Bugs item #1829276, was opened at 2007-11-09 16:31 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1829276&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: Applet Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: molvisions (molvisions) Assigned to: Miguel (migueljmol) Summary: weird color application Initial Comment: hi, this is a difficult bug to file because I can't pin down exactly when it happens (it seems random at the moment). I am loading an external file with values, and coloring atoms according to those values. a demo can be seen here: <http://www.molvisions.com/impas/> or, since my server is wicked slow, downloaded from here: <http://www.molvisions.com/impas/gly_bact_min.tar> basically, I load the external file and then use blocks of select statements to color atoms; for example: select backbone1 and (property_potc1 > 1 and property_potc1 < 3) color atoms yellow color atoms translucent 0.9 clicking a radio button in the above demo should apply a single coloring script of this form. but, even though the script and data for each button are exactly the same, often the resulting color scheme is very different. for example, sometimes I see a nice, and extremely wrong, rainbow gradient in the right-hand structure. but not always. I hope that description made sense. can anyone see a reason why this might be happening? thanks, tim driscoll ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2007-11-10 02:59 Message: Logged In: YES user_id=1082841 Originator: NO First, better try a newer Jmol version. No sense talking about bugs in 11.1.37. Comments: color atoms [75,75,75] color atoms translucent 0.9 color trace [75,75,75] select backbone1 and (property_potc1 > 0 and property_potc1 < 2) 1. You can do this and save one step: color atoms translucent 0.9 [75,75,75] 2. OK, you've got me. Why not just select backbone1 and (property_potc1 = 1) 3. With Jmol 11.4.43 you can instead make an array of your color list and process it like this: mycolors = "[xff0000],[xff2200],[xff2244],[xff44ff]".split(","); for (var i = 1; i <= mycolors.size; i = i + 1); print " " + i + " color= " + mycolors[i] + " " + mycolors[i].color; select backbone1 and property_potc1 = i; color atoms translucent 0.9 @{mycolors[i]}; color trace @{mycolors[i]}; end for; ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1829276&group_id=23629 ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
