Kavya, Does your ligand contain any heavier atom (S, P or other)? Is it possible that your ligand binds in different orientations? So your atom X could actually be atom Y?
Debasish -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kavyashree Manjunath Sent: Friday, May 24, 2013 1:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Negative FoFc around ligand Sir, I used model without ligand for MR. This happens only for some atoms not for all. So should I reduce the occupancy for all atoms? I did use occupancy refine it showed different occupancy like 0.8, 0.6 for two different atoms. Thank you Regards Kavya > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Kavya, > > I assume that you carried out molecular replacement without the ligand in the search model (otherwise you are probably looking at model bias). In that case the ligand most likely has reduced occupancy. You can either manually set all atoms in the ligand to e.g. 0.5 or use the 'occupancy' keyword in refmac to refine it. The density maps should improve. > > Best, > Tim > > On 05/24/2013 06:50 PM, Kavyashree Manjunath wrote: >> Dear users, >> >> I am using refmac 5.7.0029 for refining a structure (resolution 2.2 Ang) bound to 2 ligands. After MR There is a very clear density of ligands but after refinement, I get negative fofc map near one of the ligand upto 5 sigma. However its 2fofc map covers the whole ligand. Also for the other ligand, I do not see any 2fofc density (at 3 sigma) for 2 atoms, without these atoms the ligand is >> unrealistic. But the density comes up around these at around 0.7 sigma. Overall completeness is 99.9% Rmerge 7.5% >> >> What else I need to check in the data. Kindly provide some >> suggestions. >> >> Thanking you Regards Kavya >> >> >> >> >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFRn6QqUxlJ7aRr7hoRAmYhAJ48NmunV8jbKnctniW+06Rn8D/x2QCfd5nR DQHWl1Z5w/XhTsd3RI4+oqQ= > =EruH > -----END PGP SIGNATURE----- > > -- > This message has been scanned for viruses and dangerous content by > MailScanner, and is believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
