Re: [ccp4bb] Negative electron density

Just for completeness: BUSTER includes an automatic so-called "void correction" that tries to detect those incorrectly bulk-solvent filled cavities and correct for it. Nothing for you to do extra, since that correction is on by default ... and works as expected in a lot of cases as far as we can te

Re: [ccp4bb] AW: [ccp4bb] Negative electron density in the Fo-Fc map at the binding site

ulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von > Armando Albert > Gesendet: Freitag, 18. Juli 2014 18:04 > An: CCP4BB@JISCMAIL.AC.UK > Betreff: [ccp4bb] Negative electron density in the Fo-Fc map at the > binding site > > Dear all, > I am screening a small library

[ccp4bb] AW: [ccp4bb] Negative electron density in the Fo-Fc map at the binding site

[mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Armando Albert Gesendet: Freitag, 18. Juli 2014 18:04 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Negative electron density in the Fo-Fc map at the binding site Dear all, I am screening a small library of ligands against my protein crystals. Following a soaking

Re: [ccp4bb] Negative electron density in the Fo-Fc map at the binding site

Hi Armando, can be many reasons, a few for instance: - are you sure the ligand you modeled in is the one that is actually there? - is the positive density around or overlaps with ligand atoms you places? Then that would means ligand parameters are underrefined (need more refinement) or not corre

[ccp4bb] Negative electron density in the Fo-Fc map at the binding site

Dear all, I am screening a small library of ligands against my protein crystals. Following a soaking with different ligands, I collect datasets to 1.9A resolution and refine them against an empty model without any problem. What is the meaning of a rather large negative electron density in th

Re: [ccp4bb] Negative electron Density for Zinc

Thank You very much everyone. I took all your suggestions into consideration. I was able to solve the problem Thank You once again Deepthi On Tue, Aug 28, 2012 at 5:07 PM, Pavel Afonine wrote: > Hi Deepthi, > > 1) refine anisotropic ADPs for Zn, > 2) make sure charge is accounted for, > 3) r

Re: [ccp4bb] Negative electron Density for Zinc

I wish I could give a sensible explanation, but this feature is very common with heavy atoms. Possible problems. The default wavelength for all atomic scattering functions is Cu Ka - you can see the formula used and details in the file $CLIBD/atomsf.lib. The atomic scattering values are much t

Re: [ccp4bb] Negative electron Density for Zinc

Hi Deepthi, 1) refine anisotropic ADPs for Zn, 2) make sure charge is accounted for, 3) refine f' and f'' for Zn (that means you need to use anomalous data in refinement). If 1-3 do not help, add 4) refine occupancy of Zn, 5) make sure you visualize your map using correct levels. This should so

Re: [ccp4bb] Negative electron Density for Zinc

Please correct me if I am wrong. If I am understanding correctly, your refinement was against the data of SAD which used a wavelength to collect anomalous dispersion. Such kind of data have anomalous source atoms collected at a lower "real" atomic struc

[ccp4bb] Negative electron Density for Zinc

Hi Everybody Thank You very much for your suggestions. I did play around with Zinc occupancy by giving 0.5 to each of them. I got rid of the negative electron density. But i think it still needs to be refined. Thank You very much once again Deepthi

[ccp4bb] Negative electron Density for Zinc

Hi everybody, I am working on a mutant protein structure which is 56 aminoacids long and solved the structure using SAD( Single wavelength anomalous dispersion) with zinc ions. We used SHELX software to locate the Zinc atoms and solved phases. We got the structure as a monomer. The resolution of