From: Patrick J. C. <car...@sa...> - 2004-01-28 16:23:09
|
As per Miguel's questions about my wanting to use hbonds to draw unit cells: I realized I could do a better job with normal bonds and script commands to draw the unit cell edges thin and I can also have the applet display come up immediately with non-default atom and bond sizes by using script commands like: select all; cpk on; cpk 0.40; wireframe on; wireframe 0.15; select oxygen; cpk 0.1; wireframe 0.1 Take a look at: http://macxray.chem.upenn.edu/cell457b.html 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. 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. 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. Pat |
From: Miguel H. <mt...@mt...> - 2004-01-28 20:20:31
|
Pat, > Take a look at: > > http://macxray.chem.upenn.edu/cell457b.html This URL cannot work ... either you are using another URL or there is a bug in your Browser/Java implementation. The 'codebase' parameter is referring to a directory that cannot exist. applet codebase ="../jmol" code ="JmolApplet" archive="JmolApplet.jar" The ../jmol means to go up a directory level and down to the jmol directory. Since this page is the root of the web server, you cannot go 'up-and-over'. I see that the jmol directory *does* exist on your web server, in which case you can change it to say applet codebase ="/jmol" code ="JmolApplet" archive="JmolApplet.jar" or applet codebase ="jmol" code ="JmolApplet" archive="JmolApplet.jar" Please let me know whether or not this *really* is the URL that you are using. If so, then let me know browser/java you are using ... because if it is working then it is a bug in the java implementation. Miguel |
From: Philip B. <pb...@sa...> - 2004-01-28 18:02:25
|
Following up on this: Is there a scripting way to choose some bonds for different "fatness" than others. I am thinking of the Ferrocene example and a way to show the metal coordination bonding differently than the covalent bonding. Phil Bays On Jan 28, 2004, at 11:25 AM, Patrick J. Carroll wrote: > As per Miguel's questions about my wanting to use hbonds to > draw unit cells: I realized I could do a better job with normal bonds > and script commands to draw the unit cell edges thin and I can also > have the applet display come up immediately with non-default atom and > bond sizes by using script commands like: > > select all; > cpk on; > cpk 0.40; > wireframe on; > wireframe 0.15; > select oxygen; > cpk 0.1; > wireframe 0.1 > > Take a look at: > > http://macxray.chem.upenn.edu/cell457b.html > > > 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. 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. > 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. > > > Pat > > > > > ------------------------------------------------------- > 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 > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
From: E.L. W. <eg...@sc...> - 2004-01-31 01:56:47
|
=2D----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.=20 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 t= he > capability of displaying "original atoms only" (as the application can) a= nd > 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= =20 projects in my PhD. I would very much appreciate your help with debugging it... The ShelX code= =20 comes from CDK (cdk.sf.net), and apparently I did something wrong in the=20 conversion from notional coordinates and cartesian coordinates, and visa=20 versa...=20 There are some tests which should make sure the code is doing things=20 correctly: http://cvs.sourceforge.net/viewcvs.py/cdk/cdk/src/org/openscience/cdk/test/= geometry/CrystalGeometryToolsTest.java Sorry for the long link...=20 Download version 1.5 (with comments) or 1.4 (without comments) what is=20 tested... I would highly appreciate if you could have a look at the tests and see if= =20 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 =2D --=20 eg...@sc... PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 =2D----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAGM+1d9R8I9Yza6YRAlMmAJ9HtpHZzckD0l5Bet1Cj7W/CYjbTACfZeJl brexs61gOXu/bmxYsKCLnk8=3D =3DdyDZ =2D----END PGP SIGNATURE----- |