Actually one can make a lot of sense about e/A^3 in the absence of F(000). You actually think of the density as difference from the average and not an absolute measurement.
For an Fo-Fc style map the F(000) term is simply the difference between the number of missing electrons in the model and the number of extra electrons. Since we are probably missing all data of resolution lower than about 20 A because of the beamstop the model defects are only counted if they are within about 20 A or so of the point you are looking at. In the latter stages of refinement, when one is trying to identify strange density, the rest of the model should be pretty good and the expected mean value of the difference map very near zero. Of course your model is missing atoms for the blob itself so the difference density will tend to sink, resulting in somewhat lower peaks and negative density around the edges but this effect is usually not huge. On the other hand, contouring based on rmsd (i.e. sigma ack!) causes huge differences depending on the other things that are going on in your map. The rmsd of your first difference map can be many times larger than it is in your last. The density for a missing water molecule contoured at 3 rmsd in the first map will look very different than the same water molecule contoured at 3 rmsd in the last map. That water molecule contoured at, say, 0.18 e/A^3 would look pretty much the same. In the first difference map that water molecule will be surrounded by a huge number of other features when you contour at 0.18 e/A^3 and by very few in the last map, but isn't that as it should be? The map is supposed to be flatter at the end. Dale Tronrud On 11/28/12 12:30, Pavel Afonine wrote: > For map in e-/A^3 units to make sense one needs to obtain F000, which > may be more tricky than one may think. Interesting, how Coot does this > given just a set of Fourier map coefficients? > > Pavel > > On Wed, Nov 28, 2012 at 12:21 PM, Greg Costakes <gcost...@purdue.edu > <mailto:gcost...@purdue.edu>> wrote: > > You stated that the map is set to 3 sigma, but what is the e-/A^3? > In Coot I often find that my fo-fc map needs to be maxed out (max > sigma) in order to get to an acceptable e-/A^3. It is possible that > your fo-fc map at 3 sigma has an e-/A^3 of 0.04 or something low > like that. > > > ------------------------------------------------------------------------------- > Greg Costakes > PhD Candidate > Department of Structural Biology > Purdue University > Hockmeyer Hall, Room 320 > 240 S. Martin Jischke Drive, West Lafayette, IN 47907 > > > -------------------------------------------------------------------------------- > > > ------------------------------------------------------------------------ > *From: *"Jon Read" <jon.r...@astrazeneca.com > <mailto:jon.r...@astrazeneca.com>> > *To: *CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > *Sent: *Wednesday, November 28, 2012 10:48:04 AM > *Subject: *[ccp4bb] Strange density > > > Anyone see anything like this before? The data is 1.7Angstrom data > with good statistics. The picture shows the solid FoFc density > contoured at 3 Sigma in light brown and -3 Sigma in purple. The > density is odd as it appears to be bound to a peptide carbonyl with > no other obvious interactions with the protein. There is a > characteristic tail at one end. > > > > > > > > ------------------------------------------------------------------------ > > AstraZeneca UK Limited is a company incorporated in England and > Wales with registered number: 03674842 and a registered office at 2 > Kingdom Street, London, W2 6BD. > > *Confidentiality Notice: *This message is private and may contain > confidential, proprietary and legally privileged information. If you > have received this message in error, please notify us and remove it > from your system and note that you must not copy, distribute or take > any action in reliance on it. Any unauthorised use or disclosure of > the contents of this message is not permitted and may be unlawful. > > *Disclaimer:* Email messages may be subject to delays, interception, > non-delivery and unauthorised alterations. Therefore, information > expressed in this message is not given or endorsed by AstraZeneca UK > Limited unless otherwise notified by an authorised representative > independent of this message. No contractual relationship is created > by this message by any person unless specifically indicated by > agreement in writing other than email. > > *Monitoring: *AstraZeneca UK Limited may monitor email traffic data > and content for the purposes of the prevention and detection of > crime, ensuring the security of our computer systems and checking > compliance with our Code of Conduct and policies. > >
