Hmm - rather tricky! I would do an MR search with the crystal model v the EM density, Steps would be: 1) convert EM density to "structure factors". - there are tools which do this .. 1a) You need to go back to ccp4i - program sfall to read map to generate SFs from map - then cad or sftools to add a fake SigF column 2) Solve MR search with the model v these "structure factors" using them as Fobs 3) Calculate the structure factors from the MR positiooned model and get the difference map..
On Wed, 5 Jun 2024 at 11:46, Martin Malý <martin.maly...@email.cz> wrote: > Dear Devbrat, > > I am now playing with a similar problem but I don't have a simple solution > for you as I'm also quite stuck. You can check these software tools which > involve some scripting in Python (NumPy, SciPy) and C++: > > EMDA (for cryoEM maps, included in CCP-EM) > https://gitlab.com/ccpem/emda > https://doi.org/10.1016/j.jsb.2021.107826 > > Gemmi (mainly for crystallography, included in CCP4) > https://gemmi.readthedocs.io/en/latest/grid.html > > Maybe there are also some relevant features in CCTBX (included in CCP4 and > Phenix). > > Cheers, > Martin > > On 05/06/2024 07:00, Devbrat Kumar wrote: > > Hello Everyone, > > Greetings! > > I have a query regarding the resampling of cryoEM density to match crystal > density to obtain a density difference map. Specifically, I am trying to > determine if it is feasible to resample a cryoEM map with an XRD density > map. However, each time I attempt this, the resampling output provides an > arbitrary ASU resample map, resulting in a significant loss of major > density. > > I have been using Coot and Chimera for this process but have not achieved > the desired outcome. Please guide me or suggest how to move forward with > this. My goal is to create an accurate final density difference map. > > Thank you in advance for your help. > *Warm Regards-* > *Devbrat Kumar* > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/
