Re: [PyMOL] Ray Tracing A Protein Gallery

[Buz Barstow <buzb@ma...>]

Dear All,

Thanks for all your suggestions on ray tracing the protein gallery.

In the end, I used several of the techniques suggested, and everything  
worked out really well!

To summarize:

1. Use the grid_mode option (only available in the compiled from  
source pymols)
2. Make a fake .pdb that has the corners and centers of a 3D box to  
use for alignment
3. Use the set_view command to apply the same viewing matrix
4. Use the zoom command with a center and a distance specified.

Also, the cealign package is really helpful for aligning and  
translating very dissimilar molecules.

Thanks! and all the best,

--Buz




On Dec 16, 2008, at 4:05 PM, DeLano Scientific wrote:

> Hi Buz,
>
> You can use "center" as a selection name for input with zoom, along  
> with a
> distance value.
>
> zoom center, distance
>
> e.g.
>
> # first, get the object you want in the center of the screen
>
> orient
>
> # then zoom the viewer by a fixed amount about the center point
>
> zoom center, 10
>
> # you may also wish to move the clipping planes in/out to avoid  
> cutting into
> any of the molecular representations:
>
> clip atoms, 4, selection=all
>
> # also, depending upon the application, you might want to disable
> perspective
>
> set orthoscopic
>
> # get rid of background pixels
>
> unset opaque_background
>
> # render
>
> ray
>
> # and save
>
> save struct001.png
>
> Cheers,
> Warren
>
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:support@...
>
>
>
>> -----Original Message-----
>> From: Buz Barstow [mailto:buzb@...]
>> Sent: Monday, December 15, 2008 11:42 AM
>> To: pymol-users@...
>> Subject: [PyMOL] Ray Tracing A Protein Gallery
>>
>> Dear All,
>>
>> I'm making a gallery of protein molecules for my PhD thesis.
>> I'd like to find an automatic way to ensure that all of the
>> ray traced images have the same scale. Is there an easy way
>> to do this?
>>
>> Thanks! and all the best,
>>
>> --Buz
>>
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[PyMOL] Mutating an Ion in Pymol and Displaying van der waals Radii

[Buz Barstow <buzb@ma...>]

Dear All,

I'd like to mutate an ion in pymol from a potassium to a sodium. Is  
there an easy way to do this from the command line without having to  
edit the pdb file of the structure?

Also, when one displays an atom (for instance a K atom) using the  
spheres representation, is the radius of the sphere equal to the  
Pauling radius of the atom (under the assumption that it is ionized)?  
For K, it looks like it is.

Thanks! and all the best,

--Buz

[PyMOL] surface properties

[Mark Collins <mnc2003@co...>]

Hi All
I have searched thru the archive and couldn't find an answer, to this.  I
would like to make pymol surface(s) colored by (1) hydrophobicity and (2)
concavity/convexity.
These are easily produced in grasp, so one possibility maybe to import
some type of grasp file.
Thanks in advance for suggestions, websites, or tutorials, etc.
Mark

[PyMOL] weird visualization of a peptide structure

[annalisa bordogna <annalisa.bordogna@gm...>]