Re: [Jmol-users] java.io.IOException: Mark invalid

2002-10-11 Thread Bradley Smith
Yes, this problem was pointed out with regard to reading large PDB files. It has been fixed, and will work properly in the next version which will be released soon. Thanks, Bradley - Original Message - From: "Randall Hall" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Sent: Friday, Octo

Re: [Jmol-users] Help.

2002-10-09 Thread Bradley Smith
The problems with reading large PDB files have been fixed. The next version of Jmol will be able to read 4HIR.pdb. Thanks, Bradley - Original Message - From: "Zongming Pan" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Sent: Tuesday, October 08, 2002 6:46 PM Subject: [Jmol-users] Help.

Re: [Jmol-users] Help.

2002-10-08 Thread Bradley Smith
Because using Jmol with large molecules is rare, it is not frequently tested. The reason is does not work is not simple to answer. There are multiple problems. My suggestion is to please be patient. These problems will be corrected in future versions. Thank you for pointing out the problem. Thank

Re: [Jmol-users] "java.lang.ClassNotFoundException"

2002-10-07 Thread Bradley Smith
- From: "Jianjun Dong" <[EMAIL PROTECTED]> To: "Bradley Smith" <[EMAIL PROTECTED]> Cc: <[EMAIL PROTECTED]> Sent: Monday, October 07, 2002 6:08 AM Subject: Re: [Jmol-users] "java.lang.ClassNotFoundException" > > Hello Bradley, > > I got the er

Re: [Jmol-users] "java.lang.ClassNotFoundException"

2002-10-06 Thread Bradley Smith
What command did you run to get the error message? Bradley - Original Message - From: "Jianjun Dong" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Sent: Sunday, October 06, 2002 3:54 PM Subject: [Jmol-users] "java.lang.ClassNotFoundException" > > Hello, > > I am interested in using J

Re: [Jmol-users] JMol4: MacOS X package

2002-10-01 Thread Bradley Smith
Now also available from SourceForge. Thanks, Henry. Bradley - Original Message - From: "Rzepa, Henry" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Sent: Tuesday, October 01, 2002 11:28 PM Subject: [Jmol-users] JMol4: MacOS X package > A MacOS X package (built with the developer tool

[Jmol-users] Jmol version 4 released.

2002-10-01 Thread Bradley Smith
Jmol version 4 has been released. The following is a brief list of changes: - Reading of MOPAC 97 and 2002 files. Formerly, only MOPAC 7 files worked. - Jmol can now also read files in non-CML with the command "jmol ". - The PDB reader now also parses CONECT fields and implements Rasmol's p

Re: [Jmol-users] Reading ADF output

2002-05-22 Thread Bradley Smith
Yes, that is a problem. Extending ADF reading to recognize all elements has been added to the feature request list. It should be fixed for the next release. Thanks, Bradley - Original Message - From: "Hans Martin Senn" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Sent: Wednesday, May 2

Re: [Jmol-users] JMol fails to run with Java RE1.4.0

2002-05-22 Thread Bradley Smith
I am unable to reproduce using J2SDK 1.4.0, Jmol 3, and Windows 2000. I suggest you look on Sun's Java Bug Parade, and if you don't find it, perhaps report it there. Thanks, Bradley - Original Message - From: "T Wei" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Sent: Tuesday, May 21, 20

[Jmol-users] Jmol version 3

2002-05-12 Thread Bradley Smith
Jmol version 3 has been released. The following is a brief list of changes:   - Export of BMP and PNG images. - Rendering of multiple bonds. - Scaling of vector arrowheads by magnitude which shows significant vectors more clearly. - Fixed bugs 547574 and 548591. - Adjustable scaling of vect

Re: [Jmol-users] Re: Jmol-users digest, Vol 1 #25 - 1 msg

2002-05-06 Thread Bradley Smith
Jmol requires jdk 1.2 or later. Please upgrade, and try again. As for running on Linux, once again "java -version" should respond with a version of 1.2 or later. If that is true, Jmol should be able to run by simply executing the jmol shell script which is in the jmol-2 directory. Thanks, Brad

Re: [Jmol-users] printing from jmol

2002-05-04 Thread Bradley Smith
There are printing bugs in some versions of Java. If you look in the Jmol Console (under the Help menu), I bet an exception is displayed there when you try to print. Try upgrading to a newer version of Java. For me on Windows, Java 1.3.1_02 wouldn't print, but 1.3.1_03 does. Thanks, Bradley --

Re: [Jmol-users] Installation problem

2002-05-01 Thread Bradley Smith
What happens when you run "java -version"? Or when you run "java -Djmol.home=c:\jmol-2 -cp c:\jmol-2\jars\jmol.jar org.openscience.jmol.Jmol"? Thanks, Bradley - Original Message - From: "kerrell chia" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Sent: Tuesday, April 30, 2002 1:13 AM Sub

[Jmol-users] Jmol can now be run via Java Web Start

2002-04-17 Thread Bradley Smith
Jmol can now be run via Java Web Start. The link can be accessed via the download page http://jmol.sourceforge.net/download.html or directly at http://jmol.sourceforge.net/jws/jmol.jnlp. Thanks to Christian Ribeaud for helping develop this feature. Thanks, Bradley ___

[Jmol-users] Jmol version 2 released.

2002-04-14 Thread Bradley Smith
Jmol version 2 has been released. This release includes major changes such as simplification of the user interface, improved interaction with POV-Ray, an upgrade of CML importing and addition of MDL file reading, and more. This release reintegrates the applet and application code. The applet clas

Re: [Jmol-users] jmol 1.2 NoClassDefFound Error

2002-04-14 Thread Bradley Smith
I was unable to reproduce your problem. I am using Redhat with Java 2 SDK 1.3.1_02. Does the jars/jmol.jar file exist? Does it contain org/openscience/jmol/Jmol.class? Thanks, Bradley - Original Message - From: "Jeff Mullen" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Sent: Sunday, A