Hi Esben,

I have a list of coordinates on a regular grid with associated floating point values from a calculation that I want to visualise in PyMOL. Is it nescessary to write this to an Xplor/CNS/CCP4 file format and subsequently load it, or can it be loaded directly into a map object via some fancy python code?

It depends on how you want to visualize the data. If dots/points or other discrete representations are okay then you can use a XYZ or a modified structure file. If you want the benefit of a field (volume, gradient, isosurface) then I suggest the map.

If you already have the data in a well-formatted brick, check out the asCCP4 function in http://www.pymolwiki.org/index.php/Tiff2ccp4. That writes the CCP4 header and data (of a TIFF file, but you can modify that for your needs). 

If you want, send me a copy of your data. Or, I also have a very poorly written script that will convert raw volumes of data to CCP4 maps, similar to the aforementioned script. Email me personally and I can send you a copy if you prefer (but it's really ugly code).

Cheers,

-- Jason


On Wed, Jan 29, 2014 at 8:02 AM, Esben Jannik Bjerrum <esbenjannik@rocketmail.com> wrote:
>
> Hi All-knowing Pymol'ers.
>
> I wonder if anyone had a couple of tips/ pointers / script snippets.
>
> I have a list of coordinates on a regular grid with associated floating point values from a calculation that I want to visualise in PyMOL. Is it nescessary to write this to an Xplor/CNS/CCP4 file format and subsequently load it, or can it be loaded directly into a map object via some fancy python code?
>
> Best Regards
> Esben Jannik Bjerrum
>
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--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jason.Vertrees@schrodinger.com
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