Re: [ccp4bb] SAD: Refine against anomalous data

2007-08-12 Thread George M. Sheldrick
Dear Paul, That implies that phenix refine (like SHELXL, but unlike REFMAC) can refine against data for which I+ and I- (or F+ and F-) have not been merged. An attempt to refine f" against Friedel merged data would be very poorly determined. Am I right in guessing that phenix refine can only d

Re: [ccp4bb] SAD: Refine against anomalous data

2007-08-12 Thread Paul Adams
Dear George, you are correct - this kind of refinement only makes sense if F+ and F- are kept unmerged. The refinement of f'/f'' is performed with the FFT (from what I recall - Ralf can confirm or deny). At the very least, structure factors from non-anomalous atoms are calculated using the F

[ccp4bb] CCP4 rotation convention

2007-08-12 Thread Bernhard Rupp
Dear programmers - Phil Evans writes in acta D57 1355 (2001) on p 1358 section 5.2: "the convention used in AMoRe (Navaza, 1994) and other CCP4 programs (Collaborative Computational Project, Number 4, 1994) is to rotate by gamma around z, then by beta around the new y, then by alpha around

Re: [ccp4bb] PDB format survey?

2007-08-12 Thread Edward A Berry
Ralf W. Grosse-Kunstleve wrote: I.e. the first 9 serial numbers are represented as usual. The following atoms use a base-36 system (10 digits + 26 letters) with upper-case letters. 43670016 (26*36**4) additional atoms can be numbered this way. If there are more than 43770015 (9+43670016)

[ccp4bb] selfrot plot

2007-08-12 Thread Bernhard Rupp
Dear All: plotting a selfrotation with polarrfn. a) Seems in the GUI interface, selecting a range for a fine kappa seach (60,80,1) does not change anything? Looking at the command file, it does not contain any LIMITS statement. But the def file has them. b) I'd like to show the azimuth angle, bu