Bugs item #768973, was opened at 2003-07-10 11:09 Message generated for change (Comment added) made by egonw You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=768973&group_id=23629
Category: File Input/Output Group: None >Status: Closed >Resolution: Out of Date Priority: 5 Submitted By: Dietrich Bartel (dbartel) Assigned to: Egon Willighagen (egonw) Summary: (.jmol?) problems going from v5 -> v6, v7 Initial Comment: In version 5 Atom properties could be edited/changed. This is not possible with v6 and v7. In v5 atom properties were found in .jmol/properties. The property table is saved in v6 and v7 under .jmol/jmol_atomtypes.txt. When starting jmol without having .jmol/jmol_atomtypes.txt v7 complains about it with "readAtomTypes getResourceAsStream: jmol_atomtypes.txt" wheras v6 doesn't complain. v6 and v7 do read the history file (recent files, POVRAY path ...) but they don't update the recent files (povray path is updated!) ---------------------------------------------------------------------- >Comment By: Egon Willighagen (egonw) Date: 2005-01-04 19:26 Message: Logged In: YES user_id=25678 Dietrich, I believe most things can now easily be addressed with custom scripts. Please reopen if you have need for a different way to address the customization. ---------------------------------------------------------------------- Comment By: Miguel (michaelthoward) Date: 2003-08-14 12:35 Message: Logged In: YES user_id=608250 Dietrich , > Some scientists were accustomed to changing characteristics in ver 5. I would be very interested in starting a dialog with your Jmol users. I would like to know what type of work they are using it for and what features they want. Please have them email me [EMAIL PROTECTED] Miguel ---------------------------------------------------------------------- Comment By: Miguel (michaelthoward) Date: 2003-08-13 14:32 Message: Logged In: YES user_id=608250 Dietrich, > Had there been serious reasons to change this behaviour? We are in the process of completely rewriting the graphics rendering in Jmol. As a result there have been a lot of changes in this area. They should look at the RasMol/Chime compatible scripting commands which are now implemented in Jmol. These commands give complete control over atom diameter, bond diameter, and colors ... on an object by object basis. Write me if you have more questions. Miguel ---------------------------------------------------------------------- Comment By: Dietrich Bartel (dbartel) Date: 2003-08-13 09:28 Message: Logged In: YES user_id=119286 Miguel, I'm a "graphics" man maintaining the visualization software here in our institution for our scientists and not using Jmol deeply for myself. Some scientists were accustomed to changing characteristics in ver 5. Had there been serious reasons to change this behaviour? Dietrich ---------------------------------------------------------------------- Comment By: Miguel (michaelthoward) Date: 2003-08-12 01:26 Message: Logged In: YES user_id=608250 Dietrich, Which characteristics are you particularly interested in changing *on-the-fly*? Miguel ---------------------------------------------------------------------- Comment By: Dietrich Bartel (dbartel) Date: 2003-08-11 16:21 Message: Logged In: YES user_id=119286 Sorry to be not precise enough. I meant changing atom properties from *within* jmol itself. This was possible in ver 5: the values could be changed and the color through a color chooser. The changes worked immediatly without having to restart jmol. In ver 5 the history file is updated for opening *any new* file whereas in ver 7 the history file is read with its recent file entries but not updated with new ones. On the other hand changing the povpray path when exporting /rendering *is updated* in the same history file (just confirmed it under win98, irix and aix). ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2003-08-09 16:00 Message: Logged In: YES user_id=25678 The line "readAtomTypes getResourceAsStream" is actually not a complaint... but a remnant debug message... Moreover, I can edit the .jmol/jmol_atomtypes.txt file, restart Jmol and see the changes in the table... Could you give me the output of: java -Dcdk.debugging=true -jar jmol.jar | grep AtomType ? BTW, what about the history file? Is that a separate bug, or related to the atom types? Is it correct that the recent files list is not updated when Jmol is restarted and new files are opened? And what is the relation with the povray path? ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2003-07-10 11:39 Message: Logged In: YES user_id=25678 Thanx for reporting this. I will look into this problem. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=768973&group_id=23629 ------------------------------------------------------- The SF.Net email is sponsored by: Beat the post-holiday blues Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek. 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