I have just been trying out Jmol and found a problem with the SHELX reader.
The problem is that it balks on reading atom co-ordinates lines such as
H 1 0.0 0.0 0.0 0
in the particular case where the element has only 1 letter in its chemical
symbol and there is no number following. For example:
TITL Converted by XX2shx - Keith Refson
CELL 1.54180 8.619649 8.627482 6.9505 79.93961 103.2911 120.0852
LATT -1
SFAC Mg O
Mg 1 1.0071635310000 1.0103068320000 0.0143757880000 0
O 2 0.1412130180000 0.2240108100000 0.1585782800000 0
O 2 0.8725146790000 0.7986771140000 0.8727733560000 0
END
fails, but
TITL Converted by XX2shx - Keith Refson
CELL 1.54180 8.619649 8.627482 6.9505 79.93961 103.2911 120.0852
LATT -1
SFAC Mg O
Mg 1 1.0071635310000 1.0103068320000 0.0143757880000 0
O1 2 0.1412130180000 0.2240108100000 0.1585782800000 0
O2 2 0.8725146790000 0.7986771140000 0.8727733560000 0
END
reads in correctly.
There's an error in the source logic in procedure assumeAtomRecord()
if (atomName.length() > 1 &&
Character.isDigit(atomName.charAt(1))) {
// one letter code elementSymbol
char symbol = atomName.charAt(0);
if (symbol == 'Q' || symbol == 'q')
return; // ignore atoms named Q
elementSymbol = "" + symbol;
} else {
elementSymbol = atomName.substring(0, 2);
}
which jumps to the "else" clause if a single digit element symbol is not
followed by a digit.
Keith Refson
--
Dr Keith Refson,
Building R3
Rutherford Appleton Laboratory
Chilton
Didcot kr AT isise
Oxfordshire OX11 0QX DOT nd DOT rl DOT ac DOT uk
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