I can say that my chair is 10 meters above ground level and I can also say that it is 100 meters above sea level. The units of "meters" is equally valid in both cases. The value of any measurement is useless without both the units and the origin (or coordinate system in multidimensions). The values reported by Coot are how many e/A^3 more dense is this spot than the local average.
We are all in agreement on the main point, however. If you want people to help interpret your density map, please give us some indication how dense that density is. rmsd's or sigma's don't help much. One thing I like to do is to purposefully leave out a nearby water molecule so you can compare your mysterious blob to the density of a real atom in YOUR crystal with YOUR bulk solvent. Then we have something to talk about. Dale Tronrud On 11/28/12 14:31, Pavel Afonine wrote: > If a map was computed from map coefficients not having F000 included I > would not say it has *electron* per Angstrom cube (e/A**3) units, but > it's just a unit cell volume scaled map in some units. > > Whether such a map more useful compared to sigma scaled one is a > separate question. In fact, it is, as you and Ed pointed out. > > I was just trying to say that if one did not include F000 one should not > interpret map values too literally (thinking of them as electrons, etc). > The second point was that F000 is typically estimated (not > experimentally measured), and any estimation errors will be in turn > reflected in e/A**3 map values, which adds one more reason of > being cautious when interpreting map values. > > Pavel > > On Wed, Nov 28, 2012 at 2:13 PM, Dale Tronrud <det...@uoxray.uoregon.edu > <mailto:det...@uoxray.uoregon.edu>> wrote: > > > 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> > > <mailto: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> > > <mailto:jon.r...@astrazeneca.com > <mailto:jon.r...@astrazeneca.com>>> > > *To: *CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > <mailto: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. > > > > > >
