. Likely cause: the renaming file (path: /home/cat/miniconda3/envs/rpte/name.txt) is missing entries for these species, resulting in unloadable topology files (path: /home/cat/miniconda3/envs/rpte/param/).