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Re: [ccp4bb] Refmac 5.4.0066 versus Refmac 5.4.0034 |
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CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 03 January 2008Subject: Re: Refmac 5.4.0066 versus Refmac 5.4.0034 From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2008-01-03 anom formfactor SE If you did not then nothing was done. Garib On 3 Jan 2008, at 18:01, Ethan Merritt wrote: > On Thursday 03 January 2008 01:25, Boaz Shaanan wrote: >> >> Is the wrong value pointed out by Ethan the reason why we tend >> to nearly always see +ve difference peaks over Se-met after >> refinement ? > > Could be. > I have attached a plot of the net scattering factor for the two > sets of values. > > I am curious as to exactly which version[s] of atomsf had the wrong > value for A1. The various old copies I have lying around on my disks > all contain the correct value. > > Ethan > > > > >> >> Just curious. >> >> Regards, >> >> Boaz >> >> ----- Original Message ----- >> From: Garib Murshudov >> Date: Wednesday, January 2, 2008 19:19 >> Subject: Re: [ccp4bb] Refmac 5.4.0066 versus Refmac 5.4.0034 >> To: CCP4BB@JISCMAIL.AC.UK >> >>> On 2 Jan 2008, at 17:15, Ethan Merritt wrote: >>> >>>> On Tuesday 01 January 2008 06:40, Mark A Saper wrote: >>>>> >>>>> Well, I guess one shouldn't change versions of refmac in the >>>>> middle >>>>> of a structure refinement. What are the major >>> differences between . >>>>> 0034 and .0066 ? I noted that form factors for the Se >>> atom have >>>>> changed dramatically even though I'm using the same " anom >>> formfactor>> SE -8.13 5.05 " command. Is this because the >>> program is now using >>>>> the wavelength on the .MTZ file ? >>>>> >>>>> with .0034: >>>>> >>>>> SE 8.8706 >>> 2.4098 5.8196 0.2726 >>> 3.9731 15.2372 >>>>> 4.3543 43.8163 2.8409 >>>> >>>> The first coefficient here is wrong. >>>> >>>>> with .0066: >>>>> >>>>> SE 17.0006 >>> 2.4098 5.8196 0.2726 >>> 3.9731 15.2372 >>>>> 4.3543 43.8163 -11.7969 >>>> >>>> These are the values given for a1, b1, ... a4, b4 in Table 6.1.1.4 >>>> of International Tables for Crystallography Volume C (1995). >>>> >>>> The value of c (-11.7969) corresponds to an f' value of >>>> -14.6378 (= -11.7969 - 2.8409) >>>> >>>> This could only be possible at the inflection point of the Se >>>> anomalous scattering curve, and only for a beam with a very narrow >>>> bandwidth. Current generation beamlines more >>> typically yield an >>>> effective f' of -5e to -10e in practice. >>> >>> We have corrected it. It was due to double addition of f' (one >>> from >>> anom formfactor and one from a la crossec calculation). Now it >>> should >>> not happen >>> >>> Garib >>> >>> >>>> >>>> -- >>>> Ethan A >>> Merritt Courier Deliveries: 1959 NE Pacific >>>> Dept of Biochemistry >>>> Health Sciences Building >>>> University of Washington - Seattle WA 98195-7742 >>>> >>> >> >> Boaz Shaanan, Ph.D. >> Dept. of Life Sciences >> Ben-Gurion University of the Negev >> Beer-Sheva 84105 >> Israel >> Phone: 972-8-647-2220 ; Fax: 646-1710 >> Skype: boaz.shaanan‎ >> > > -- > Ethan A Merritt Courier Deliveries: 1959 NE Pacific > Dept of Biochemistry > Health Sciences Building > University of Washington - Seattle WA > 98195-7742 CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 03 January 2008 |
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