Hi Robbie, I guess that solves part of the problem. But when I generate a new set of maps with F1=FWT and PHI=PHWT and load them into Pymol, they are still not comparable to those in Coot. Again, the maps for ligands 1 and 2 in Pymol look about the same.
Best, 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 1:26 PM Robbie Joosten <robbie_joos...@hotmail.com> wrote: > 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 > > <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> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
