Hi Filipe, 

together with James' comment (thanks, James, too!!)

"Once you have the cubes in CCP4 format you should be able to use coot
to align the maps after aligning two PDB files corresponding to the 
coordinates of interest. Its the "Transform map by LSQ model fit ..." 
menu under Map Tools..."

your cub->mrc converter would be a great start (it seems faster than
converting the stream with James' floatgen)

As for the rest: one map does not have this matrix, since it was
derived experimentally, and the grids are not identical. But I suppose
Coot will deal with the different grids properly :-)

Thanks to both you and James!

Tim

On Fri, 17 Jan 2025 07:30:28 +0000
Filipe Miguel Cardoso Micu Menezes <filipe.mene...@helmholtz-munich.de>
wrote:

> Hi there,
> 
> depending on the level of theory you use, there should be an
> electronic density matrix behind the electrostatic potential
> calculation. I think this is the best metric you can possibly
> have/define to come up with an index like ">60% similarity": subtract
> the density matrices and then use algebra to determine whether the
> matrix has norm numerically different from zero.
> 
> On the other hand, cub is just a simple text format to store
> densities on a 3D grid. If it helps, I have a simple python script
> that converts the cub files to mrc format and you can open anywhere.
> Chimera and ChimeraX open cub too. In this case, if the two molecules
> are perfectly aligned, you can calculate the differential
> electrostatic potential. Since this is defined over a grid, and
> assuming that the grids of the two calculations coincide, then do one
> minus the other. Delta_MEP = MEP1 - MEP2
> 
> If you plot this and the quantity is numerically indistinguishable
> from zero, you prove your point too. You can also sum the norm of
> this difference over the whole grid. This should also define a metric
> of relative difference. But this requires that the grids are
> identical and in the same coordinate space. Otherwise things get
> complicated because you need to interpolate.
> 
> I hope this helps. Let me know if you want the cub->mrc converter.
> 
> Best
> Filipe
> 
>  [...]  
> 
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-- 
--
Tim Gruene
Head of the Core Facility Crystal Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

https://ccsa.univie.ac.at

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