Dear all,
Thanks for your suggestions on rendering thermal ellipsoids. What I found
worked easiest was to use Pymol 1.1 beta 3 to display the ellipsoids and for
now color them based on the isotropic equivalent B factor by using
spectrum b, minimum=10, maximum=30
which uses the default bgr gradient and worked pretty well to color atoms
with B< Bmin blue , atoms with B>Bmax red and those in between shaded
smoothly from blue to red. There is also a script color_b.python on Robert
Campbell‚s pymol web page that allows setting many options such as the
coloring scheme or how the colors are binned which may be useful.
Charu
On 9/15/08 3:12 AM, "Warren DeLano" <[log in to unmask]> wrote:
> I don't fully understand the nature of the challenge being faced by the
> original poster, but FYI, just in case: Current PyMOL open-source code and
> executable builds can also render temperature-factor ellipsoids from CIF and
> PDB files, both interactively and using the built-in ray tracer.
>
> There's an example figure on the current home page about 2/3 of the way down:
> http://pymol.sf.net
>
> Cheers,
> Warren
On 9/15/08 2:42 AM, "Ethan A Merritt" <[log in to unmask]> wrote:
> On Sunday 14 September 2008, Chaudhry, Charu (NIH/NICHD) [F] wrote:
>> Hello,
>>
>> Does anyone know how to render thermal ellipsoids in rastep in a specific
>> view, not the one arbitrarily chosen by the program? How to do this is not
>> well documented as far as I have seen. What I have tried is to write out the
>> rotation/transformation matrix of the view I want using molscript –gl, and
>> put the matrix or its transpose (as a test) into the raster3d header file
>> automatically used as input for raster3d if it is in the current directory.
>> This changes the view from the default automatic view but does not match the
>> view I want. My header.r3d file looks like -
>> by rotation
>> -0.155113 0.406792 0.900256
>> -0.861109 0.390958 -0.325027
>> -0.48418 -0.825635 0.28965
>> translate -4.6120 -21.2290 -16.6985;
>> but it is not clear to me if this is the correct format to be using, or if
>> there is a different issue as to why the views don’t match. The 4th line of
>> the matrix is from render output in raster3d.
>
> Here is what I do:
>
> 1) Create a Raster3D Header file with the identity rotation matrix.
> Let's call this file header.r3d
> Sample is here:
> http://skuld.bmsc.washington.edu/raster3d/html/render.html#sample_header
>
> 2) Matrix element [4,4] (= 0.6 in the sample) describes the total width,
> in Angstroms, of the field of view. You can tweak this later on the
> command line to "render" by using the -zoom option.
>
> 3) Choose a preferred view in molscript -gl, and save the matrix directly
> (*not* the transpose) to a separate file in the form of a global
> rotation matrix. Example is here:
> http://skuld.bmsc.washington.edu/raster3d/html/render.html#obj16
> The whole file will look like this:
>
> 16
> ROTATION
> M11 M12 M13
> M21 M22 M23
> M31 M32 M33
>
> 6) Create a description of the ellipsoids themselves using rastep.
> The -h flag tells it not to create a new header.
>
> rastep -Bcolor 10 30 -prob .25 < test.pdb > ellipsoids.r3d
>
>
> 7) Finally, make a file that joins all of these together into
> a picture description that can be rendered. Let's call this
> file picture_1.r3d. It will contain pointers to the
> individual components:
>
> @header.r3d
> @matrix.r3d
> @ellipsoids.r3d
>
>
> 8) Now you can render this in one command:
>
> render < picture_1.r3d > png.r3d
>
> The individual component files can be changed independently.
> That is, you can swap another view matrix into the matrix.r3d
> file, or change parameters in the header file, etc.
> The master picture description picture_1.r3d and the render
> command that calls it will remain the same.
>
> Alternatives:
>
> - This whole process can be automated from the Raster3D panel
> of Xfit, capturing the current orientation and scale of the
> molecule in the graphics window.
>
> - You can do something similar using Coot, but so far as I know
> it won't render the ellipsoids. (Maybe the current version does?)
> But you could take the 20 lines of header records at the top of
> the file created by Coot, and append them to the front of the
> ellipsoids file created above.
>
>> I run rastep from the command line using
>> rastep -Bcolor 10 30 -prob .25 < test.pdb | render -png test.png
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