[ccp4bb] map and model do not fit when using Turbo-Frodo
Dear All, I am refining a structure of Se-protein solved with MAD using phenix. The unit cell is P 21 21 21 with a=36.898, b=59.450, c=393.909 and alpha=beta=gamma=90. There are two molecules in A.U. The problem is that when I use Turbo-Frodo for molecular modeling, the map does not fit to the model. There is a shift (translation) between the map and the model. However, if I use coot every thing is OK. I don't know why this happens only with Turbo. Any suggestion or any trick for this problem are welcome. Thanks in advance. Youssef
Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.
Hi all, I just want to ask another question related to this topic: Based on the example given by Jerry McCully and if the data has alternate strong and weak reflections, how can we split it into two different files; one containing the weak reflections and the other containing the strong reflections? Youssef
Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.
One paper in Acta. Cryst. (2006) D62, 1369-1374 described the same problem of pseudo-symmetry. To lower the Rfactor they used (h+k+l=2n+1) odd reflections for rigid body refinement and (h+k+l=2n) even reflections for restrained refinement. By this way they could decrease R/Rfree from (0.425/0.434) to (0.235/0.311). Youssef Anastassis Perrakis wrote: On Sep 4, 2009, at 11:04, Ben Ammar Youssef wrote: Hi all, I just want to ask another question related to this topic: Based on the example given by Jerry McCully and if the data has alternate strong and weak reflections, how can we split it into two different files; one containing the weak reflections and the other containing the strong reflections? I guess what you mean is to separate different layers along a reciprocal direction in two files? (and not simply strong vs weak reflections ...) These are be possible to do in sftools with a bit of playing and rtfm, but I am not sure where it would lead you. Tassos Youssef *P** **please don't print this e-mail unless you really need to* Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
Re: [ccp4bb] Zalman LCD availability
Hi Francois, Zalman LCD (21") is available in Japan. We already bought 2 sets one month ago and both are working perfectly with mac pro, windows and Linux. For William: I think the best way to get extra glasses is to go, in the weekend (or late night show if you like), to the nearest movie theater with 3D projection. Personally I did this way, and I got two pairs of glasses just for ~3US$ extra/pair and of course enjoyed the 3D movie. Youssef Francois Berenger wrote: Hello, By the way, does anyone got this LCD in Japan? My team is interested to know the model's exact reference as well as from where you ordered it. Thanks a lot, Francois.
