From pietro.roversi@path.ox.ac.uk Mon Jan 10 09:24:07 2011 From: Pietro Roversi To: phenixbb@phenix-online.org Subject: [phenixbb] The phenix autobuilder does not find buccaneer Date: Mon, 10 Jan 2011 17:21:45 +0000 Message-ID: <1584BD53851F1449A9AEB6065750318530D2D660F9@EXMBX02.ad.oak.ox.ac.uk> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============6828848358300975295==" --===============6828848358300975295== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Dear all, I have Buccaneer 1.5.0: partyring:~/Projects/Japanin/autoBUSTER> $CBIN/cbuccaneer 
=20
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.1: cbuccaneer             version 1.5.0 : 28/05/10##
 ###############################################################
 User: pietro  Run date: 10/ 1/2011 Run time: 17:18:57=20


and yet the phenix autobuilder fails - saying I need 1.3.0 or higher (see bel=
ow)

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=20
BUCCANEER version 1.3.0 or higher

****************************************
________________________________________
From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.=
org] On Behalf Of Pavel Afonine [pafonine(a)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.

_______________________________________________
phenixbb mailing list
phenixbb(a)phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb

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From terwilliger@lanl.gov Mon Jan 10 11:30:37 2011
From: "Thomas C. Terwilliger" 
To: phenixbb@phenix-online.org
Subject: Re: [phenixbb] The phenix autobuilder does not find buccaneer
Date: Mon, 10 Jan 2011 12:30:10 -0700
Message-ID: <57844.128.165.0.81.1294687810.squirrel@webmail.lanl.gov>
In-Reply-To:
 <1584BD53851F1449A9AEB6065750318530D2D660F9@EXMBX02.ad.oak.ox.ac.uk>
MIME-Version: 1.0
Content-Type: multipart/mixed; boundary="===============8428258642738656880=="

--===============8428258642738656880==
Content-Type: text/plain; charset="utf-8"
Content-Transfer-Encoding: 7bit

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  
 <'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
>> 
>>  
>> 

>> 
>>
>>  ###############################################################
>>  ###############################################################
>>  ###############################################################
>>  ### 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(a)phenix-online.org
>> [phenixbb-bounces(a)phenix-online.org] On Behalf Of Pavel Afonine
>> [pafonine(a)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.
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb(a)phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb(a)phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>


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