Ok, that helped. Now I'm stuck on step 2, if you can believe that!
the data command seems to be failing. I put the following in my
javascript code:
jmolScript('x=load("foldx.dat"); select *; data "property_foldx @x";
color red;');
I verified that the "load" command worked, but the "data" command
doesn't (atoms do not turn red, indicating failure in that step).
Can you see anything wrong with my syntax? I verified that there are
the correct number of rows in foldx.dat.
Many thanks,
Sam
On May 3, 2007, at 2:09 PM, Bob Hanson wrote:
> 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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