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 > On 17. Jan 2025, at 01:02, Tim Gruene <tim.gru...@univie.ac.at> wrote: > > Dear Paul, dear everyone, > > I need to compare two Gaussian Cube files (Paul Bourke's > page https://paulbourke.net/dataformats/cube/ is the best description I could > find), and my first approach would be a map correlation coefficient at the > van der Waals surface. Does anyone know how to do this? > > Details: > The cube files contain the electrostatic potential map of a single > Tyrosine molecule (derived in two different ways). Both files include > the tyrosine coordinates. They are oriented differently. Also the grid > spacing is different, requiring map interpolation. > > I would superpose tyrosine A onto tyrosine B and transform map A the > same way to superpose it with map B. Then I would calculate their > mapCC, ideally in certain sub-volumes, and with the possibility to > define the surface as van-der-Waals-surface. I coded something myself, > but I am not sure how long it would take me to debug the code so that I > trust the result. > > I did not find a way to read a cube file with coot, and ccp4mg > (from ccp4 8.0, admittedly) crashes with a segmentation fault when > opening either map. > > The background: > My PhD student and I think the two maps look quite comparable, given > their different origin, but two reviewers think they do not look alike. > I was hoping for a CC that gives a number to the looks (ideally a > number > 60% ;-)) > > Best wishes, > Tim > > > -- > Tim Gruene > Head of the CF Crystal Structure Analysis > Faculty of Chemistry > University of Vienna > > Phone: +43-1-4277-70202 > > 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/ 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 ######################################################################## 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/
