Hi Dale,

this tells me that phenix.refine does not see the free-r flags in exptl_fobs_freeR_flags.mtz file. I'm not sure how Autobuild managed to run phenix.refine in this case.

Tom is not available until Jan 21. Meanwhile I can try to debug it myself. To do so I need to reproduce this problem. Could you please send me the model and data and the exact commands (for autobuild and phenix.reifne) you used (send it to my mailbox and not to bb)? If the model / data are confidential feel free to manipulate them somehow (randomize the data, remove half of the model, ...) but make sure the program still fail.

Also, I noticed that you are using an old version of PHENIX (I replaced "main.high_resolution=" with "xray_data.high_resolution=" a while ago). Since we keep improving things and many bugs were fixed since that time, it could be a good idea to try to run this with the latest version of PHENIX (I can do this if you send me the data).

Thanks!
Pavel.


On 1/2/2008 4:47 PM, Dale Tronrud wrote: 
Thomas C. Terwilliger wrote:
  
Hi Dale,

Can you try something else:

phenix.refine    AutoBuild_run_12_/overall_best.pdb \
 refinement.input.xray_data.file_name=\
 AutoBuild_run_12/exptl_fobs_freeR_flags.mtz \
  refinement.main.high_resolution=2.2 refinement.main.low_resolution=20 \
           /usr/users/dale/geometry/chromophores/bcl_tnt.cif


This differs from your run only by substituting

AutoBuild_run_12/exptl_fobs_freeR_flags.mtz

for your 2 refinement data files.  This is the exact file that is used in
refinement by AutoBuild.

    

    I tried this command, very similar to yours:

  phenix.refine AutoBuild_run_12_/overall_best.pdb \
   refinement.input.xray_data.file_name=AutoBuild_run_12_/exptl_fobs_phases_freeR_flags.mtz \
   refinement.main.high_resolution=2.2 refinement.main.low_resolution=20 \
   /usr/users/dale/geometry/chromophores/bcl_tnt.cif output.prefix=junk2

The final output was:

F-obs:
   AutoBuild_run_12_/exptl_fobs_phases_freeR_flags.mtz:FP,SIGFP

If previously used R-free flags are available run this command again
with the name of the file containing the original flags as an
additional input. If the structure was never refined before, or if the
original R-free flags are unrecoverable, run this command again with
the additional definition:

refinement.main.generate_r_free_flags=True

If the structure was refined previously using different R-free flags,
the values for R-free will become meaningful only after many cycles of
refinement.

Sorry: Please try again.

The output from mtz.dump for your .mtz is

Processing: AutoBuild_run_12_/exptl_fobs_phases_freeR_flags.mtz
Title: Resolve mtz file.
Space group symbol from file: P
Space group number from file: 212
Space group from matrices: P 43 3 2 (No. 212)
Point group symbol from file: 43
Number of crystals: 2
Number of Miller indices: 38159
Resolution range: 75.6238 2.14896
History:
   From resolve_huge, 27/12/07 15:07:56
Crystal 1:
   Name: HKL_base
   Project: HKL_base
   Id: 0
   Unit cell: (169.1, 169.1, 169.1, 90, 90, 90)
   Number of datasets: 1
   Dataset 1:
     Name: HKL_base
     Id: 0
     Wavelength: 0
     Number of columns: 0
Crystal 2:
   Name: allen-
   Project: FMO-ct
   Id: 2
   Unit cell: (169.1, 169.1, 169.1, 90, 90, 90)
   Number of datasets: 1
   Dataset 1:
     Name: 1
     Id: 1
     Wavelength: 0
     Number of columns: 9
     label      #valid  %valid    min      max type
     H           38159 100.00%   0.00    38.00 H: index h,k,l
     K           38159 100.00%   2.00    78.00 H: index h,k,l
     L           38159 100.00%   0.00    55.00 H: index h,k,l
     FP          38159 100.00%  32.00 15171.00 F: amplitude
     SIGFP       38159 100.00%  23.00  1716.00 Q: standard deviation
     PHIM        38159 100.00% -90.00    45.00 P: phase angle in degrees
     FOMM        38159 100.00%   0.00     0.00 W: weight (of some sort)
     FreeR_flag  38159 100.00%   0.00    19.00 I: integer
     FC          38159 100.00%   0.00     0.00 F: amplitude

Dale Tronrud

  
I agree that you should be able to use your original data file instead.  A
possible reason why this has failed is that the original data file has a
couple reflections for which there is no data...and which were tossed by
AutoBuild before creating exptl_fobs_freeR_flags.mtz . Two files that
differ only in reflections with no data will still give different
checksums, I think.

All the best,
Tom T

    
Hi Dale,

      
1) Why you specify reflection MTZ file twice in phenix.refine script?


          
    I put the mtz in twice because if I put it in once phenix.refine
complains that I have no free R flags.  It seems to want one file with
the amplitudes and another with the flags.  Since I have both in the
same file I put that file on the line twice and phenix.refine finds
everything it needs.

        
phenix.refine looks for free-R flags in your main data file
(1M50-2.mtz). Optionally you can provide a separate file containing
free-R flags (I have to write about this in the manual). However, if
your  1M50-2.mtz contains free-R flags then you don't need to give it
twice. So clearly something is wrong at this step and we need to find
out what is wrong before doing anything else. Could you send the result
of the command "phenix.mtz.dump 1M50-2.mtz" to see what's inside of your
data file? Or I can debug it myself if you send me the data and model.

      
    If the MD5 hash of the test set depends on the resolution then
certainly
I could be in trouble.
        
No. It must always use the original files before any processing.

      
    Does the resolution limit affect the MD5 hash of the test set?

        
No.  If it does then it is a very bad bug. I will play with this myself
later tonight.

      
3) Does this work:

(...)
          
    I'll try these but it will take a bit of time.

        
Don't run it until completion. Just make sure it passed through the
processing step.

Pavel.

_______________________________________________
phenixbb mailing list
[email protected]
http://www.phenix-online.org/mailman/listinfo/phenixbb

      
_______________________________________________
phenixbb mailing list
[email protected]
http://www.phenix-online.org/mailman/listinfo/phenixbb
    
_______________________________________________
phenixbb mailing list
[email protected]
http://www.phenix-online.org/mailman/listinfo/phenixbb