Dear Paul, Herman, Robbie, and Santosh, Thanks for your quick replies.
The FFT-generated maps and mtz maps look roughly equivalent in Coot, but there are minor differences even at the same e/A^3 level (the mtz maps actually look a bit weaker). I generated them using the default settings in FFT: simple map, format to cover asymmetric unit, F1=F_XDSdataset, Sigma=SIGF_XDSdataset, PHI=PHIC. Perhaps, as Robbie mentioned, the problem lies in column selection, since Coot uses FWT and PHWT. I can assign F1 and PHI to these values, respectively, but what should I choose for Sigma? My version of Pymol doesn't support loading of mtz files. I think it's only in the incentive version. Paul wrote: "No need to do this - just export the map (or the map fragment)." I'm not sure how to do this without going through FFT! I can also try generating maps in Phenix, as Santosh suggested. However, if the maps can be directly exported, as Paul suggested, I would prefer to follow that route. Best wishes, Chris <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Mon, Sep 30, 2019 at 12:49 PM Santhosh Gatreddi <santhoshgl2...@gmail.com> wrote: > Hi Chris, > > I also observed similar thing when I have generated 2Fo-Fc maps in CCP4 > FFT. But when I have generated 2Fo-Fc maps in Phenix then my maps were > similar in Pymol and Coot. I request you to generate maps with Phenix and > verify it in Pymol. It worked for me. > > One possible reason for this is map averaging in Pymol. Make sure that you > uncheck it before loading your map in Pymol. > > I hope that above suggestion works for you. > > Regards, > Santhosh > > On Mon, Sep 30, 2019 at 4:06 PM Chris Fage <fage...@gmail.com> wrote: > >> Dear All, >> >> I recently obtained structures of a protein bound to two different small >> molecules. When viewing the structures in Coot with a similar contour >> setting, the 2Fo-Fc map around ligand 1 is clearly much weaker than that >> around ligand 2.However, after generating 2Fo-Fc maps in FFT and loading >> them in Pymol (again, choosing equal contour levels), the maps surrounding >> ligands 1 and 2 have nearly the same quality. Is there a difference in >> scaling between the two programs that can account for this? Thanks for any >> advice! >> >> Best wishes, >> Chris >> >> >> <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> >> Virus-free. >> www.avg.com >> <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> >> <#m_-501199200969567658_m_-8793236030949751887_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> > > > -- > > > > > > > > > > > > *With regards....Santhosh Gatreddi (Research Scholar)c/o Dr.Insaf Ahmed > Qureshi, Dept. of Biotechnology & Bioinformatics,School of > lifesciences,University of > Hyderabad,Hyderabad-500046(A.P),India.Ph.no-9160628684.* > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
