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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