Re: [PyMOL] Ray Tracing A Protein Gallery

[Buz B. <bu...@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:su...@de...
>
>
>
>> -----Original Message-----
>> From: Buz Barstow [mailto:bu...@ma...]
>> Sent: Monday, December 15, 2008 11:42 AM
>> To: pym...@li...
>> 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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