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 > > [...] > > Helmholtz Zentrum München – Deutsches Forschungszentrum für > Gesundheit und Umwelt (GmbH) Ingolstädter Landstraße 1, D-85764 > Neuherberg, https://www.helmholtz-munich.de Geschäftsführung: Prof. Dr. med. > Dr. h.c. Matthias H. Tschöp, Dr. Michael Frieser | Aufsichtsratsvorsitzende: > MinDir’in Prof. Dr. Veronika von Messling > Registergericht: Amtsgericht München HRB 6466 | USt-IdNr. DE 129521671 -- -- 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 GPG Key ID = A46BEE1A ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
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