Dear Chris, The first thing I would do is to load the FFT map (not the mtz) in coot and see how densities of both ligands compare in that case. Also in FFT, did you calculate exactly one unit cell, or did you select a region just around the protein? If you contour the maps in terms of RMSD, the amount of solvent included in the maps influences the RMSD level. For comparison it would be better to look at contour levels in electrons/Å**3. Finally, you could also look at the contour levels of the surrounding protein atoms, to get an idea how the ligand density compares to the protein density.
Best, Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Chris Fage Gesendet: Montag, 30. September 2019 12:37 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk> 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 [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-green-avg-v1.png]<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com_email-2Dsignature-3Futm-5Fmedium-3Demail-26utm-5Fsource-3Dlink-26utm-5Fcampaign-3Dsig-2Demail-26utm-5Fcontent-3Dwebmail&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=JB0q0dL5k3brkVlvZ6JtwS2ZgxG16MYZHEuyyCKXl5I&s=LrW_ht7LQyzaIgiOBBTPFBShwT1cX8B1f7mRfDZRJtg&e=> Virus-free. www.avg.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.avg.com_email-2Dsignature-3Futm-5Fmedium-3Demail-26utm-5Fsource-3Dlink-26utm-5Fcampaign-3Dsig-2Demail-26utm-5Fcontent-3Dwebmail&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=JB0q0dL5k3brkVlvZ6JtwS2ZgxG16MYZHEuyyCKXl5I&s=LrW_ht7LQyzaIgiOBBTPFBShwT1cX8B1f7mRfDZRJtg&e=> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=JB0q0dL5k3brkVlvZ6JtwS2ZgxG16MYZHEuyyCKXl5I&s=_jWAHzSBesMuvzCcRU6p1pxSgs__xBafHFiGWsOZR8Y&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
