On Thursday, 14 November, 2013 18:58:27 Niu Tou wrote:
> Dear Phil,
>
> I used PHASER to do the task. I have double checked and both files have
> the same prefix, so they are from the same output. I have also checked the
> headers again, they have the same spacegroup. Actually I was trying to
> search for two different molecules but only one was found. The spacegeoup
> is P2 and I am quite sure it is not P21 from system absence.
P21 is 100 times more common than P2.
There are only 160 protein structures in P2 in all of the PDB
So although it is of course possible for it to be P2, it is more likely from
a priori expectations to be P21 with "prohibited" large intensities for the
0k0 relections. You definitely need to consider P21 as a possibility
when running MR.
Ethan
>
> One possibility is that the space group was wrong, since there is a 95% off
> origin peak. There are several choices from data processing, P1, P2, C2
> C222, all have this large off origin peak. I wonder if this 95% peak can
> tell some information?
>
> It will not surprise me if this result is incorrect, however how could
> these regular density be?
>
> Best,
> Niu
>
>
> On Thu, Nov 14, 2013 at 5:47 PM, Phil Jeffrey <pjeff...@princeton.edu>wrote:
>
> > Hello Niu,
> >
> > 1. We need extra information. What program did you use ? What's the
> > similarity (e.g. % identity) of your model. What's your space group ? Did
> > you try ALL the space groups in your point group in ALL the permutations
> > (e.g. in primitive orthorhombic there are 8 possibilities).
> >
> > 1a. My best guess on limited info is that you've got a partial solution
> > in the wrong space group with only part of the molecules at their correct
> > position.
> >
> > 2. I recently had a very unusual case where I could solve a structure in
> > EITHER P41212 or P43212 with similar statistics, but that I would see
> > interpenetrating electron density for a second, partial occupancy molecule
> > no matter which of these space groups I tried (and it showed this when I
> > expanded the data to P1). Might conceivably be a 2:1 enantiomorphic twin,
> > in retrospect, but we obtained a more friendly crystal form. I hope you
> > don't have something like that, but it's possible.
> >
> > Phil Jeffrey
> > Princeton
> >
> >
> > On 11/14/13 5:22 PM, Niu Tou wrote:
> >
> >> Dear All,
> >>
> >> I have a strange MR case which do not know how to interpret, I wonder if
> >> any one had similar experiences.
> >>
> >> The output model does not fit into the map at all, as shown in picture
> >> 1, however the map still looks good in part regions. From picture 2 we
> >> can see even clear alpha helix. I guess this could not be due to some
> >> random density, and I have tried to do MR with a irrelevant model
> >> without producing such kind of regular secondary structure.
> >>
> >> This data has a long c axis, and in most parts the density are still not
> >> interpretable. I do not know if this is a good starting point. Could any
> >> one give some suggestions? Many thanks!
> >>
> >> Best,
> >> Niu
> >>
> >>
> >>
> >
