[phenixbb] autobuild wizard question

Tom Terwilliger terwilliger at lanl.gov
Sun Aug 19 16:47:29 PDT 2007

Hi Jeff,

I'm sorry for the trouble with the AutoBuild Wizard!

I was not able to duplicate the problem with my 
version and putting in a model with 2 chains and 
trying to do rebuild_in_place of just a few 
residues, unfortunately.  Everything seemed to 
work as it is supposed to.  Can you check a couple things:

1. Make sure you have the latest version of 
PHENIX (development version) from the website.
2. Make sure that the range of residues you want 
to rebuild is at least 2 in from each end of the 
chain (so if the chain is 1-350, you can rebuild 
3-6 or 347-348 but not 340-350).
3. If you accidentally give the Wizard a range 
that is too big, it should give you an error 
message and stop, but if you fix the range then it should go on.
4. Try running the Wizard from the command line, 
and specify "verbose=True debug=True" which will 
help because it gives you a lot of output that 
may help figure out what is going on. You will 
need to add also " |tee debug.log" to catch the output from this run.

If none of those things help, then if you can 
send me the AutoBuild_run_xx_.output file from 
your GUI-version run and the output from running 
from the command line; that may help me figure out what is going wrong.

-Tom T

Jeff Habel wrote:

>I’m a new PHENIX user and having trouble with the Autobuild wizard.
>The structure has 2 molecules in the asymmetric 
>unit and I am trying to build a small portion 
>(286-297) of both chains.  I have tried building 
>both at the same time and trying just chain A 
>but always receive the error about needing 2 
>amino acids on either end for anchoring the 
>build.  Every time I alter the build range (284
 etc) the error persists.
>Any suggestions would be appreciated.

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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