[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [ccp4bb]: AMORE question
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
"Eleanor J. Dodson" wrote:
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> Wei Zhang wrote:
> >
> > *** For details on how to be removed from this list visit the ***
> > *** CCP4 home page http://www.ccp4.ac.uk ***
> >
> > Dear CCP4 users,
> >
> > I am now trying to solve a protein structure by MR using Amore. There are
> > four molecules in the au, based on the Matthews'coefficient and
> > self-rotation calculation.
> >
> > The rotation and translation results are quiet puzzling. Here is the four
> > solutions for each molecules, after fixing them one by one
> >
> > SOLUTIONTF1 1 77.01 90.00 271.21 0.1013 0.4771 0.3473 46.1 52.5 41.1 2 58.5
> > SOLUTIONTF2 1 15.47 48.52 87.74 0.4730 0.1005 0.1464 51.3 51.4 49.9 2 58.5
> > SOLUTIONTF3 1 72.38 32.04 96.38 0.8958 0.5205 0.3605 54.2 50.6 52.7 1 59.0
> > SOLUTIONTF4 1 81.25 38.07 83.60 0.0458 0.4842 0.3609 56.0 49.5 56.6 1 49.0
> >
> > These solutions are the best,even though there is no clear gap.
> >
> > After fiting, the CC and R-factor are also improved
> >
> > TABLE Alpha Beta Gamma Tx Ty Tz Corr_F Rfac
> > SOLUTIONF 1 76.96 86.29 269.96 0.0895 0.4795 0.3503 57.2 47.8 57.3
> > SOLUTIONF 1 17.28 42.06 86.32 0.4720 0.1061 0.1464 57.2 47.8 57.3
> > SOLUTIONF 1 73.14 32.34 95.17 0.8981 0.5195 0.3576 57.2 47.8 57.3
> > SOLUTIONF 1 79.16 45.90 83.17 0.0539 0.4895 0.3601 57.2 47.8 57.3
> >
> > Considering the model I used contains only 60% amino acids of my protein,
> > I think it is close to the solution.
> >
> > But, problem appears when I check their packing. Molecules overlap to each
> > other, either directly or to their symmetry mates.
> >
> > My questions are
> >
> > 1.Could someone know why such CC and R-f doesn't produce right
> > solution?
>
> Many reasons.. CC and R-f are indicators only.
>
> Have you got the right space group? Is there translational non-cryst
> symmetry? Look at the native 4A Patterson and see if there is a large
> peak off the origin.. With 4 molecules in the asymm unit it is common to
> find a peak with on coordinate 0.5. And that will generate apparent
> absences for a 21 screw although your space group may well have not got
> one.
>
> You need then to run the TRAFUN in all possible space groups.
> eg P 21 21 21 and P 2 21 21 if your NCS gave you a peak at x=0.5, ...
>
> Your solution would appear OK because you may well have 2 molecules
> correctly placed in the wrong space group..
> If that is true you will probably have found a solution which is half
> right -
>
> OK?
> Eleanor
Alternatively you could give Molrep a try with the option _PST Y or _PST C
http://www.ysbl.york.ac.uk/~alexei/molrep.html
Juergen
--
Juergen Bosch Tel -49 -89 8578 2648
Max Planck Institut fuer Biochemie Fax -49 -89 8578 2641
Abt. Molekulare Strukturbiologie bosch@biochem.mpg.de
Am Klopferspitz 18a http://www.biochem.mpg.de/
D-82152 Martinsried, Germany