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:[log in to unmask]] On Behalf Of
> Chris Fage
> Sent: Monday, September 30, 2019 14:00
> To: [log in to unmask]
> 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
>
>
>
>
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> On Mon, Sep 30, 2019 at 12:49 PM Santhosh Gatreddi
> <[log in to unmask]> 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 <[log in to unmask]>
> 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
>
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> --
>
> 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.
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