[phenixbb] AutoSol problem

Tom Terwilliger terwilliger at lanl.gov
Tue Jul 31 09:57:30 PDT 2007

Hi Ben,

I'm sorry for the problem!   No, the separate installation of SOLVE 
should not affect the running of SOLVE in phenix. All the 
environmental variables in phenix are set on the fly.

Can you try a couple things for me:

1. Just run solve by itself:


Does this load up? If you then say


does it end nicely?

2.  If that works, can you send me the output where SOLVE bombed in 
phenix. There should be a log file like: LAST.LOG in the working 
directory that should have error messages at the end.  Alternatively, 
if you can send the very last log files written to the TEMP0 
subdirectory of the working directory that would do it.

3. If you can send me the whole logfile that would be great too.

thank you!
-Tom T

At 10:33 AM 7/31/2007, you wrote:

>One of my users is running the Linux 64-bit version of Phenix-1.3b and
>they are getting the following message at the end of their logfile:
>Failed to carry out AutoSol_scale_and_analyze_mad:
>None of the solve versions worked
>The solve part of Phenix looks like it built correctly:
>  $ ls -l phenix-1.3b/build/intel-linux-2.6-x86_64/solve_resolve/exe/
>-rwxr-xr-x 1 sbgrid sbgrid  1561344 Jun 27 16:55 extract_segment
>-rwxr-xr-x 1 sbgrid sbgrid  1561344 Jun 27 16:55 extract_segment_pair
>-rwxr-xr-x 1 sbgrid sbgrid  3483160 Jun 27 16:55 resolve
>-rwxr-xr-x 1 sbgrid sbgrid  3483576 Jun 27 16:55 resolve_extra_huge
>-rwxr-xr-x 1 sbgrid sbgrid  3483256 Jun 27 16:55 resolve_giant
>-rwxr-xr-x 1 sbgrid sbgrid  3482968 Jun 27 16:55 resolve_huge
>-rwxr-xr-x 1 sbgrid sbgrid  1768392 Jun 27 16:55 resolve_pattern
>-rwxr-xr-x 1 sbgrid sbgrid  1768392 Jun 27 16:55 resolve_pattern_extra_huge
>-rwxr-xr-x 1 sbgrid sbgrid  1768392 Jun 27 16:55 resolve_pattern_giant
>-rwxr-xr-x 1 sbgrid sbgrid  1768392 Jun 27 16:55 resolve_pattern_huge
>-rwxr-xr-x 1 sbgrid sbgrid  1547840 Jun 27 16:55 segment_library
>-rwxr-xr-x 1 sbgrid sbgrid  1575648 Jun 27 16:55 side_chains
>-rwxr-xr-x 1 sbgrid sbgrid  1566208 Jun 27 16:55 side_chains_update
>-rwxr-xr-x 1 sbgrid sbgrid  5327984 Jun 27 16:55 solve
>-rwxr-xr-x 1 sbgrid sbgrid 11331152 Jun 27 16:55 solve_extra_huge
>-rwxr-xr-x 1 sbgrid sbgrid  6529136 Jun 27 16:55 solve_giant
>-rwxr-xr-x 1 sbgrid sbgrid  7729424 Jun 27 16:55 solve_huge
>-rwxr-xr-x 1 sbgrid sbgrid 11393392 Jun 27 16:55 solve_mx
>  $ file phenix-1.3b/build/intel-linux-2.6-x86_64/solve_resolve/exe/solve
>phenix-1.3b/build/intel-linux-2.6-x86_64/solve_resolve/exe/solve: ELF 64-bit
>LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.4.0, statically
>linked, for GNU/Linux 2.4.0, stripped
>We do have a standalone Solve install with its corresponding SOLVEDIR, etc,
>environment variables.  Could that be confusing Phenix?
>I have the complete logfile, but it's rather long.  If it would help, it
>can be made available.
>Any ideas on what I should do to troubleshoot this?
>Ben Eisenbraun
>Structural Biology Grid
>phenixbb mailing list
>phenixbb at phenix-online.org

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

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