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PDB Conversion and Converters |
PDB conversion within the Maestro interface is carried out using the
mmpdb library. Access to this library is also available through the
pdbconvert utility—see the General Utilities document.
The PDB conversion library converts PDB files to Maestro or
MacroModel files, or the reverse. It uses three sets of criteria for the
placement of bonds in the conversion from PDB: a set of standard
residue templates, the CONECT records of the PDB file, and
geometry. pdbconvert makes an effort to read and understand as many
non-standard PDB conventions as possible. It also writes PDB files
that comply with the standard conventions as much as possible.
Maestro has a color scheme that is based on the PDB conversion error reporting that can be used to call attention to parts of the molecule that may need correction. The color error codes are described below. The use of this scheme to color PDB structures on import is controlled by a preference.
The following color codes are used in the error reporting scheme for PDB conversion.
| Color | Meaning |
|---|---|
| orange | Non-standard residues connected by geometry and/or CONECT records. Unless duplicate CONECT records are specified, only single order bonds are added, so multiple bonds will need to be added. |
| red | Standard residue, but the input PDB file had missing atoms. |
| blue | A standard residue that has some atom names unknown to the standard connection template. The unrecognized atom names were connected by geometry. |
| cyan | An adjacent residue is listed in the SEQRES records but is entirely missing from the ATOM records, indicating a gap in the structure. |
| green | A residue with alternate positions for some of its atoms. |
| gray | Standard residues connected by standard templates. Confidence in bond orders assigned to these residues is high. |
Maestro displays the following warning messages to indicate the status of an attempted PDB conversion:
| Status | Message |
|---|---|
| OK | Nothing is displayed. This indicates what appears to be a successful conversion. |
| WARNING | Dialog box displays "Problems found while converting file". A temporary PDB output file was generated successfully, but the quality of the conversion is suspect. |
| ERROR | Dialog box displays: "Could not convert file to format Format". The conversion failed. Most likely the temporary output file could not be created, possibly due to permissions or a full disk. Another reason for failure is the attempt to convert a file that has varying number of atoms in different MODELs. |
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