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.
2) Select those atoms:
select 1.2 # only the second model in the first file
3) Read the file data into a variable:
myData = load("data.txt")
4) Create a data set based on that variable:
DATA "property_whatever @myData"
5) Now you can, for instance, use this as part of the atom label:
select 1.1; label "%a %4.2{property_whatever}"
(That would be 4 characters right-justified with 2 decimal places.)
6) For an isosurface, just use either of these commands to map those
numbers onto the solvent surface:
ISOSURFACE saSurface map property_whatever
or
ISOSURFACE saSurface map property @myData
These do the same thing. So you really don't need the DATA command
unless you want labels.
To color the van der Waals surface, use:
ISOSURFACE VDW 100% saSurface map property @myData
I thought that this might be a nice default, so you can even just do the
following:
isosurface property_whatever
or for a slightly smoother rendition:
ISOSURFACE VDW 100% molecular map property @myData
If all you are interested in is a quick-and-dirty mapping, then all you
need is:
x = load("data.txt")
isosurface property @x
That's it! I'll get this uploaded in a bit.
Bob
-------- Original Message --------
Subject: Re: Jmol color question
Date: Tue, 6 Mar 2007 11:57:53 -0600
From: Jeffrey Tseng <[EMAIL PROTECTED]>
Reply-To: [EMAIL PROTECTED]
To: Bob Hanson <[EMAIL PROTECTED]>
References:
<[EMAIL PROTECTED]>
<[EMAIL PROTECTED]>
<[EMAIL PROTECTED]>
<[EMAIL PROTECTED]>
Thanks for your idea.
But I need surface coloring.
I show you a picture. You will know why I need the surface.
(It is rendered by VMD)
Other structure Visualization viewers, such as VMD,
it could render surface with any color you like. It needs some work
too. But it can.
Jmol has such nice web properties. It should come with it.
I believe if dots could, isosurface can do better.
Cheers,
On 3/6/07, Bob Hanson <[EMAIL PROTECTED]> wrote:
It's certainly an interesting idea. But isosurfaces are not properties
of atoms; they are properties of the molecule.
Try dots instead. They look pretty cool, and they can be colored all of
these ways, because they are associated with atoms.
Bob
Jeffrey Tseng wrote:
> Thanks for your quick responding.
>
> Based on the description on http://jmol.sourceforge.net/jscolors/,
> the color "object" could be isosurface.
>
>
> I try to color a "surface" with the different values of B-factor
> embedded in PDB file's records.
>
> My intention is to render a surface ( a set of selection of atoms)
> with different properties. In this case, the property is B-factor.
> Other property could be the conservation of amino acid residues. But
> this needs some work to modify the pdb file for obtain other
> properties.
>
>> because Isosurface isn't associated with any atoms, and all those
>> color schemes are based on knowing what the properties of the associated
>> atoms are (temperature, CPK color, etc.)
>
>
> I try
> color isosurface cpk
> It dosen't work, either.
>
> ##You said isosurface isn't associated with any atoms.
> then, I swith the order of commands.
>
> color relativeTemperature
> isoSurface molecular
>
> It dosen't work because isosurface switch the temperature color back
> to default (purple).
>
>
> ##################################
> Is it possible to color it by temperature and render the surface with
> isosurface at the same time.
>
> I think I try to tell you that
>
> Is there any variable in Jmol so users could define such that
> isosurface could be associated with ?
>
> Thanks very much,
>
> Cheers
>
>
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> On 3/6/07, Bob Hanson <[EMAIL PROTECTED]> wrote:
>
>> right, because Isosurface isn't associated with any atoms, and all those
>> color schemes are based on knowing what the properties of the associated
>> atoms are (temperature, CPK color, etc.)
>>
>> Explain to me more about what you are trying to do.
>>
>> Bob
>>
>>
>> Jeffrey Tseng wrote:
>>
>> > Hi, Bob
>> >
>> > Thanks your effort for maintaining Jmol. It is a very good
>> > visualization tool for view protein structures.
>> >
>> > After playing around Jmol on structures, I encounter a Jmol coloring
>> > problem.
>> > I try to color an isosurface in relativeTemperature or any kind
>> > pre-defined color scheme described in Jmol website
>> > http://jmol.sourceforge.net/jscolors/
>> >
>> >
>> > For example, I type
>> >
>> > color isosurface relativeTemperature
>> > ##################################
>> > The object (isosurface) shows ALL "black".
>> >
>> > The only works for "isosurface" is:
>> >
>> > color isosurface lightgreen
>> >
>> > #################################
>> > "lightgreen" is regular color name.
>> >
>> > Any predefined such as CPK, relativeTemperature, structure ....... in
>> > Jmol dose NOT work for isosurface.
>> >
>> >
>> >
>> > Is there anything I miss or a bug ?
>> > Currently, I adopt Jmol applet with version 11.0RC4
>> >
>> >
>> > Thanks for your kind help !!
>> >
>> >
>> >
>>
>>
--
Yan Yuan Tseng
UIC Bioinformatics
218 Science and Engineering Offices
851 S. Morgan Street, MC 063
Chicago, Illinois 60607
(312) 4135725
http://manta.bioengr.uic.edu/predict/
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