Sam, you should be doing all this testing from a Jmol console -- pull
that up from the popup menu and work from it.
It's far easier than trying to get it going this way.
you can't say
color atoms cartoons property_foldx
one or the other:
select *
color atoms property_foldx
color cartoons property_foldx
Samuel Flores wrote:
>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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