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Hi Lijun, once you solved and refined the structure, and you used for this the anisotropy truncated data, please PDB deposit both: manipulated data (the one you used for refinement the model), and the original dataset. This is very important. One day the software will be able to handle highly anisotropic datasets correctly, so you would not need to apply some suspicious manipulations to it anymore. Pavel. On 7/21/10 4:18 PM, Lijun Liu wrote: > Ed, > > Thanks for the comment! Anisotropic correction hits the problem, and > makes good > improvement! > > You suggestion about one strong reflection around 2.1 Å is very > interesting. > However, one single reflection's (along c*) ripples passes along c and > give sin/cos > pattern along c, which means along c everywhere should give such a > residual map > pattern throughout the unit cell, which is not observed. As I > mentioned, only several > small regions showed such residual maxima (please do not argue with me > I also had > lost 1 or 2 big low ordered reflections, :). Also, this reflection > needs to be very strong and > should not be overload-ignored during processing. Anyway, reflections > (0 0 39-41) are > pretty weak or normal. Cheers, the great FT!!! > > Lijun > > On Jul 21, 2010, at 2:28 PM, Edward A. Berry wrote: > >> Another possible cause of this "layering" might be a single strong >> "rogue" reflection at about 2.1A along the C* axis. Since hex ice >> has a lattice spacing around here, a single crystal of ice (a snowflake >> captured from the LN2 or growing on the crystal in the cold stream) >> could result in such spots. If one of them was close enough to the >> predicted spot of your crystal, it could get integrated and show up >> in your data list. >> Not an ice ring, you understand, but an ice diffraction spot >> appearing to be a protein diffraction spot. I think this is >> what Phoebe was referring to. >> >> If the anisotropy correction doesn't give a good map, try making >> a map with resolution limited to 2.3 A. If that looks ok, extend >> the resolution in small steps through the 2.1A range. If you layers >> suddenly returns with one of these steps, you could eliminate a thin >> shell, or narrow it down to the particular spot and eliminate that. >> -ed- >> >> Lijun Liu wrote: >>> No. No ice ring! Sorry I meant the strongest amplitudes of (Fo-Fc) at >>> the 2.1 A around region in the reciprocal space, not the strongest >>> densities on real space images. As Pavel suggested, this is a good case >>> of anisotropicity. In my original email, I used "polarized" pattern to >>> address this---I used the wrong nomenclature to address the same thing, >>> I think. Lijun >>> >>> >>>> Could any of those strong spots at 2.1 be ice? >>>> >>>> ---- Original message ---- >>>>> Date: Tue, 20 Jul 2010 16:13:31 -0700 >>>>> From: Lijun Liu <[log in to unmask] <mailto:[log in to unmask]>> >>>>> Subject: Re: [ccp4bb] Residual densities! >>>>> To: [log in to unmask] <mailto:[log in to unmask]> >>>>> >>>>> Pavel, >>>>> Thanks for the quick response. I just listed out >>>>> the Fo-Fc column of the reflection files, and it >>>>> looks the strongest densities are mostly along c* >>>>> and many located in the 2.1A region. I think you >>>>> may be right. >>>>> Lijun >>>>> On Jul 20, 2010, at 4:05 PM, Pavel Afonine wrote: >>>>> >>>>> Hi, >>>>> >>>>> It looks like the data is highly anisotropic - >>>>> I've seen it many times. You can either apply >>>>> anisotropy correction >>>>> (http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/ >>>>> <http://www.doe-mbi.ucla.edu/%7Esawaya/anisoscale/>) >>>>> or use PHENIX tools to compute the maps - anyone >>>>> of both should help. The major difference between >>>>> the two is that PHENIX will not modify your >>>>> original data in any way. Let me if using PHENIX >>>>> map calculation tools does not help. >>>>> >>>>> Cheers, >>>>> Pavel. >>>>> >>>>> On 7/20/10 3:19 PM, Lijun Liu wrote: >>>>> >>>>> Hi all, >>>>> I solved a structure and the refinement is close >>>>> to complete. However, some residual density >>>>> puzzles me. >>>>> The SG is P212121, and the c is 84.8 Å. Along >>>>> c, in several small but not all regions, there >>>>> are some layered, alternately appeared positive >>>>> and negative residual density pieces (c is the >>>>> norm of these plane-like pieces; 3-sigma contour >>>>> for pos and neg difference densities). The >>>>> distance between the neighboring positive pieces >>>>> is measured to be ~2.1 Å, corresponding to >>>>> ~1/40 *c. In one of such region, there is an >>>>> indole ring of Trp that is approximately >>>>> parallel to the plane-like residual density >>>>> pieces (attached figure). In two other regions, >>>>> there are Leu or else but not ring structure. >>>>> The data is complete to 1.9 Å. Reflection >>>>> check did not show any special imcompleteness >>>>> (ice ring loss, wedge loss, other resolution bin >>>>> loss, etc). It looks like to me that there is a >>>>> systematic loss of information which made it is >>>>> specially sensitive to ~2.1 Å reflections >>>>> (especially those along c*). It does not look >>>>> like to me to be radiation damage. Crystal was >>>>> needle and showed somehow polarized (but never >>>>> serious) diffraction pattern along c*. >>>>> Attached is a piece of map with the >>>>> above-mentioned Trp included. I would like to >>>>> know if some one also met something like this >>>>> before. Thanks for any comments. >>>>> Lijun Liu >>>>> Cardiovascular Research Institute >>>>> University of California, San Francisco >>>>> 1700 4th Street, Box 2532 >>>>> San Francisco, CA 94158 >>>>> Phone: (415)514-2836 >>>>> >>>>> Lijun Liu >>>>> Cardiovascular Research Institute >>>>> University of California, San Francisco >>>>> 1700 4th Street, Box 2532 >>>>> San Francisco, CA 94158 >>>>> Phone: (415)514-2836 >>> >>> Lijun Liu >>> Cardiovascular Research Institute >>> University of California, San Francisco >>> 1700 4th Street, Box 2532 >>> San Francisco, CA 94158 >>> Phone: (415)514-2836 >>> >>> >>> >> > > Lijun Liu > Cardiovascular Research Institute > University of California, San Francisco > 1700 4th Street, Box 2532 > San Francisco, CA 94158 > Phone: (415)514-2836 > > >