[phenixbb] Fix for autobuild/ligandfit problem with long $PATH

Tom Terwilliger 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

echo $PATH

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,
Tom T

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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