all files loaded by an applet must be from the current directory of
subdirectory. Can't have "../"
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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