Homology modeling servers: Difference between revisions
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==Problems== | ==Problems== | ||
===Sequence Numbering Anomalies=== | ===Sequence Numbering Anomalies=== | ||
It is common for the sequences of proteins in [[PDB]] structures to begin with a number other than 1 ([[2fsr]]:A). Discontinuities in sequential numbering may occur ([[1igt]]:B, [[2fsr]]:A). Residues in the same chain may have the same sequence number, notably in the case of "insertions" relative to a reference sequence. These inserted residues may all have the same number, but are distinguished by insertion codes, typically letters in alphabetical order. However, in rare cases, the letters may not be in alphabetical order, e.g. chain J in [[1ucy]]. An overview of sequence numbering anomalies in the [[PDB]], including further examples, is at [http://firstglance.jmol.org/seqspecs.htm Specification for Interactive Sequence Listings] (in [[FirstGlance in Jmol]]). | It is common for the sequences of proteins in [[PDB]] structures to begin with a number other than 1 ([[2fsr]]:A), and to include zero ([[1avq]]:A, [[1bxw]]:A). Discontinuities in sequential numbering may occur ([[1igt]]:B, [[2fsr]]:A). Residues in the same chain may have the same sequence number, notably in the case of "insertions" relative to a reference sequence. These inserted residues may all have the same number, but are distinguished by insertion codes, typically letters in alphabetical order. However, in rare cases, the letters may not be in alphabetical order, e.g. chain J in [[1ucy]]. An overview of sequence numbering anomalies in the [[PDB]], including further examples, is at [http://firstglance.jmol.org/seqspecs.htm Specification for Interactive Sequence Listings] (in [[FirstGlance in Jmol]]). | ||
* '''Phyre2''': In early April, 2011, Phyre2 numbered the aligned portion of the template sequence incorrectly when the above kinds of sequence anomalies occur in the template [[PDB]] file. The development team has acknowledged the problem and is working on a fix. | * '''Phyre2''': In early April, 2011, Phyre2 numbered the aligned portion of the template sequence incorrectly when the above kinds of sequence anomalies occur in the template [[PDB]] file. The development team has acknowledged the problem and is working on a fix. | ||