Dear Niu, To me, it looks like random density. Since coot contours are based on sigma levels, you will always see features. I do not think you can do anything with your current map. As others have said, it is always a good idea to test ALL possible space groups, even if you are convinced it is P2. It only takes CPU time and, compared to trying to build in uninterpretable maps, very little time of yourself. Make sure to run the jobs in different directories, so the results do not get mixed up.
The other thing to do would be to look at the diffraction images: are all spots sharp, or are some spots smeared? Are the spots with even L much stronger then the spots with odd L? Is your off-origin peak at c=0.5 (fractional) or at some random position? How many molecules do you expect based on a Matthews calculation? Are you sure the protein in the crystals is the protein you think it is? Since P2 is a very low-symmetry space group, the first thing I would do is to process the data in P1 and run Phaser in P1. In that case you do not have to worry about the space group etc. Once you get a solution, you can use Zanuda to find the correct space group. If you have a pseudo-translation (all L=odd reflections weak), you could also consider processing the data with the c-axis forced to be half the current length and running molecular replacement with that data. The solution will be approximate but can give you valuable information about the true packing. With an off-origin peak of 95% of the origin peak, the solution will not be far off. Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Niu Tou Gesendet: Freitag, 15. November 2013 00:58 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Weird MR result 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. 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<mailto: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
