-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Wednesday 28 January 2004 17:25, Patrick J. Carroll wrote: > Of course, the better way to draw unit cells would be the > capability to read shelxl .res files (which was introduced into Jmol with > version 7). These files have all the necessary information. Unfortunately, > Jmol 7 has a bug that reads the cell angles incorrectly (Jmol reports > alpha, beta, gamma as beta, gamma, alpha). Jmol 8 has an additional bug in > that it represents the cell angles in radians rather than degrees.
How does this bug manifest itself? > So the > Jmol 7 application will only display a correct unit cell for orthogonal > cells (all cell angles 90 degrees). But the Jmol 7 applet does not have the > capability of displaying "original atoms only" (as the application can) and > so it will not draw any atoms that are outside the boundaries of the cell. Patrick, I'm sorry that I have not fixed this yet... I've been quite busy with other projects in my PhD. I would very much appreciate your help with debugging it... The ShelX code comes from CDK (cdk.sf.net), and apparently I did something wrong in the conversion from notional coordinates and cartesian coordinates, and visa versa... There are some tests which should make sure the code is doing things correctly: http://cvs.sourceforge.net/viewcvs.py/cdk/cdk/src/org/openscience/cdk/test/geometry/CrystalGeometryToolsTest.java Sorry for the long link... Download version 1.5 (with comments) or 1.4 (without comments) what is tested... I would highly appreciate if you could have a look at the tests and see if there is anything out of order... > So for drawing unit cells right now, I don't need anything added > to the hbond functionality, but it would be nice to fix the shelxl.res > bugs. I will try to do this asap. Kind regards, Egon Willighagen - -- [EMAIL PROTECTED] PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAGM+1d9R8I9Yza6YRAlMmAJ9HtpHZzckD0l5Bet1Cj7W/CYjbTACfZeJl brexs61gOXu/bmxYsKCLnk8= =dyDZ -----END PGP SIGNATURE----- ------------------------------------------------------- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
