Re: [phenixbb] Using PyMOL-1.8 with PHENIX-dev-2306

Hi, Billy It works, after I added the flags in that file. I also created a patch file. Please check the attach file. Just put it in the root folder of PHENIX, and type "patch -p0 < install_base_packages.py.patch" Thanks for your help. By A.C. 2016-02-15 16:34 GMT+08:00 Billy Poon :

Hi,

Since you are installing from source, the easiest way would be to edit the Python script that installs all the base dependencies. To do so,

1) Open install_base_packages.py located in phenix-installer-dev-2306-source/modules/cctbx_project/libtbx/auto_build 2) Add 'configure_args.append("--enable_unicode=ucs4")' after line 644. That section just adds our flags to the configure step for installing Python. After editing, your section should look like,

configure_args.append("--enable-shared") configure_args.append("--enable-unicode=ucs4") configure_args.append("LDFLAGS=-Wl,-rpath=\$$ORIGIN/../lib")

3) Just run the Phenix install program (./install --prefix=<installation directory>) like normal and Python will be compiled with your new flag.

Let me know if you have any issues. Thanks!

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

On Sun, Feb 14, 2016 at 5:55 PM, acyang wrote:

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Hi Billy

Thanks for your reply. I installed phenix from source (phenix-installer-dev-2306-source.tar.gz). And I used scientific linux 7.1 for my workstation. I noticed that SCONS is adopted in the installation of phenix, and phenix will download a modified version of python (python_2.7.8_cci). I think the problem can be solved by adding a flag "--enable-unicode=ucs4" in configuring Python-2.7.8_cci.

I'd appreciate if you can tell me how to modify the SCONS script file.

by A.C.

2016-02-12 16:52 GMT+08:00 Billy Poon :

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Hi,

Are you installing phenix from source or from a binary distribution? And which operating system are you using? I can give you the flags (in addition to the --prefix flag for installing into the base directory) for the configure step for either OS X or Linux.

You can basically install Phenix normally, and then recompile our Python from scratch with our regular flags and your extra flag.

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

On Wed, Feb 3, 2016 at 3:05 AM, acyang wrote:

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Hi everyone

I've installed pymol and phenix on my scientific linux7.1 workstation. I can launch pymol via the launching script($PYMOL_HOME/pymol) normally. But when I launched pymol in phenix GUI, I got some error as followed:

********************************************************************************************************************************* Traceback (most recent call last): File "/opt/PyMOL/modules/pymol/__init__.py", line 71, in <module> import pymol File "/opt/PyMOL/modules/pymol/__init__.py", line 521, in <module> import pymol._cmd ImportError: /opt/PyMOL/modules/pymol/_cmd.so: undefined symbol: PyUnicodeUCS4_SetDefaultEncoding

********************************************************************************************************************************* After STFW*, *I knew the problem is about unicode variant (UCS2, UCS4). I also checked the configuration of two python. For /bin/python (adopted by pymol)

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> import sys>>> print sys.maxunicode1114111

And for $PHENIX_HOME/base/bin/python (adopted by phenix)

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> import sys > print sys.maxunicode 65535

My question is : How do I add the flag --enable-unicode=ucs4 in configuring Python-2.7.8_cci.

I'd appreciate if any reply on this.

acyang

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