well, that's your clue. Use message @x
to see the whole message (115 bytes). It will say, "HTTP Error 500 - Internal server error" That's an indicator that you have the wrong URL or something is amiss with your server. See http://www.checkupdown.com/status/E500.html I think it's nothing to do with Jmol. x got loaded with an error message instead of the file. That can certainly happen. We aren't checking for that, so it goes ahead and tries to assign colors. All green, I would have guessed, but maybe red because it reads that one number "500" and all the rest are 0. Make sure the file name capitalization is exact, directories are right, etc. Something is wrong on that server. Try just reading that file directly as a URL in your browser. Bet you get the same error message. Try changing the file extension to "txt" -- your server may be treating "dat" extensions in some bizarre way. Bob Samuel Flores wrote: >Hi Bob, > >I can do all of this on my local install (except, yes, the color >syntax was wrong -- least of my worries ;).) The problem is that >none of it works on the applet on my web server. > >My first problem is just loading foldx.dat. If I do this through the >console of my web applet, I get: > >x=load("foldx.dat") >pending >script 5 started >x = "Error:java.io.IOException: Server returned HTTP response code: >500 for URL: htt >#...(115 bytes -- use SHOW x or MESSAGE @x to view) >Script completed >Jmol script terminated > >The DATA command results in: > >DATA "property_foldx @x" >pending >script 9 started >Script completed >Jmol script terminated > >Any help is much appreciated. Is there an example on the web of an >applet that does this? > > > Don't worry -- you are doing it right in Jmol. Call your IT guys and have them check that URL. >Many thanks > >Sam > >On May 3, 2007, at 10:38 PM, Bob Hanson wrote: > > > >>Sam, you should be doing all this testing from a Jmol console -- pull >>that up from the popup menu and work from it. >>It's far easier than trying to get it going this way. >> >>you can't say >> >>color atoms cartoons property_foldx >> >>one or the other: >> >>select * >>color atoms property_foldx >>color cartoons property_foldx >> >> >> >>Samuel Flores wrote: >> >> >> >>>Cool, this helps. >>> >>>I am still having trouble with getting the DATA command to work, >>>though. Is there something obviously wrong with the following? I >>>verified that execution stops due to the DATA statement. >>> >>>jmolScript('x=load("foldx.dat"); select *; DATA "property_foldx >>>@x" ; color atoms cartoons property_foldx; '); >>> >>>Many thanks, >>> >>>Sam >>> >>>On May 3, 2007, at 6:43 PM, Bob Hanson wrote: >>> >>> >>> >>> >>> >>>>Yes, certainly. Macs and PCs are different, though. Can you find the >>>>Java Console (PC) or >>>>System logs (I think) directory on your Mac. Macs dump this to a >>>>file; >>>>PCs just display in on a >>>>console. >>>> >>>>Use >>>> >>>>loglevel = 5 >>>> >>>>to get voluminous reports of what is going on, and use >>>> >>>>message @x >>>> >>>>or >>>> >>>>show x >>>> >>>>to display the value of any variable any time in the Jmol console >>>>(from >>>>the popup menu). >>>> >>>>Bob >>>> >>>> >>>> >>>>Samuel Flores wrote: >>>> >>>> >>>> >>>> >>>> >>>>>Also, is there some way to access the error log? Debugging applets >>>>>without error messages is painful. >>>>> >>>>>Sam >>>>> >>>>> >>>>>On May 3, 2007, at 1:09 PM, Samuel Flores wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>Hi Bob, >>>>>> >>>>>>I am trying to follow this advice you gave Tim. I have an applet >>>>>>and want to color my molecule by a parameter which I store in a >>>>>>file called 'foldx.dat.' I am stuck on the first step, though -- >>>>>>loading the data file. I have the following line in my >>>>>>javascript: >>>>>> >>>>>>jmolScript('x=load("../foldx.dat"); select *; color red;'); >>>>>> >>>>>>The 'color red' command is only a flag to show me that the load >>>>>>command didn't incur an error. However the molecule does not >>>>>>change color, indicating that the load command failed. Is >>>>>>there an >>>>>>obvious problem with my syntax? I will write the rest of the code >>>>>>once the load command is working. >>>>>> >>>>>>Sam >>>>>> >>>>>>On Apr 30, 2007, at 11:01 PM, Bob Hanson wrote: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>Tim, I think you will like how this works. The idea is to set >>>>>>>up a >>>>>>>property (like temperature, but of your own definition) and then >>>>>>>use it >>>>>>>in the command >>>>>>> >>>>>>>color atoms property_x >>>>>>> >>>>>>>To set up "property_x", you load the values into a variable and >>>>>>>then use >>>>>>>the DATA command >>>>>>>to assign that variable to a property. "x" here is arbitrary: >>>>>>> >>>>>>>x = load("myfile.dat") >>>>>>>select * >>>>>>>data "property_tim @x" >>>>>>> >>>>>>>Make sure the data are a single column -- the second of what you >>>>>>>show >>>>>>>below. Then just >>>>>>> >>>>>>>color atoms [cartoons, trace, etc.] property_tim >>>>>>> >>>>>>>The idea is that once you have assigned the property to the atoms >>>>>>>with >>>>>>>the data statement, then >>>>>>>you can color them using it. >>>>>>> >>>>>>>If you don't have data for all the atoms, just supply the >>>>>>>necessary data >>>>>>>for the SELECED atoms. >>>>>>>So, for example, if you are only coloring the alpha carbons, you >>>>>>>can do >>>>>>>that using >>>>>>> >>>>>>>select *.CA >>>>>>>data "property_ca @x" >>>>>>> >>>>>>>The color scheme will be roygb. >>>>>>> >>>>>>>Bob >>>>>>> >>>>>>> >>>>>>>Timothy Driscoll wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>>hi, >>>>>>>> >>>>>>>>I have a set of charge values for atoms in a pdb file. I'd >>>>>>>>like to >>>>>>>>color the structure according to those charges, but I'm a bit >>>>>>>>confused how to do that. I have this, from an email in march >>>>>>>>2007: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>Jmol 11.1.18 will allow a broad range of customized >>>>>>>>>colorings for >>>>>>>>>isosurfaces as well as new capabilities for labels. Basically >>>>>>>>>you can >>>>>>>>>read in any number of sets of atom-based data (charges, >>>>>>>>>distances >>>>>>>>>from a >>>>>>>>>given point, anything) and then you can display that either >>>>>>>>>in a >>>>>>>>>label >>>>>>>>>or as a coloration of an isosurface. It's very simple: >>>>>>>>> >>>>>>>>>1) In a file, construct a list of the numbers you want to >>>>>>>>>associate >>>>>>>>>with >>>>>>>>>atoms. Just any list separated by lines or spaces or tabs -- >>>>>>>>>any >>>>>>>>>white >>>>>>>>>space is fine. Just numbers. It does not have to be for ALL the >>>>>>>>>atoms, >>>>>>>>>just whatever ones you wish to SELECT. >>>>>>>>> >>>>>>>>>2.5 2e-3 >>>>>>>>>-2.54 3 6 >>>>>>>>>etc. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>I grasp how to load the external dataset into Jmol, but how do I >>>>>>>>associate a particular charge with the correct atom? for >>>>>>>>example: >>>>>>>> >>>>>>>>atomnum charge >>>>>>>>1 -0.33 >>>>>>>>2 0.32 >>>>>>>>3 0.55 >>>>>>>>4 -0.55 >>>>>>>>5 0 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>thanks for any help, >>>>>>>> >>>>>>>>tim >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>----------------------------------------------------------------- >>>>>>>-- >>>>>>>-- >>>>>>>---- >>>>>>>This SF.net email is sponsored by DB2 Express >>>>>>>Download DB2 Express C - the FREE version of DB2 express and take >>>>>>>control of your XML. No limits. Just data. Click to get it now. >>>>>>>http://sourceforge.net/powerbar/db2/ >>>>>>>_______________________________________________ >>>>>>>Jmol-users mailing list >>>>>>>[email protected] >>>>>>>https://lists.sourceforge.net/lists/listinfo/jmol-users >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>------------------------------------------------------------------- >>>>>-- >>>>>---- >>>>>This SF.net email is sponsored by DB2 Express >>>>>Download DB2 Express C - the FREE version of DB2 express and take >>>>>control of your XML. No limits. Just data. Click to get it now. >>>>>http://sourceforge.net/powerbar/db2/ >>>>>_______________________________________________ >>>>>Jmol-users mailing list >>>>>[email protected] >>>>>https://lists.sourceforge.net/lists/listinfo/jmol-users >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>-------------------------------------------------------------------- >>>>-- >>>>--- >>>>This SF.net email is sponsored by DB2 Express >>>>Download DB2 Express C - the FREE version of DB2 express and take >>>>control of your XML. No limits. Just data. Click to get it now. >>>>http://sourceforge.net/powerbar/db2/ >>>>_______________________________________________ >>>>Jmol-users mailing list >>>>[email protected] >>>>https://lists.sourceforge.net/lists/listinfo/jmol-users >>>> >>>> >>>> >>>> >>>--------------------------------------------------------------------- >>>---- >>>This SF.net email is sponsored by DB2 Express >>>Download DB2 Express C - the FREE version of DB2 express and take >>>control of your XML. No limits. Just data. Click to get it now. >>>http://sourceforge.net/powerbar/db2/ >>>_______________________________________________ >>>Jmol-users mailing list >>>[email protected] >>>https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >>> >>> >>---------------------------------------------------------------------- >>--- >>This SF.net email is sponsored by DB2 Express >>Download DB2 Express C - the FREE version of DB2 express and take >>control of your XML. No limits. Just data. Click to get it now. >>http://sourceforge.net/powerbar/db2/ >>_______________________________________________ >>Jmol-users mailing list >>[email protected] >>https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > >------------------------------------------------------------------------- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
