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
>>
>>
>
>
> ----------------------------------------------------------------------
> ---
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
-------------------------------------------------------------------------
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
