Sir, It has two 'P's. This is the one which shows different occupancy one of them 0.64 and another 1. I checked to confirm that it is not P but water but it is too close to ligand to be water.
Thank you Regards Kavya > 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. > > -- > 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.
