[phenixbb] refinement with several twins / modulated data / pseudo-translational symmetry

iulek iulek at interponta.com.br
Sun Jun 29 09:24:14 PDT 2008


Hi, Paul,

    Thanks four you reply.
    In summary, some warnings, I think the main ones are the off-origin 
peaks in the native Patterson and the twinning operators. I can send you 
the whole output (or snipping the intermediate twin analyses) if you 
like, or post to the bb if appropriate. Concerning twin, I have below:

Statistics depending on twin laws
------------------------------------------------------------------
| Operator  | type | R obs. | Britton alpha | H alpha | ML alpha |
------------------------------------------------------------------
| -k,h+k,l  |  PM  | 0.120  | 0.380         | 0.388   | 0.385    |
| h+k,-h,l  |  PM  | 0.120  | 0.376         | 0.388   | 0.349    |
| -h-k,h,l  |  PM  | 0.120  | 0.371         | 0.388   | 0.350    |
| k,-h-k,l  |  PM  | 0.120  | 0.379         | 0.388   | 0.370    |
| -h,-k,l   |  PM  | 0.106  | 0.391         | 0.408   | 0.392    |
| k,h,-l    |  PM  | 0.108  | 0.382         | 0.399   | 0.401    |
| h,-h-k,-l |  PM  | 0.121  | 0.372         | 0.388   | 0.370    |
| h+k,-k,-l |  PM  | 0.124  | 0.377         | 0.388   | 0.362    |
| -h-k,k,-l |  PM  | 0.123  | 0.377         | 0.387   | 0.373    |
| -k,-h,-l  |  PM  | 0.109  | 0.390         | 0.399   | 0.430    |
| -h,h+k,-l |  PM  | 0.122  | 0.377         | 0.387   | 0.370    |
------------------------------------------------------------------

    Please, let me know if appropriate to send the whole output or ask 
for any further information you find necessary.
    Many thanks once again.

Jorge

> Hi Jorge,
>
>    what does phenix.xtriage say about the data processed in P1?
>
>    Cheers,
> 	Paul
>
> On Jun 29, 2008, at 6:43 AM, iulek wrote:
>
>   
>> Dear all,
>>
>>     I have a strongly modulated dataset as can be observed in the  
>> truncate output below. Specially, the modulation is higher for L  
>> odd/even and at lower resolution:
>>
>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>>
>>   Analysis of mean intensity by parity for reflection classes
>>
>>   For each class, Mn(I/sig(I)) is given for even and odd parity  
>> with respect to the condition,
>> eg group 1: h even & odd; group 7 h+k+l even & odd; group 8 h+k=2n  
>> & h+l=2n & k+l=2n or not
>>
>>  Range    Min_S    Dmax    Nref     1           2            
>> 3           4           5           6           7           8
>>                                     h           k            
>> l          h+k         h+l         k+l        h+k+l    h+k,h+l,k+l
>>      1   0.00018  20.85     519 13.2  8.9   13.9  8.2   22.3  2.4    
>> 13.3  8.9   12.5  9.6   12.9  9.0   12.6  9.5   16.5  9.2
>>      2   0.00230  15.04     994 15.9 16.0   15.3 16.5   30.1  2.3    
>> 15.7 16.2   15.1 16.7   14.9 16.8   15.1 16.7   13.5 16.6
>>      3   0.00442  12.36    1289 17.2 16.0   17.0 16.2   33.8  3.7    
>> 17.2 16.0   14.9 18.0   14.7 18.2   14.9 18.0   13.1 17.4
>>      4   0.00655  10.74    1568 20.7 18.9   20.3 19.2   35.5  4.9    
>> 20.4 19.2   18.7 20.7   18.3 21.0   18.5 20.9   17.7 20.3
>>      5   0.00867   9.63    1759 20.3 15.8   20.1 16.0   33.2  4.9    
>> 20.1 15.9   18.7 17.3   18.6 17.4   18.8 17.2   21.6 16.9
>>      6   0.01079   8.80    2042 19.6 15.4   19.3 15.7   30.5  5.8    
>> 19.5 15.5   17.6 17.3   17.5 17.4   17.6 17.3   19.9 16.7
>>      7   0.01291   8.15    2206 15.9 12.0   15.8 12.1   22.6  5.0    
>> 15.5 12.4   14.3 13.5   14.1 13.7   14.0 13.8   16.2 13.2
>>      8   0.01504   7.63    2393 11.8  9.0   11.5  9.3   18.6  3.6    
>> 11.7  9.1   10.5 10.2   10.3 10.3   10.4 10.3   12.0  9.9
>>      9   0.01716   7.20    2526  9.8  6.5    9.8  6.5   13.8   
>> 3.2    9.8  6.6    9.0  7.3    9.0  7.3    9.0  7.4   11.6  7.1
>>     10   0.01928   6.83    2747 11.1  7.5   11.0  7.6   15.7  3.0    
>> 10.8  7.8   10.0  8.5    9.9  8.6    9.8  8.6   12.3  8.3
>>     11   0.02141   6.52    2867 10.3  7.3   10.2  7.3   14.4  3.0    
>> 10.3  7.3    9.4  8.1    9.4  8.1    9.4  8.2   11.7  7.9
>>     12   0.02353   6.24    3122  8.6  5.8    8.5  5.8   11.6   
>> 3.0    8.4  5.9    7.3  6.9    7.3  6.9    7.2  7.0    8.8  6.6
>>     13   0.02565   6.00    3124  7.9  5.7    7.7  5.9   11.1   
>> 2.9    7.7  5.9    6.8  6.7    6.8  6.8    6.8  6.7    7.8  6.5
>>     14   0.02777   5.78    3346  9.8  6.7    9.7  6.7   12.7   
>> 3.5    9.6  6.8    8.8  7.7    8.7  7.8    8.6  7.9   10.7  7.5
>>     15   0.02990   5.59    3428  9.0  5.6    8.9  5.7   11.2   
>> 3.1    8.8  5.8    7.9  6.7    7.8  6.8    7.7  6.9    9.9  6.4
>>     16   0.03202   5.41    3633  8.3  5.5    8.2  5.5   10.9   
>> 3.5    8.2  5.6    7.1  6.6    7.1  6.6    7.1  6.6    8.8  6.2
>>     17   0.03414   5.25    3658  9.6  6.2    9.4  6.3   12.4   
>> 3.7    9.4  6.4    8.4  7.3    8.4  7.3    8.2  7.5   10.6  7.0
>>     18   0.03627   5.10    3696 10.2  6.4   10.1  6.5   12.5   
>> 4.3    9.8  6.7    8.8  7.8    8.7  7.9    8.6  7.9   10.8  7.4
>>     19   0.03839   4.97    3955 10.1  6.9    9.9  7.0   12.6   
>> 4.5    9.8  7.1    8.8  8.2    8.6  8.3    8.6  8.3   10.4  7.9
>>     20   0.04051   4.84    3902 10.9  7.2   10.9  7.2   13.4  4.6    
>> 10.7  7.4    9.7  8.4    9.7  8.4    9.7  8.4   12.1  8.0
>>     21   0.04263   4.73    4207 11.4  6.8   11.3  6.9   13.7  4.8    
>> 11.1  7.0    9.5  8.5    9.4  8.6    9.5  8.6   12.0  8.1
>>     22   0.04476   4.62    4169  9.7  6.8    9.6  6.9   12.4   
>> 4.6    9.5  7.0    8.3  8.1    8.3  8.2    8.2  8.2    9.7  7.8
>>     23   0.04688   4.52    4100 11.1  6.7   11.0  6.8   12.6  5.5    
>> 10.8  7.0    9.0  8.8    8.9  8.8    8.9  8.9   11.0  8.2
>>     24   0.04900   4.42    4605 10.8  6.5   10.7  6.5   12.3  4.9    
>> 10.5  6.8    9.5  7.8    9.4  7.9    9.3  7.9   12.2  7.5
>>     25   0.05113   4.33    4449  9.6  6.1    9.5  6.2   11.1   
>> 4.6    9.4  6.3    8.3  7.4    8.2  7.5    8.2  7.5   10.2  7.0
>>     26   0.05325   4.25    4528  9.1  5.8    9.1  5.8   10.0   
>> 4.8    8.8  6.0    7.6  7.2    7.5  7.3    7.5  7.3    9.2  6.8
>>     27   0.05537   4.17    4782  8.6  5.3    8.6  5.3    9.7   
>> 4.6    8.5  5.4    7.5  6.5    7.4  6.5    7.4  6.5    9.5  6.1
>>     28   0.05749   4.10    4774  8.3  5.2    8.2  5.3    9.6   
>> 3.9    8.0  5.4    7.0  6.4    7.0  6.4    6.9  6.5    8.6  6.1
>>     29   0.05962   4.02    4837  8.1  5.6    8.1  5.7    9.7   
>> 4.4    7.9  5.8    7.2  6.6    7.2  6.6    7.2  6.6    8.6  6.4
>>     30   0.06174   3.96    5066  8.2  4.9    8.2  4.9    8.9   
>> 4.2    8.0  5.1    6.9  6.2    6.8  6.2    6.7  6.3    8.6  5.8
>>     31   0.06386   3.89    4954  7.4  4.7    7.3  4.8    7.9   
>> 4.1    7.2  4.9    6.2  5.9    6.1  6.0    6.2  5.9    7.5  5.6
>>     32   0.06599   3.83    5052  7.6  4.6    7.6  4.6    8.2   
>> 4.0    7.4  4.8    6.4  5.8    6.4  5.8    6.3  5.9    8.0  5.5
>>     33   0.06811   3.77    5159  6.9  4.4    6.8  4.5    7.2   
>> 4.0    6.6  4.6    5.8  5.4    5.7  5.5    5.6  5.6    6.9  5.2
>>     34   0.07023   3.72    5226  6.7  4.1    6.7  4.2    7.2   
>> 3.8    6.6  4.2    5.6  5.2    5.6  5.2    5.6  5.2    7.0  4.9
>>     35   0.07236   3.66    5359  6.6  4.1    6.6  4.2    6.7   
>> 4.1    6.4  4.4    5.4  5.3    5.4  5.3    5.3  5.4    6.6  5.0
>>     36   0.07448   3.61    5293  6.4  3.9    6.3  3.9    6.9   
>> 3.5    6.2  4.1    5.4  4.8    5.4  4.9    5.4  4.8    6.7  4.6
>>     37   0.07660   3.56    5633  6.7  4.4    6.7  4.4    7.4   
>> 3.7    6.6  4.5    5.8  5.3    5.7  5.4    5.7  5.4    7.0  5.1
>>     38   0.07872   3.52    5479  5.9  3.8    5.9  3.8    6.2   
>> 3.6    5.8  3.9    5.0  4.7    5.0  4.7    5.0  4.7    6.1  4.5
>>     39   0.08085   3.47    5578  5.2  3.3    5.2  3.3    5.4   
>> 3.1    5.0  3.5    4.4  4.0    4.4  4.0    4.3  4.1    5.4  3.8
>>     40   0.08297   3.43    5580  5.3  3.3    5.3  3.3    5.3   
>> 3.3    5.2  3.4    4.6  4.0    4.6  4.1    4.6  4.1    5.8  3.8
>>     41   0.08509   3.39    5936  5.3  3.3    5.3  3.2    5.4   
>> 3.2    5.1  3.4    4.5  4.0    4.5  4.0    4.4  4.1    5.5  3.8
>>     42   0.08722   3.35    5783  4.7  3.0    4.7  3.0    4.5   
>> 3.3    4.6  3.1    3.9  3.8    4.0  3.8    3.9  3.8    4.8  3.6
>>     43   0.08934   3.31    5889  4.4  3.0    4.4  2.9    4.5   
>> 2.9    4.3  3.1    3.8  3.6    3.8  3.5    3.7  3.6    4.5  3.4
>>     44   0.09146   3.27    5966  4.4  2.8    4.5  2.8    4.5   
>> 2.8    4.3  2.9    3.8  3.5    3.8  3.5    3.8  3.5    4.7  3.3
>>     45   0.09358   3.23    6145  4.0  2.6    4.0  2.6    4.1   
>> 2.5    3.9  2.8    3.5  3.2    3.5  3.2    3.5  3.2    4.2  3.0
>>     46   0.09571   3.20    6202  3.6  2.3    3.7  2.3    3.6   
>> 2.3    3.6  2.4    3.2  2.8    3.2  2.7    3.2  2.7    4.0  2.6
>>     47   0.09783   3.16    6042  3.7  2.3    3.8  2.2    3.5   
>> 2.5    3.7  2.3    3.1  2.9    3.1  2.9    3.1  2.9    4.0  2.7
>>     48   0.09995   3.13    6198  3.5  2.2    3.5  2.1    3.3   
>> 2.4    3.4  2.2    2.9  2.8    2.9  2.8    2.9  2.8    3.6  2.6
>>     49   0.10208   3.10    6421  3.3  2.1    3.3  2.1    3.1   
>> 2.3    3.2  2.1    2.7  2.6    2.7  2.6    2.7  2.6    3.4  2.4
>>     50   0.10420   3.07    6403  3.2  2.2    3.3  2.1    3.1   
>> 2.3    3.2  2.2    2.8  2.6    2.8  2.6    2.8  2.6    3.3  2.5
>>     51   0.10632   3.04    6357  2.9  2.0    3.0  1.9    2.8   
>> 2.1    2.9  2.0    2.6  2.4    2.6  2.3    2.6  2.4    3.1  2.2
>>     52   0.10844   3.01    6389  2.6  1.9    2.6  1.9    2.6   
>> 2.0    2.6  1.9    2.4  2.2    2.4  2.2    2.3  2.2    2.8  2.1
>>     53   0.11057   2.98    6580  2.8  1.9    2.8  1.9    2.7   
>> 2.0    2.8  2.0    2.5  2.3    2.4  2.3    2.4  2.3    2.9  2.2
>>     54   0.11269   2.95    6663  2.8  1.9    2.8  1.8    2.7   
>> 1.9    2.7  1.9    2.5  2.1    2.5  2.1    2.5  2.1    3.1  2.0
>>     55   0.11481   2.92    6582  2.6  1.9    2.7  1.8    2.6   
>> 1.9    2.6  1.9    2.4  2.1    2.4  2.1    2.4  2.1    2.9  2.0
>>     56   0.11694   2.90    6572  2.6  1.8    2.6  1.8    2.5   
>> 1.9    2.6  1.8    2.3  2.1    2.3  2.1    2.3  2.1    2.7  2.0
>>     57   0.11906   2.87    6820  2.4  1.7    2.4  1.7    2.3   
>> 1.8    2.4  1.8    2.1  2.0    2.1  2.0    2.1  2.0    2.5  1.9
>>     58   0.12118   2.85    6970  2.3  1.6    2.3  1.6    2.2   
>> 1.8    2.3  1.6    2.0  1.9    2.0  1.9    2.0  2.0    2.3  1.8
>>     59   0.12330   2.82    6717  2.4  1.7    2.5  1.6    2.2   
>> 1.8    2.4  1.7    2.0  2.0    2.0  2.0    2.0  2.0    2.4  1.9
>>     60   0.12543   2.80    5677  2.1  1.6    2.1  1.6    2.0   
>> 1.7    2.0  1.6    1.8  1.8    1.8  1.8    1.8  1.8    2.0  1.8
>>
>>          Totals:         277916  6.4  4.3    6.4  4.3    7.6   
>> 3.2    6.3  4.4    5.5  5.2    5.5  5.2    5.5  5.2    6.6  4.9
>>
>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 
>> !
>>
>>     As you can imagine, I have pseudo-translation peaks , the  
>> strongest at 48 % height (of the origin peak) at 0.0 0.0 0.5, other  
>> two at ~ 30 % height at 0.0 0.5 0.0 and 0.5 0.0 0.0 (and so at 0.5  
>> 0.0 0.5, etc.). The cell is large, 229 229 72 90 90 120, data  
>> processed at several space group options with good statistics; the  
>> highest  symmetry is P622. With much struggle, some solutions from  
>> molecular replacement came out. Basically, the monomers (~274  
>> residues each) makes "strings" (pack of one monomer over the other  
>> in one dimension), then these strings seem to be able to pack  
>> themselves in parallel (within them there must be an up/down  
>> feature) and parallel to the shorter cell axis. Given the cell  
>> dimensions, it seems most probable that I have 48 mol/au, although  
>> I cannot discard 36 mol/au (or even something between, depending  
>> upon the symmetry). I attach a picture of the supposed pack in case  
>> of 48 mol/au, viewed down to the 120 angle. The packing has made me  
>> practically rule out space groups P622 and P312, yet the need for a  
>> 2-fold axis passing through both 0, 1, 0 and 1, 0 0. Whenever I  
>> process the data in a lower space group, xtriage suggests strongly  
>> twinning, and close to 50 % in almost any operation. Also, whatever  
>> space group I choose for refinement, the results are all some how  
>> alike, R-free stucks (with any twinning operation that I can use to  
>> refine) at  about 40/41 %; non-twinned refinement stucks R-free  
>> around 48 %.  The investigated space groups include P321, P6, P3,  
>> P2, C222, C2 and P1 (besides, of course, at the beginning, P622 and  
>> P312), with several combinations of molecules/au (I there might be  
>> screw axes, although no systematic absences). With P1, I have the  
>> lowest reason between R and R-free (because R is higher). I must  
>> add that I have already tested some refinement alternatives, such  
>> as bulk solvent models, fix these, etc., but of course not all  
>> alternatives. Much information has been produced; one other  
>> highlight I think is the fact that most of the time atomic B- 
>> factors are refined to the ground, I suppose because of the  
>> abnormal intensity distribution/data modulation.
>>     I have a couple of questions and other information which I  
>> prefer to number since from now.
>> a) Is there a source of information for refinement of such  
>> modulated data? Or previous cases reported in the literature?
>> b) I have not tried yet P1 with 48 molecules. I run out of chain  
>> ID's, what does phenix accept besides the alphabet and 0-9?
>> c) For P3, with any of the 3  twin operators the result is  
>> practically the same. To my knowledge, only shelxl can deal,  
>> currently, with more that one twinned domain, but  these can only  
>> be produced in a iterative fashion. So, what might be the other way  
>> round? Is this development expected for phenix? For P1, I would  
>> have 11 pseudo-merohedral twin operations... I think the kind of  
>> packing is quite prone to twinning.
>> d) Concerning what is raised in c, how necessary is to combine the  
>> 3 possible twin operators with the 3 reindexing possibilities....
>> e) How can I convince phenix to use the suggested twin operation  
>> 1/2*h-1/2*k,3/2*h+1/2*k,l in C222 (and some others with the *  
>> symbol in C2)?
>>     Much more information is available; I think I could pick the  
>> main ones.
>>     Thanks for any help.
>>
>> Jorge
>>
>> <snapshot35_ed.png>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>     
>
>   
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20080629/d1424f95/attachment-0003.htm>


More information about the phenixbb mailing list