No such luck! If one calculated the Root Mean Square Deviation from the Mean then F(000) makes no difference, but everyone I know calculates the Deviation from 0.0. I guess that makes it an "rms" and not an "rmsd".
We can use maps calculated w/o the F(000) because we are generally more interested in the shape of the density than its height. We use the shape to come up with interpretations, which is the hard part. The height can give us a clue about the occupancy an atom would have if we refined one there - It is a shortcut to avoid building and refining models that are destined to be nonsense. If the molecule you are building will refine to an occupancy of 0.1 you could spend you time better by doing something else. Dale Tronrud On 11/28/12 15:13, Lijun Liu wrote: > F000 contributes to the whole map as a level (F000/V). If calculated > with a only difference of with or w/o F000, should the sigma levels of > the two maps be the same? That is why we could rely on maps for > modeling that are calculated w/o F000 item. Lijun > > > On Nov 28, 2012, at 2:30 PM, 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. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >
