[cctbxbb] Re: electron density value near an atom

Hi Rob, to do this you need to make the following choices: - map to use: exact model calculated map (infinite resolution) or a finite resolution Fourier map; - kind of map (form-factors: electron, x-ray, neutron). Fourier map can be calculated using phenix.fmodel Exact model calculated map can be calculated using phenix.model_map You should be able to set form-factors of your choice in both tools. phenix.map_value_at_point  and  phenix.map_values_along_line are the tools that you seem to be asking for. For anything custom, see how the above tools are implemented and use CCTBX building blocks to do specifically what you want (I know you are fluent in Python and CCTBX)! Hope that gives enough hints to get started! Pavel On 10/14/24 10:34, Nigel Moriarty wrote:

Rob

I'm cc'ing Pavel who would be best to answer this question.

Cheers

Nigel

--- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : [email protected] Web  : CCI.LBL.gov http://CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 https://orcid.org/0000-0001-8857-9464

On Thu, Oct 10, 2024 at 9:34 AM wrote:

Dear CCTBX users/developers

I would like to calculate the theoretical electron density value at a point in space as a function of an atom specified by its coordinate and its form factor. I’ll assume it’s for a certain X-ray wavelength, say 1.0Å. If someone would have the time to give me a few pointers on how to do this using the CCTBX I'd be very grateful.

Thanks in advance,

Rob _______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]