[phenixbb] Fix for autobuild/ligandfit problem with long $PATH
terwilliger at lanl.gov
Thu Jun 25 08:26:16 PDT 2009
Hi Phenix users,
Several of you have had trouble with phenix.autobuild (or
phenix.ligandfit) failing if you had a very long $PATH. The problem
seems to be that if your $PATH is very long, then adding more to it
and re-setting it can lead to a string that is too long (on some
systems). Starting with PHENIX version 1.4-100 (today's version) you
can add the keyword
remove_path_word_list=" cns xiaroot ccp4 phaser"
to shorten your $PATH. This keyword will selectively remove all paths
from $PATH that include any of the words you specify, and that do not
include the word "phenix", when running that phenix job. The log file
will list what paths were removed.
To figure out what paths to remove, type
and choose the ones that identify other programs that are not part of
phenix. I hope that will do it! Please let me know if this doesn't
solve the problems.
All the best,
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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