[sharp-discuss] problems in running autoSHARP

[Clemens Vonrhein]

Dear Huanwang,

it seems that your CCP4 binaries are not working properly. Have a look
at the file IF3-C.2/UNIQUEIFY/unique.log: it generates a complete set of
reflections BUT keeps all systematic absent reflections (for C2) in
there, so the file has 12824 reflections! When I run this script:

unique hklout dummy.mtz <<end_ip
CELL     72.4178   30.1989   43.3259   89.9999  100.1119   90.0001
SYMM 5
RESO 2.000
LABO F=FUNI SIGF=SIGFUNI
END
end_ip

I get a file with 6413 reflections - no matter if I use CCP4 4.1.1 or
the latest 4.2. Obviously, from that point onwards your MTZ file is
wrong. So let's try fixing this problem first (which hopefully will
fix the crash in SHARP later on).

Things I could think of that might have gone wrong:

  1. using a buggy compiler for compilation (see RedHat/Linux specific
     discussions on CCP4BB and the CCP4 webpage)

  2. not using the latest CCP4 version, i.e. either the 4.1.1 patch
     release or the latest 4.2 (binaries are available for both from
     www.ccp4.ac.uk)

  3. maybe your $BDG_home/database/symop file got corrupted? The C2
     entry should look like this:

     5 4 2 C2 PG2 MONOCLINIC 'C 1 2 1' 
       X,Y, Z 
      -X,Y,-Z 
      1/2+X,1/2+Y,Z 
      1/2-X,1/2+Y,-Z

  4. some other random problems (general Linux OS bugs like glibc
     etc).

  5. maybe you could try to get in contact with the CCP4
     people/community.

I would upgrade your CCP4 version to at least 4.1.1 or (probably
better) 4.2 (although some incompatibilities are still not finally
resolved on my side ... SUSHI 3.0.10 is kind of imminent!).

Let me know if this helps.

Cheers

Clemens



On Thu, Jun 27, 2002 at 09:56:30AM -0500, Huanwang Yang wrote:
> Dear Clemens:
> 
> I thought that the autoSHARP was working. Actually, it is not. I directly
> used the provided
> data IF3-C. I selected this file and started autoSHARP. After about 1 hour
> and half. It stopped
> at step 4.2 .
> 
>    4.2 Run first round of SHARP
> 
>    (details)    (explanation)    (2 seconds)
> 
>  ERROR   : (see    SHARP_INIT/LISTautoSHARP.html)
> 
> I  looked at SHARP_INIT/LISTautoSHARP.html. It gives the following message:
> 
> 
> 1. running SHARP to refine initial set of sites
> 
>    [directory IF3-C.2] SHARP log file
> 
>  ERROR   : in running SHARP
> 
> I really do not know what is the problem.

-- 

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