Dear Guillaume I will keep that in mind while trying.
Thank you Regards Devbrat On Wed, Jun 5, 2024, 5:21 PM Guillaume Gaullier < guillaume.gaull...@kemi.uu.se> wrote: > 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> 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 > ######################################################################## 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/
