From: Bob H. <ha...@st...> - 2007-05-06 06:39:35
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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 > > |