With a cryoEM map, it's easier to do the rigid-body fitting of step 2 in real space (this is trivial to do interactively in ChimeraX) rather than by MR.
________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Sent: Wednesday, June 5, 2024 1:39:56 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map 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<mailto: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 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ######################################################################## 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/
