[phenixbb] Analyzing MIR datasets

[Tom Terwilliger]

Hi Sena,

I'm sorry for the trouble! There is supposed to be an earlier error  
message that helps you more than that one, and it is not getting  
printed here.

Can you try these things:

1.  What version of phenix is this (hopefully 1.5-2, if not...that is  
the place to start).
2. Try these commands

phenix.autosol show_labels= iafinal_d212121.mtz
phenix.autosol show_labels=s10final_d212121.mtz
phenix.autosol show_labels=s23final_d212121.mtz

3. You can then use the labels="xxxx" that are output from step 2 (see  
the labels for "autosol")  from this as an extra line for each input  
file in your parameters file like this:

   native {
     data = iafinal_d212121.mtz
     labels="I,SIGI"
  }

Also if you want to send me directly (terwilliger at lanl.gov) these data  
files it may help me fix autosol so that it gives a better error  
message...

All the best,
Tom T

On Nov 5, 2009, at 3:43 PM, Rajagopalan, Senapathy wrote:

> Hi All,
>
> I am a new user to Phenix and am trying to process MIR datasets from  
> a parameter file typing ‘phenix.autosol mir.eff’ and keep running  
> into the error message saying:
>
>
> _______________
> Possible choices:
>   /Users/sena/data/crystallography/raw1025/Processing/ 
> iafinal_d212121.mtz:I,SIGI,merged
>   /Users/sena/data/crystallography/raw1025/Processing/ 
> iafinal_d212121.mtz:IPR,SIGIPR,merged
>
> Please use scaling.input.xray_data.obs_labels
> to specify an unambiguous substring of the target label.
>
> Unable to get range of aniso B from xtriage output
> Multiple equally suitable arrays of observed xray data found.
>
> ********************************************************************************
> Failed to carry out AutoSol_scale_and_analyze_mir:
>
> Sorry, there is something wrong with the file /Users/sena/data/ 
> crystallography/raw1025/Processing/iafinal_d212121.mtz ... xtriage  
> cannot analyze it?
> ********************************************************************************
> ___________________
>
> The ‘mir.eff’ file contains:
>
> ------------------
> #
> autosol {
>   seq_file = sequence.dat
> #scaling.input.xray_data.obs_labels='I SIGI'
> #  xray_data_labels = FP, SIGFP
> #  autosol.input.xray_data.labels=FP
> labels='I SIGI'
>   crystal_info {
>     space_group = p212121
>     unit_cell = 49.020  73.140 187.350  90.000  90.000  90.00
>   }
>   native {
>     data = iafinal_d212121.mtz
>  }
>   deriv {
>     data = s10final_d212121.mtz
>     atom_type = I
> sites = 2
>     inano = noinano *inano anoonly
>   }
>   deriv {
>     data = s13final_d212121.mtz
>     atom_type = I
>     sites = 1
>     inano = noinano *inano anoonly
>   }
> deriv {
>     data = s23final_d212121.mtz
>     atom_type = I
>     sites = 1
>     inano = noinano *inano anoonly
>   }
> }
> -----------------
>
> I guess the error comes because the program is not able to make a  
> choice as to which columns to take from the mtz file. But no matter  
> what ‘label’ syntax I use or where I use it, it doesn’t seem to  
> help. Obviously, I am missing something here. So could someone  
> please help me with this. Also, I tried the same thing using the  
> phenix wizard and it still gives me the same error.
>
> Thanks
> Sena
>
>
>
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss




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