From: Samuel F. <sam...@ya...> - 2007-05-06 08:48:01
|
Hi Bob, I figured out how to get it to color the trace by residue.. trace off; select alpha ;hidenotselected=true; x=load ("foldx_data.cgi?ID=$ID&type=HingeMaster");show x; DATA "property_hingemaster \@x"; trace on; color trace property_hingemaster; This is good enough, at least for now. If by-residue numbering gets easier hopefully I'll hear about it, so I can do cartoons and so on. Thanks for the help.. Sam On May 6, 2007, at 2:39 AM, Bob Hanson wrote: > It would be nice to be able to write a Jmol "macro" to do it: > > residueData = load("mydata.dat") > nResidues = {*}[{*}].resno #{*}[{*}] is "the last atom" > n = 1 > message _start > if (n > nResidues);goto _end;endif > select resno = n > ....what here....? > n = n + 1 > goto _start > message _end > > Hmm. Say, maybe we need > > select xxxx > set property_x [some value] > > ? > > Bob > > > > > Samuel Flores wrote: > >> Hi All, >> >> Many thanks for prior help received on this. >> >> Is there a way to assign the coloration based on residue number >> rather than atom number? I have flexibility information associated >> with each residue and would like to shade the protein according to >> this scheme. My current "fix" is to select only alpha carbons, then >> color by this property, then turn on the trace. However the result >> looks clownish and unprofessional, like a snake with mumps. I could >> do some database work and count the number of atoms in each residue, >> then generate the color data appropriately. But that seems so >> clunky.. >> >> Does anyone have an alternative? >> >> For any party willing to look at it, I have this set up at: >> http://molmovdb.org/cgi-bin/morph.cgi?ID=f419381-29700 >> Click on the Hinge anallysis tab, then on: "Color by HingeMaster >> score (Jmol window)" >> >> Sam >> >> On May 4, 2007, at 11:25 AM, Samuel Flores wrote: >> >> >> >>> Ah, so that was the problem. apache of course tries to execute all >>> files in cgi-bin. The page with my jmol applet is actually a CGI >>> script. The data file will not be served up because it is not >>> executable. I finally fixed the problem by making a program called >>> "foldx_data.cgi" which does nothing more than serve up a web page >>> with a CR-delimited list of numbers. The following is my code: >>> >>> x=load("foldx_data.cgi"); DATA "property_foldx @x"; color >>> property_foldx; >>> >>> Thanks for all your help! Hopefully this will be of use to someone >>> else, and my suffering will not have been in vain, amen. >>> >>> Sam >>> >>> On May 3, 2007, at 11:27 PM, Bob Hanson wrote: >>> >>> >>> >>>> 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 >>>>>>>>>>> Jmo...@li... >>>>>>>>>>> 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 >>>>>>>>> Jmo...@li... >>>>>>>>> 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 >>>>>>>> Jmo...@li... >>>>>>>> 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 >>>>>>> Jmo...@li... >>>>>>> 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 >>>>>> Jmo...@li... >>>>>> 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 >>>>> Jmo...@li... >>>>> 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 >>>> Jmo...@li... >>>> 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 >>> Jmo...@li... >>> 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 >> Jmo...@li... >> 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 > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |