[Biopython-dev] [Bug 3166] Bio.PDB.DSSP fails to work on PDBs with HETATM

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Jan 18 11:11:51 UTC 2011


macrozhu+biopy at gmail.com changed:

           What    |Removed                     |Added
Attachment #1562 is|0                           |1
           obsolete|                            |

------- Comment #7 from macrozhu+biopy at gmail.com  2011-01-18 06:11 EST -------
Created an attachment (id=1563)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1563&action=view)
handle DSSP shifted output when there are too many res in a PDB

In this version, one more issue is fixed when reading DSSP output:

Sometimes DSSP output is not in the correct format. Column 34 to 38, which are
supposed to be occupied by solvent accessibility (acc), are partially occupied
by the elongated field before it. Thus, the conversion of the string in col 34
to 38 to integer will raise a ValueError exception. e.g. 3kic chain T res 321,
or 1VSY chain T res 6077. 
>python DSSP.py 3kic.pdb

In such cases, the acc value, and all the following values in the same line are
shifted to the right because residue sequence number is too long (more than 4
digits). Normally, only 4 digits are allocated to seq num in DSSP output. When
there are too many residues, this problems appears. 

Now the ValueError exception is caught and the line is re-examined for shifted
acc values. 

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