> I don't know if this helps, but when I type "show spacegroup" from the
> console for your mol2 file, it says "could not identify space group
> from
> name: 14 1". (The pdb file shows the correct spacegroup, P 21/c,
> and 14
> does correspond to P 21/c)
>
> I think this is a bug. Looking at the code it looks like
> Mol2Reader.readCrystalInfo must be reading "14 1" instead of just
> "14".
> Should be a simple fix. Bob?
I think you're right Dean. The code in question looks like this:
void readCrystalInfo() throws Exception {
// 4.1230 4.1230 4.1230 90.0000 90.0000 90.0000
221 1
readLine();
ichNextParse = 0;
for (int i = 0; i < 6; i++)
setUnitCellItem(i, parseFloat(line, ichNextParse));
setSpaceGroupName(line.substring(ichNextParse, line.length
()).trim());
}
But the specification for this record (CRYSIN) is this:
@<TRIPOS>CRYSIN
Each data record associated with this RTI consists of a single data
line.
The data line contains 6 crystallographic cell constants followed by the
space group number and space group setting.
Format:
cell cell cell cell cell cell space_grp setting
Fields:
cell (real) = one of the 6 crystallographic cell constants.
space_grp (integer) = the space group number.
setting (integer) = defines the axial orientation with respect to the
standard setting defined in the International Tables for X-Ray
Crystallography. For the setting number value see the tables in
Chapter 3.2 of this manual.
Example:
12.312000 4.959000 15.876000 90.000000 99.070000 90.000000 4 1
The first six real numbers are the crystallographic cell constants
(a, b,
c, α, β, γ). The space group number is 4 and the space group
setting is
1.
So the code can assume that the last two elements are integers. I
have had a look through the code but I'm not sure how the space group
is parsed so I couldn't come up with any working code. I tried just
passing the number, and the number:setting, but neither worked.
Cheerio
Aidan
--
Research School of Chemistry
Australian National University
ACT 0200, Australia
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