[phenixbb] phenix installation problem

princeadam at 163.com princeadam at 163.com
Fri Dec 3 19:11:05 PST 2021

Hi Billy and Pavel,
The latest version is also not working with smilar error. 
In the "base_tmp" directory, I found "binary.log"(see the attachment). And it showed: /bin/sh: 1: /usr/local/phenix -1.20-4438/conda_base/bin/python: not found/.
I check the "conda_base" directory under "usr/local/phe...", I can see "python2.7" and "python2.7-config" files.
So, the problem is "python2.7" is not the required "python" ?


在 2021-12-03 05:35:54,"Billy Poon" <BKPoon at lbl.gov> 写道:

Hi Adam,

In the installer directory, there should be a "base_tmp" directory with some log files. Can you send me those log files? They will show the actual error.

Billy K. Poon

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

On Thu, Dec 2, 2021 at 12:11 PM Pavel Afonine <pafonine at lbl.gov> wrote:


try latest version:



On 11/30/21 18:10, princeadam at 163.com wrote:

Dear all

I tried to install Phenix on my virtual machine(Ubuntu) in win11. And got the following error message.


                          Phenix Installation


                          version: 1.19.2-4158

                     machine type: intel-linux-2.6-x86_64

                       OS version: 5.11.0-40-generic

                      destination: /usr/local/phenix-1.19.2-4158

                  # of processors: 1



Configuring Phenix components...

Traceback (most recent call last):

  File "./bin/install.py", line 245, in <module>


  File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 200, in install


  File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 349, in install_from_binary


  File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 431, in reconfigure

    call(args=args, log=log, verbose=self.options.verbose)

  File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 55, in call

    raise RuntimeError("Call to &apos;%s&apos; failed with exit code %d" % (args, rc))

RuntimeError: Call to &apos;/usr/local/phenix-1.19.2-4158/conda_base/bin/python /usr/local/phenix-1.19.2-4158/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-1.19.2-4158/build --command_version_suffix 1.19.2-4158 phenix phaser solve_resolve labelit dials xia2 iota prime amber_adaptbx --use_conda&apos; failed with exit code 127

I searched phenixbb, and got the similar information from http://www.phenix-online.org/pipermail/phenixbb/2015-November/022456.html

It's a pity , that the answer was not suiable for me.

I have root access to write to usr/local. And under /usr/local/phenix-1.19.2-4158 , I can see four folders:build, conda_base, doc, modules.

Any one has suggestions?

all the best


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