Bugs item #2107269, was opened at 2008-09-12 06:13
Message generated for change (Settings changed) made by hansonr
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2107269&group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: File Input/Output
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: dan (danwilson4)
>Assigned to: Bob Hanson (hansonr)
Summary: CML reader loses crystal lattice information if no symmetry
Initial Comment:
Jmol (11.6RC14) seems to lose the lattice parameters information if space group
information isn't present.
In the attached CML file (UO3.cml), the system has a primitive cell, and hence
it's not valid to attach a spaceGroup="..." attribute to the <symmetry> tag.
However, in such cases, Jmol doesn't read or display the lattice parameters,
assuming the system is molecular.
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2008-09-13 11:41
Message:
Are you saying that the system is no known space group?
I see in that file:
<symmetry>
<transform3>
1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0
0.000000000000e0 1.000000000000e0 0.000000000000e0 0.000000000000e0
0.000000000000e0 0.000000000000e0 1.000000000000e0 0.000000000000e0
0.000000000000e0 0.000000000000e0 0.000000000000e0
1.000000000000e0</transform3>
<transform3>
1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0
0.000000000000e0 -1.000000000000e0 0.000000000000e0 0.000000000000e0
0.000000000000e0 0.000000000000e0 -1.000000000000e0 0.000000000000e0
0.000000000000e0 0.000000000000e0 0.000000000000e0
1.000000000000e0</transform3>
<transform3>
1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0
0.000000000000e0 -1.000000000000e0 0.000000000000e0 0.000000000000e0
0.000000000000e0 0.000000000000e0 1.000000000000e0 0.000000000000e0
0.000000000000e0 0.000000000000e0 0.000000000000e0
1.000000000000e0</transform3>
<transform3>
1.000000000000e0 0.000000000000e0 0.000000000000e0 0.000000000000e0
0.000000000000e0 1.000000000000e0 0.000000000000e0 0.000000000000e0
0.000000000000e0 0.000000000000e0 -1.000000000000e0 0.000000000000e0
0.000000000000e0 0.000000000000e0 0.000000000000e0
1.000000000000e0</transform3>
</symmetry>
That to me reads:
x,y,z;x,-y,-z;x,-y,z;x,y,-z;
But when I use those symmetry operators with this data set I get
nonsense.
In the wurtzite example you sent, these transformation matrices are very
odd
they are in fractional coordinates, but the rotational components use
angles defined
in terms of cartesian coordinates. So they are useless to Jmol.
Since Jmol then cannot read the transform3 entries, it must depend upon a
defined
unit cell and proper spacegroup name.
Say again why it would be inappropriate to have a spacegroup defined
here.
Bob
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2107269&group_id=23629
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Jmol-developers mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
