Re: [ccp4bb] unbiased electron density map
Am 10.01.2008 um 01:53 schrieb Dale Tronrud: ... Your quote bring up another matter. An initial map, i.e. before refinement, is unbiased if it is an omit map. If you have done no refinement and you leave the interesting part out of the calculation of Fc there can not be any bias in either the Fo-Fc or the 2Fo-Fc map. This is why an initial map is more reliable for proving binding of a compound, for example, than a bias reduced map after refinement. ... But isn't this only true, if the model that is put in was not refined against a related data set before? If the new Fobs are related to the old Fobs (against which the model was refined before) then you carry any model bias over to the new data, because a simple omit-map using the old data will have model bias. Best regards, Dirk. *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: [EMAIL PROTECTED] ***
Re: [ccp4bb] unbiased electron density map
Dirk Kostrewa wrote: Am 10.01.2008 um 01:53 schrieb Dale Tronrud: ... Your quote bring up another matter. An initial map, i.e. before refinement, is unbiased if it is an omit map. If you have done no refinement and you leave the interesting part out of the calculation of Fc there can not be any bias in either the Fo-Fc or the 2Fo-Fc map. This is why an initial map is more reliable for proving binding of a compound, for example, than a bias reduced map after refinement. ... But isn't this only true, if the model that is put in was not refined against a related data set before? If the new Fobs are related to the old Fobs (against which the model was refined before) then you carry any model bias over to the new data, because a simple omit-map using the old data will have model bias. Right you are, and it's an important point too. My only defense is that I said If you have done no refinement I don't think of the refinement of several models to data from isomorphous crystals as separate refinements, but sometimes forget to mention this when talking to others. I should be more careful. Dale Tronrud
[ccp4bb] unbiased electron density map
In my understanding, unbiased electron density map usually refers to the Fo-Fc map.But I have seen in some papers sentences like that The initial, unbiased 2FoFc map is contoured at.I was a bit confused since I was told by my instructor that the 2Fo-Fc was usually biased. Can anyone clear up this concept for me? Mike - Looking for last minute shopping deals? Find them fast with Yahoo! Search.
Re: [ccp4bb] unbiased electron density map
A 2Fo-Fc map is simply an Fc map with two times the Fo-Fc map added to it. ( Fc + 2(Fo-Fc) = Fc + 2Fo - 2Fc = 2Fo - Fc ) The phase comes from the Fc's. The basic formulation is biased toward the model used to calculate the Fc's. You did, after all, start with a pure Fc map! Various techniques are used to reduce bias in these maps. Usually a technique that reduces bias in one kind of map reduces the bias in the other, since they are so closely related. The procedures I know of work by changing the calculation of Fc (and the weights on the individual reflections, which aren't mentioned when using the simple name Fo-Fc but are there none-the-less) and since the Fc is in both maps both maps are debiased. These methods reduce bias. Unbiased is a stronger claim and if you use that word you should state clearly how you know the bias is gone. Your quote bring up another matter. An initial map, i.e. before refinement, is unbiased if it is an omit map. If you have done no refinement and you leave the interesting part out of the calculation of Fc there can not be any bias in either the Fo-Fc or the 2Fo-Fc map. This is why an initial map is more reliable for proving binding of a compound, for example, than a bias reduced map after refinement. Dale Tronrud michael nelson wrote: In my understanding, unbiased electron density map usually refers to the Fo-Fc map.But I have seen in some papers sentences like that The initial, unbiased 2F_o -F_c map is contoured at.I was a bit confused since I was told by my instructor that the 2Fo-Fc was usually biased. Can anyone clear up this concept for me? Mike Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://us.rd.yahoo.com/evt=51734/*http://tools.search.yahoo.com/newsearch/category.php?category=shopping
