Hi Chris, You made an Fobs map not a 2Fo-Fc map. You can leave sigma empty if you want to make a map in this case.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Chris Fage > Sent: Monday, September 30, 2019 14:00 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol > > 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> > > > 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> > > > ________________________________ > > > 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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
