[phenixbb] Rosetta refine compilation issue Centos 7
ludovic.pecqueur at college-de-france.fr
Fri Apr 29 07:52:14 PDT 2016
Dear Phenix developers,
This is a feedback from a previous post started a long time ago when I was trying to install the rosetta interface for phenix in Centos 7.
As a reminder, I could compile Rosetta with './scons.py -j8' without problem but
rosetta.build_phenix_interface exited with an error message related to python.
I had given up for some time but I tried again today with more luck.
setting up PYTHONHOME as previously suggested was breaking something:
python -c "import site" returns no error
> export PYTHONHOME=/usr/bin/python (so the distribution's python)
python -c "import site" returns "no module named site"
python -c "import site" returns no error message.
adding the path to my local PYTHON with
export PATH=/where my local Python 2.7 is/bin/:$PATH
was the correct fix and I could finally run rosetta.build_phenix_interface without errors.
On Sep 28, 2015, at 3:24 AM, phenixbb-request at phenix-online.org wrote:
> Message: 8
> Date: Thu, 24 Sep 2015 16:43:40 +0200
> From: ludovic Pecqueur <ludovic.pecqueur at college-de-france.fr>
> To: Paul Adams <pdadams at lbl.gov>
> Cc: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] Rosetta refine compilation issue Centos 7
> <0CB7F2F9-4E89-4598-92FA-58AE2526FF8D at college-de-france.fr>
> Content-Type: text/plain; charset=us-ascii
> Hi Paul, Nigel,
> Thank you for the suggestion.
> I tried to set PYTHONHOME with
> export PYTHONHOME=/usr/bin/python
> export PYTHONHOME=to PHENIX's python
> export PYTHONHOME=to a local python compiled from source that I use to compile programs like Pymol
> to no avail, I get the same error message.
> As I can compile Rosetta without phenix using : ./scons.py -j6 mode=release bin, do you think the problem could reside in the way rosetta.build_phenix_interface works?
> On Sep 23, 2015, at 11:09 PM, Paul Adams <pdadams at lbl.gov> wrote:
>> Hi Ludovic,
>> the problems seem to occur when scons is called to compile Rosetta. I notice that the scons.py file uses the python that appears first in your path (#! /usr/bin/env python). Is it possible that this is a python that is broken in some way?
>>> On Sep 23, 2015, at 9:11 AM, ludovic Pecqueur <ludovic.pecqueur at college-de-france.fr> wrote:
>>> Dear Developers,
>>> I have a fresh Centos 7 system and after installing Phenix I wanted to compile the Rosetta.refine module. (Rosetta from source version 2015.31.58019)
>>> I have succesfully compiled Rosetta but when I try to build the dedicated Rosetta for Rosetta_refine with rosetta.build_phenix_interface after setting up PHENIX_ROSETTA_PATH and ROSETTA3_DB I get the following error message:
>>> [XXX at ...]$ rosetta.build_phenix_interface nproc=6
>>> scons: Reading SConscript files ...
>>> Running versioning script ... Done. (0.1 seconds)
>>> Could not find platform independent libraries <prefix>
>>> Could not find platform dependent libraries <exec_prefix>
>>> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
>>> ImportError: No module named site
>>> CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1:
>>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 172:
>>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 163:
>>> SConscript("SConscript", "build")
>>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614:
>>> return method(*args, **kw)
>>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551:
>>> return _SConscript(self.fs, *files, **subst_kw)
>>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260:
>>> exec _file_ in call_stack[-1].globals
>>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConscript", line 28:
>>> File "/usr/local/PROGRAMS/XTAL/PHENIX/phenix-1.10-2155/base/lib/python2.7/subprocess.py", line 540:
>>> raise CalledProcessError(retcode, cmd).
>>> If you have any idea of what could cause the problem, I would welcome any suggestions.
>>> I updated Phenix and I could compile phenix.rosetta_refine without problems on Centos 6.7.
>>> Thank you very much for your time and help.
>>> Kind regards,
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> Unsubscribe: phenixbb-leave at phenix-online.org
>> Paul Adams
>> Interim Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab
>> Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
>> Adjunct Professor, Department of Bioengineering, U.C. Berkeley
>> Vice President for Technology, the Joint BioEnergy Institute
>> Laboratory Research Manager, ENIGMA Science Focus Area
>> Building 33, Room 347
>> Building 80, Room 247
>> Building 978, Room 4126
>> Tel: 1-510-486-4225, Fax: 1-510-486-5909
>> Lawrence Berkeley Laboratory
>> 1 Cyclotron Road
>> BLDG 33R0345
>> Berkeley, CA 94720, USA.
>> Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov ][ 1-510-495-2506 ]
> Message: 9
> Date: Mon, 28 Sep 2015 01:21:21 +0000 (UTC)
> From: Smith Lee <smith_lee123 at yahoo.com>
> To: PHENIX User Mailing List <phenixbb at phenix-online.org>
> Subject: [phenixbb] on Phenix10
> <615863586.1820571.1443403281522.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
> Dear All,
> With the EM cryo data, I have compared the function of phenix.real_space_refine of Phenix10 and Phenix1.9-1692. For the Ramachandran favored, the new version is about 90%, the old version is about 92%. For the clashscore by Molprobity, the new version is about 30, the old version is about 20. Molprobity indicated the clashing atoms were systematically existing in the whole molecule, rather than on specific parts of the protein which may be indication of bad modelling.
> Clearly the clashscore of 30 is unacceptable. Will you please give some advise on how to improve the function of new version of Phenix, considering adding H was not suitable as for the resolution was poorer than 4.0 A?
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