Re: [ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?
Remember you need to look at half the contour height in a mFo map compared to a 2mFo-DFc map - the same domain should show up but at a lower relative contour level in both maps. REFMAC calculates a similar WCNG and you can look at the graph of m after refinement to see how close it is to 1. If the structure is well refined except for a missing domain I suspect it will be ~ 1 Eleanor Hailiang Zhang wrote: Actually I cut a small domain from the well-defined structure (just for a test). The missing part showed in 2mFo-DFc map but not in both mFo and Fo maps, and the mFo and Fo maps are so close so that I wonder whether figure of merit generated by SIGMAA helps or not in this situation... Best Regards, Hailiang On Tue, 2010-08-31 at 13:15 -0400, Hailiang Zhang wrote: Is the difference between mFo and Fo maps supposed to be very small? For an essentially correct model, yes. The major advantage of (2mFo-DFc) maps is suppression of model bias, so if you don't see much difference then your model is very well refined. For illustration, introduce a systematic error on purpose and see which map gives you better result. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?
On Wed, Sep 1, 2010 at 4:26 AM, Ed Pozharski epozh...@umaryland.edu wrote: The reason you see the missing region in (2mFo-DFc) map is because it is effectively the sum of model map (mFo) which shows you the parts of the model you have already placed and difference map (mFo-DFc) which shows you the regions which are still missing. This is not true. The 'model map' (i.e. the map calculated from the model) is obviously the one with coefficient DFc. The mFo map represents the model (i.e. the structure already placed) + *half* of the missing structure (represented by mFo-DFc), for acentric reflections. To get the 'minimally biased' map you have to make it up by adding the other half of the missing structure so we have (for acentrics): 2mFo-DFc = DFc + (mFo-DFc) + (mFo-DFc) = DFc + 2(mFo-DFc) For centrics mFo represents the model + *all* of the missing structure, so in that case no further contribution is needed, We had this discussion a while back: it seems to me that it is precisely this confusion that is engendered by thinking in terms of 2mFo-DFc = mFo + (mFo-DFc). Cheers -- Ian
Re: [ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?
Ian is, as always, absolutely right. The only comment/correction I have is that Hailang was apparently referring to severely incomplete model, for which the poor phases will dominate the mFo map. Under such circumstances, even 2fo-fc map will not correctly reflect the actual relative contribution of the missing and already modeled regions into electron density. On Wed, 2010-09-01 at 10:49 +0100, Ian Tickle wrote: This is not true. The 'model map' (i.e. the map calculated from the model) is obviously the one with coefficient DFc. The mFo map represents the model (i.e. the structure already placed) + *half* of the missing structure (represented by mFo-DFc) -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
[ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?
Hi, I want to see how the mFo maps (NOT 2mFo-DFc) compare against Fo maps. In the SIGMAA documentation, it says WCMB is the figure of merit; however, I opened in coot with FP PHIC WCMB combination, and for lots of systems, I didn't see too much difference against FP PHIC maps. Is the difference between mFo and Fo maps supposed to be very small? Best Regards, Hailiang
Re: [ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?
Hi Hailiang, m is typically determined per resolution bin using test reflections and it can range from 0 to 1, so the difference between corresponding mFo and Fo can range accordingly. You can read more on this, for example: Acta Cryst. A42 (1986) 140-149. Acta Cryst. (1995). A51, 880-887. J. Appl. Cryst. (1996). 29, 741-744. and numerous references therein. Pavel. On 8/31/10 10:15 AM, Hailiang Zhang wrote: Hi, I want to see how the mFo maps (NOT 2mFo-DFc) compare against Fo maps. In the SIGMAA documentation, it says WCMB is the figure of merit; however, I opened in coot with FP PHIC WCMB combination, and for lots of systems, I didn't see too much difference against FP PHIC maps. Is the difference between mFo and Fo maps supposed to be very small? Best Regards, Hailiang
Re: [ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?
On Tue, 2010-08-31 at 13:15 -0400, Hailiang Zhang wrote: Is the difference between mFo and Fo maps supposed to be very small? For an essentially correct model, yes. The major advantage of (2mFo-DFc) maps is suppression of model bias, so if you don't see much difference then your model is very well refined. For illustration, introduce a systematic error on purpose and see which map gives you better result. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?
Actually I cut a small domain from the well-defined structure (just for a test). The missing part showed in 2mFo-DFc map but not in both mFo and Fo maps, and the mFo and Fo maps are so close so that I wonder whether figure of merit generated by SIGMAA helps or not in this situation... Best Regards, Hailiang On Tue, 2010-08-31 at 13:15 -0400, Hailiang Zhang wrote: Is the difference between mFo and Fo maps supposed to be very small? For an essentially correct model, yes. The major advantage of (2mFo-DFc) maps is suppression of model bias, so if you don't see much difference then your model is very well refined. For illustration, introduce a systematic error on purpose and see which map gives you better result. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?
If I understand correctly, the only difference between mFo and Fo map will be weighting in different resolution shells according to figure-of-merit. While this will presumably downweigh the less reliable resolution shells, it will hardly make up for the heavy model bias. The reason you see the missing region in (2mFo-DFc) map is because it is effectively the sum of model map (mFo) which shows you the parts of the model you have already placed and difference map (mFo-DFc) which shows you the regions which are still missing. On Tue, 2010-08-31 at 15:20 -0400, zhan...@umbc.edu wrote: Actually I cut a small domain from the well-defined structure (just for a test). The missing part showed in 2mFo-DFc map but not in both mFo and Fo maps, and the mFo and Fo maps are so close so that I wonder whether figure of merit generated by SIGMAA helps or not in this situation... Best Regards, Hailiang On Tue, 2010-08-31 at 13:15 -0400, Hailiang Zhang wrote: Is the difference between mFo and Fo maps supposed to be very small? For an essentially correct model, yes. The major advantage of (2mFo-DFc) maps is suppression of model bias, so if you don't see much difference then your model is very well refined. For illustration, introduce a systematic error on purpose and see which map gives you better result. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
