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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