[phenixbb] The phenix autobuilder does not find buccaneer

Mon Jan 10 11:30:10 PST 2011

Hi Pietro,

autobuild looks for:

1. cbuccaneer
2. ability to run cbuccaneer with
$PHENIX/phenix/phenix/autosol/run_buccaneer.py

Can you try running buccaneer with:

phenix.python $PHENIX/phenix/phenix/autosol/run_buccaneer.py <mtz> <seq>
<output_file> <'labin-line'>

Does that run?

If not, and your standard command-line version of cbuccaneer runs...then I
need to update run_buccaneer.py.

Let me know!
All the best,
Tom T

>> Dear all,
>>
>> I have Buccaneer 1.5.0:
>>
>> partyring:~/Projects/Japanin/autoBUSTER> $CBIN/cbuccaneer
>> <B><FONT COLOR='#FF0000'><!--SUMMARY_BEGIN-->
>> <html> <!-- CCP4 HTML LOGFILE -->
>> <hr>
>> <pre>
>>
>>  ###############################################################
>>  ###############################################################
>>  ###############################################################
>>  ### CCP4 6.1: cbuccaneer             version 1.5.0 : 28/05/10##
>>  ###############################################################
>>  User: pietro  Run date: 10/ 1/2011 Run time: 17:18:57
>>
>>
>> and yet the phenix autobuilder fails - saying I need 1.3.0 or higher (see
>> below)
>>
>> What environment variable is being checked and what should I
>> set for the phenix autobuilder to be able to detect buccaneer?
>>
>> Thanks
>>
>> Regards
>>
>> Pietro
>>
>>
>> ****************************************
>> AutoBuild Input failed
>> Sorry, the necessary version of BUCCANEER does not seem to be available..
>>  For BUCCANEER model building you need CCP4 version 6.1.2 or higher and
>> BUCCANEER version 1.3.0 or higher
>>
>> ****************************************
>> ________________________________________
>> From: phenixbb-bounces at phenix-online.org
>> [phenixbb-bounces at phenix-online.org] On Behalf Of Pavel Afonine
>> [pafonine at lbl.gov]
>> Sent: 07 September 2010 17:56
>> To: PHENIX user mailing list
>> Subject: Re: [phenixbb] will phenix.fmodel automatically generates and
>> takes into account the TLS B by reading the TLS REMARK from pdb?
>>
>>   Hi Hailiang,
>>
>>> For the pdb file generated by refmac which contains only the residual-B,
>>> will phenix.fmodel automatically generates and takes into account the
>>> TLS
>>> B by reading the TLS REMARK from pdb? Thanks a lot!
>>
>> phenix.tls
>>
>> is the tool to convert between total and residual ADPs. It can recognize
>> Refmac and phenix.refine formats of TLS records.
>>
>> phenix.model_vs_data does this internally to compute correct R-factors
>> and ADP statistics.
>>
>> phenix.fmodel takes the PDB file as is, so it is your responsibility to
>> provide the correct input B-factors.
>>
>> Pavel.
>>
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