[phenixbb] Creating files with positive and negative map peaks

Pavel Afonine PAfonine at lbl.gov
Wed Jul 23 14:36:52 PDT 2008


Hi Jennifer,

ok, I can add this option.

Just curious... why you need to format it this way? Also, what is in 
B-factor column?

Pavel.


On 7/23/2008 2:26 PM, Jennifer Ekstrom wrote:
> Hi Pavel,
> I'm actually looking for a way to get that peak data into the the format 
> given by cns.  I've pasted an example below... 
>
> Thanks,
> Jennifer
>
> ......................
>
> REMARK DATE:16-Jan-2008  04:53:47       created by user: ekstrom
> REMARK VERSION:1.1
> ATOM   6706 PEAK PEAK    1       2.936 -26.732   8.585  1.00 12.12      PEAK
> ATOM   6707 PEAK PEAK    2     -29.892 -17.631  49.107  1.00 11.30      PEAK
> ATOM   6708 PEAK PEAK    3     -22.298 -14.560  50.705  1.00  9.38      PEAK
> ATOM   6709 PEAK PEAK    4      -0.284 -37.687  22.843  1.00  8.50      PEAK
> ATOM   6710 PEAK PEAK    5     -26.184 -10.173  38.207  1.00  8.43      PEAK
> ATOM   6711 PEAK PEAK    6     -27.455 -11.757  37.651  1.00  7.88      PEAK
> ATOM   6712 PEAK PEAK    7       0.251 -36.207  17.111  1.00  7.54      PEAK
> ATOM   6713 PEAK PEAK    8     -36.967   7.877  42.542  1.00  7.44      PEAK
> ATOM   6714 PEAK PEAK    9       1.491 -38.169  16.878  1.00  7.44      PEAK
> ATOM   6715 PEAK PEAK   10     -27.501 -10.922  37.959  1.00  7.35      PEAK
> ATOM   6716 PEAK PEAK   11       4.477 -45.133  14.678  1.00  7.21      PEAK
> ATOM   6717 PEAK PEAK   12      -0.963 -25.803  18.167  1.00  7.04      PEAK
> ATOM   6718 PEAK PEAK   13     -26.482 -13.615  36.693  1.00  6.93      PEAK
> ATOM   6719 PEAK PEAK   14     -26.015 -10.239  30.585  1.00  6.86      PEAK
> ATOM   6720 PEAK PEAK   15     -30.002 -26.868  20.550  1.00  6.69      PEAK
> ATOM   6721 PEAK PEAK   16     -27.396 -11.906  38.698  1.00  6.65      PEAK
> ATOM   6722 PEAK PEAK   17     -31.373  -6.638  28.568  1.00  6.64      PEAK
> ATOM   6723 PEAK PEAK   18      -8.221 -55.948   9.682  1.00  6.53      PEAK
> ATOM   6724 PEAK PEAK   19     -28.291 -23.724  37.848  1.00  6.28      PEAK
> ATOM   6725 PEAK PEAK   20     -30.468 -30.466  41.446  1.00  6.18      PEAK
> ATOM   6726 PEAK PEAK   21     -31.063 -29.443  40.172  1.00  6.12      PEAK
> ATOM   6727 PEAK PEAK   22     -26.755 -11.332  32.107  1.00  6.07      PEAK
> ATOM   6728 PEAK PEAK   23       1.773 -36.238  17.792  1.00  6.05      PEAK
> ATOM   6729 PEAK PEAK   24     -29.413 -25.920  38.032  1.00  6.04      PEAK
> ATOM   6730 PEAK PEAK   25     -28.233 -22.681  37.519  1.00  6.03      PEAK
> ATOM   6731 PEAK PEAK   26     -16.125 -21.401  26.461  1.00  5.99      PEAK
> ATOM   6732 PEAK PEAK   27       0.732 -34.913  18.222  1.00  5.98      PEAK
> ATOM   6733 PEAK PEAK   28     -27.046  -9.637  32.604  1.00  5.90      PEAK
> ATOM   6734 PEAK PEAK   29     -29.019 -24.193  39.115  1.00  5.87      PEAK
> ATOM   6735 PEAK PEAK   30       2.977 -35.032  16.644  1.00  5.76      PEAK
> END
>
>
> Pavel Afonine wrote:
>   
>> Hi Jennifer,
>>
>> phenix.refine reports the list of highest peaks and deepest holes 
>> found at difference map. Look towards the end of .log file for lines 
>> like this:
>>
>> ========== residual map mFobs-DFmodel: highest peaks and deepst holes 
>> =========
>>
>>
>>                            
>> ----------peaks----------                          
>>
>> Number of peaks found at mFobs-DFmodel map (map cutoff=3.50 sigma)= 
>> 21         
>> Filter by distance & map next to the model:
>>    mapped sites are within: 1.002 - 3.227
>>    number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 20 
>> from: 21
>>    mapped sites are within: 1.002 - 3.227
>>
>> peak=    4.154 closest distance to pdb=" N   VAL     2 " =    2.881
>> peak=    3.572 closest distance to pdb=" O   VAL     2 " =    2.663
>> peak=    3.895 closest distance to pdb=" CB  ARG     5 " =    2.743
>> peak=    4.186 closest distance to pdb=" N   GLU     7 " =    2.237
>> peak=    4.958 closest distance to pdb=" OE1 GLU     7 " =    2.920
>>
>> Same for negative peaks.
>>
>> Please let us know if you have any questions!
>>
>> Pavel.
>>  
>>
>>
>> On 7/23/2008 1:22 PM, Jennifer Ekstrom wrote:
>>     
>>> I would like to obtain a file with a listing of positive and negative 
>>> difference map peaks, similar in formatting and content to the files 
>>> that would come out of cns: 
>>>
>>>          positive peaks in: <output_root>_positive.peaks
>>>          negative peaks in: <output_root>_negative.peaks
>>>
>>>
>>> We need this for use in DDQ at the jcsg validation server 
>>> (http://www.jcsg.org/prod/scripts/validation/sv2.cgi).  Is there an easy 
>>> way to create these peak files in phenix.refine?  We'd prefer to not 
>>> re-refine in CNS as we have *many* alternate conformations... 
>>>
>>> Thanks, Jennifer
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>   
>>>       
>
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