when these kind of things occur to me it always is a silly mistake like:
- occupancies of the new residues set to 0.0
- reading in the old pdb-file when running refmac instead of the new one
- calculating the map with the old refmac output instead of the new output
- reading in and/or displaying the old map in coot instead of the new map
but I guess you checked all this...
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecular/mvraaij/index.php?l=1
On 1 Mar 2011, at 17:32, Judith Reeks wrote:
> Dear All,
>
> I am currently refining a structure using the latest experimental version of Refmac (5.6) and there seems to be a problem with my Fo-Fc map. There is a region where I have fitted residues to the electron density but after refinement there is still positive electron density assigned to the region despite the fact that residues fit the electron density (see link below for a screenshot). Multiple rounds of refinement have yet to get rid of this problem. I have checked the PDB file and there does not appear to be any problems with this region. Has anybody seen something like this before?
>
> http://i1083.photobucket.com/albums/j382/jreeks/Screenshot2011-03-01at1613402.png
>
> Regards,
>
> Judith Reeks
> [log in to unmask]
> School of Chemistry
> University of St Andrews
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