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
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
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