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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