Another factor might be that ccpem uses a different axis order to gemmi and ccp4 ;-0
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android -------- Original Message -------- On 05/06/2024 12:51, Guillaume Gaullier 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/
