Re: [Jmol-users] Cell "blocks" available with mol2 formatted files?

[Aidan H. <ai...@rs...>]

> 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 =20=

> from
> name: 14 1".  (The pdb file shows the correct spacegroup, P 21/c, =20
> 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 =20
> "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   =20=

221     1
     readLine();
     ichNextParse =3D 0;
     for (int i =3D 0; i < 6; i++)
       setUnitCellItem(i, parseFloat(line, ichNextParse));
     setSpaceGroupName(line.substring(ichNextParse, line.length=20
()).trim());
   }

But the specification for this record (CRYSIN) is this:

@<TRIPOS>CRYSIN
Each data record associated with this RTI consists of a single data =20
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) =3D one of the 6 crystallographic cell constants.
space_grp (integer) =3D the space group number.
setting (integer) =3D 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 =20
(a, b,
c, =CE=B1, =CE=B2, =CE=B3). The space group number is 4 and the space =
group =20
setting is
1.

So the code can assume that the last two elements are integers. I =20
have had a look through the code but I'm not sure how the space group =20=

is parsed so I couldn't come up with any working code. I tried just =20
passing the number, and the number:setting, but neither worked.

Cheerio

Aidan

--
Research School of Chemistry
Australian National University
ACT 0200, Australia