[phenixbb] error message running example

Tom Terwilliger terwilliger at lanl.gov
Wed Nov 7 13:49:58 PST 2007

Hi Norman,

I'm very sorry for this problem!  I am puzzled...it sounds like somehow
SOLVE cannot write to the directory it is working in. (I have never seen
this one before!)

Can you try this: go to your home directory, make a subdirectory "test"
there, get in the directory, and copy $PHENIX/examples/nsf-d2-sad/peak.sca
to this subdirectory.  Then run autosol by hand. Then (fail or not) do an
ls -lt to show what the permissions are. Like this:

mkdir test
cd test
cp $PHENIX/examples/nsf-d2-sad/peak.sca .
phenix.autosol peak.sca quick=True build=False debug=True |tee test.log
ls -lt

If this works (you'll know because it gets past scaling and starts doing
phasing)...it is file permissions of some sort.  If it fails, hopefully
something in test.log or AutoSol_run_1_/LAST.log or the "ls -lt" output
will tell me something...

Thank you!
-Tom T
ps. I did get your email yesterday on the help BB, but I replied to 
an incorrect email address. I'm sorry about that too!

At 06:01 AM 11/7/2007, you wrote:
>Content-class: urn:content-classes:message
>Content-Type: multipart/alternative;
>         boundary="----_=_NextPart_001_01C8213E.3EA9AF22"
>Hi -
>I tried to run the example:
>phenix.run_example gene-5-mad
>However, it stopped, with following error messages:
>Done with gene-5-mad ...Your results are in the directory: 
>Missing the summary file: gene-5-mad/AutoSol_run_1_/
>Something did not work properly...not all output files produced
>and the LAST.LOG reports:
>  ***************************************************************************
>    6769                     SOLVE STATUS      07-nov-07 12:47:15
>    6770
>    6771  DATASET TITLE: 
> SOLVE     07-Nov-07                                           STATUS
>    6773 
> ---------------------------------------------------------------------------
>    6774  Sorry -- ERROR ENDING.  SEE the end of  your log file or 
> output   STATUS
>    6775   and solve.log
>    6776   for more information    STATUS
>Any idea what is going wrong? (phenix version 1.3 beta rc4, 64bit 
>computer, 2 dual core proc.)
>Many thanks,
>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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