[phenixbb] Running Phenix Gui on Debian 8

Chow, Martin mchow1 at uky.edu
Wed Feb 8 06:24:15 PST 2017


I am having troubling running Phenix 1.11.1.2575 gui under Debian 8 (Jessie), and have same results with different computers that are running the same system.
I have no problem with previous versions like 1.9 and 1.10. However, with 1.11, Phenix guy won’t run. It complains about Gtk+ or Glib etc and quits. I know these are related to gui tool kits. 
I have tried Centro5, Centro6, and even compiled it, they all give similar or same complaints. 
I believe command-line works, but never try. However, simple commands like —version or —-help etc work.
I just tried it on Red Hat, 1.11 works without issues. Clearly, it is a problem with the Linux Distro.

Thank you.

Martin Chow, Ph.D.
Biochemistry
University of Kentucky
________________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of phenixbb-request at phenix-online.org [phenixbb-request at phenix-online.org]
Sent: Tuesday, February 07, 2017 3:20 PM
To: phenixbb at phenix-online.org
Subject: phenixbb Digest, Vol 135, Issue 4

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Today's Topics:

   1. Computational Crystallography Newsletter, Volume 8,       Number 1
      (Nigel Moriarty)
   2. Re: Phenix installation on manjaro (Murpholino Peligro)
   3. Re: Phenix installation on manjaro (Billy Poon)
   4. Re: Phenix installation on manjaro (Murpholino Peligro)
   5. Re: Phenix installation on manjaro (Murpholino Peligro)
   6. pdbtools atom_selection behavior (wtempel)


----------------------------------------------------------------------

Message: 1
Date: Mon, 6 Feb 2017 13:21:05 -0800
From: Nigel Moriarty <nwmoriarty at lbl.gov>
To: PHENIX user mailing list <phenixbb at phenix-online.org>,      ccp4bb
        <CCP4BB at jiscmail.ac.uk>, developers at phenix-online.org,
        industry at phenix-online.org
Subject: [phenixbb] Computational Crystallography Newsletter, Volume
        8,      Number 1
Message-ID:
        <CANkP=2eK6S4MWS=UJ=wZLXfC5qR9vQpgZEyi91gVv47EvdWQjA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

I am pleased to announce the publication of the latest issue of the
Computational Crystallography Newsletter:

       http://www.phenix-online.org/newsletter/

A listing of the articles and short communications is given below. Please
note that the newsletter accepts articles of a general nature of interest
to all crystallographers. Please send any articles to me at
NWMoriarty at lbl.gov noting that there is a Word Template on the website to
streamline production.

January 2017 <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf>

Articles
- Deploying *cctbx.xfel* in Cloud Computing and High Performance Computing
Environments
<http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=10>

Short Communications
- multi_core_run(), yet another simple tool for embarrassingly parallel jobs
<http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=6>
- Phenix tool to compute a difference map for cryo-EM
<http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=8>

Fitting tips #13 ? O-pairs: The love-hate relationship of carboxyl oxygens
<http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=2>

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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Message: 2
Date: Mon, 6 Feb 2017 18:04:38 -0600
From: Murpholino Peligro <murpholinox at gmail.com>
To: Billy Poon <bkpoon at lbl.gov>
Cc: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] Phenix installation on manjaro
Message-ID:
        <CAMdBu0VkEfZPNxw1aGne1Zcypte=ON+7Ar5GjzWHmH-7qOFozw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

[eva03 phenix-installer-dev-2666-intel-linux-2.6-x86_64-centos5]#
/usr/local/phenix-dev-2666/base/bin/python
/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py
--current_working_directory /usr/local/phenix-dev-2666/build
--command_version_suffix dev-2666 phenix phaser solve_resolve labelit dials
xia2 iota prime
Traceback (most recent call last):
  File
"/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py",
line 22, in <module>
    if not run():
  File
"/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py",
line 17, in run
    libtbx.env_config.cold_start(sys.argv)
  File
"/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/env_config.py",
line 2294, in cold_start
    " --current_working_directory %s" % show_string(build_path))
RuntimeError: Not equivalent to the current working directory:
--current_working_directory "/usr/local/phenix-dev-2666/build"

I am trying the centos5 version. I'll try the centos6 ...

2017-02-03 15:39 GMT-06:00 Billy Poon <bkpoon at lbl.gov>:

> Hi,
>
> Can you provide the output for
>
> '/usr/local/phenix-dev-2666/base/bin/python /usr/local/phenix-dev-2666/
> modules/cctbx_project/libtbx/configure.py --current_working_directory
> /usr/local/phenix-dev-2666/build --command_version_suffix dev-2666 phenix
> phaser solve_resolve labelit dials xia2 iota prime'
>
> That is the command that is failing.
>
> Also, which installer are you using? The CentOS 6 installer is generally
> more compatible with more recent versions.
>
> --
> 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 Thu, Feb 2, 2017 at 2:02 PM, Murpholino Peligro <murpholinox at gmail.com>
> wrote:
>
>> Dear all.
>> has anyone been lucky with the installation of phenix in manjaro or any
>> other archlinux-based distribution?
>>
>> Thanks
>> Ps. Error looks like http://pastebin.com/WzwrbK8W
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>>
>
>
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Message: 3
Date: Mon, 6 Feb 2017 16:23:30 -0800
From: Billy Poon <bkpoon at lbl.gov>
To: Murpholino Peligro <murpholinox at gmail.com>
Cc: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] Phenix installation on manjaro
Message-ID:
        <CAHmYUcZuF+MFnNaeYc-EaDUseKyefcTqi3JKTET-khVyA2i1pA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Sorry, can you try running that command again, but in the

/usr/local/phenix-dev-2666/build

directory? The command needs to run in the same directory specified by the
--current_working_directory 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 Mon, Feb 6, 2017 at 4:04 PM, Murpholino Peligro <murpholinox at gmail.com>
wrote:

> [eva03 phenix-installer-dev-2666-intel-linux-2.6-x86_64-centos5]#
> /usr/local/phenix-dev-2666/base/bin/python /usr/local/phenix-dev-2666/
> modules/cctbx_project/libtbx/configure.py --current_working_directory
> /usr/local/phenix-dev-2666/build --command_version_suffix dev-2666 phenix
> phaser solve_resolve labelit dials xia2 iota prime
> Traceback (most recent call last):
>   File "/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py",
> line 22, in <module>
>     if not run():
>   File "/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py",
> line 17, in run
>     libtbx.env_config.cold_start(sys.argv)
>   File "/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/env_config.py",
> line 2294, in cold_start
>     " --current_working_directory %s" % show_string(build_path))
> RuntimeError: Not equivalent to the current working directory:
> --current_working_directory "/usr/local/phenix-dev-2666/build"
>
> I am trying the centos5 version. I'll try the centos6 ...
>
> 2017-02-03 15:39 GMT-06:00 Billy Poon <bkpoon at lbl.gov>:
>
>> Hi,
>>
>> Can you provide the output for
>>
>> '/usr/local/phenix-dev-2666/base/bin/python
>> /usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py
>> --current_working_directory /usr/local/phenix-dev-2666/build
>> --command_version_suffix dev-2666 phenix phaser solve_resolve labelit dials
>> xia2 iota prime'
>>
>> That is the command that is failing.
>>
>> Also, which installer are you using? The CentOS 6 installer is generally
>> more compatible with more recent versions.
>>
>> --
>> 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 Thu, Feb 2, 2017 at 2:02 PM, Murpholino Peligro <murpholinox at gmail.com
>> > wrote:
>>
>>> Dear all.
>>> has anyone been lucky with the installation of phenix in manjaro or any
>>> other archlinux-based distribution?
>>>
>>> Thanks
>>> Ps. Error looks like http://pastebin.com/WzwrbK8W
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>>
>>
>>
>
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------------------------------

Message: 4
Date: Mon, 6 Feb 2017 18:33:15 -0600
From: Murpholino Peligro <murpholinox at gmail.com>
To: Billy Poon <bkpoon at lbl.gov>
Cc: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] Phenix installation on manjaro
Message-ID:
        <CAMdBu0UQFduxG_vCNZ73ofmUA1m9AwXSxQY87u2J2OdpT=eqrw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Here is the output
http://pastebin.com/tEimEaF2

Thanks


2017-02-06 18:23 GMT-06:00 Billy Poon <bkpoon at lbl.gov>:

> Sorry, can you try running that command again, but in the
>
> /usr/local/phenix-dev-2666/build
>
> directory? The command needs to run in the same directory specified by the
> --current_working_directory 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 Mon, Feb 6, 2017 at 4:04 PM, Murpholino Peligro <murpholinox at gmail.com>
> wrote:
>
>> [eva03 phenix-installer-dev-2666-intel-linux-2.6-x86_64-centos5]#
>> /usr/local/phenix-dev-2666/base/bin/python /usr/local/phenix-dev-2666/mod
>> ules/cctbx_project/libtbx/configure.py --current_working_directory
>> /usr/local/phenix-dev-2666/build --command_version_suffix dev-2666
>> phenix phaser solve_resolve labelit dials xia2 iota prime
>> Traceback (most recent call last):
>>   File "/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py",
>> line 22, in <module>
>>     if not run():
>>   File "/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py",
>> line 17, in run
>>     libtbx.env_config.cold_start(sys.argv)
>>   File "/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/env_config.py",
>> line 2294, in cold_start
>>     " --current_working_directory %s" % show_string(build_path))
>> RuntimeError: Not equivalent to the current working directory:
>> --current_working_directory "/usr/local/phenix-dev-2666/build"
>>
>> I am trying the centos5 version. I'll try the centos6 ...
>>
>> 2017-02-03 15:39 GMT-06:00 Billy Poon <bkpoon at lbl.gov>:
>>
>>> Hi,
>>>
>>> Can you provide the output for
>>>
>>> '/usr/local/phenix-dev-2666/base/bin/python
>>> /usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py
>>> --current_working_directory /usr/local/phenix-dev-2666/build
>>> --command_version_suffix dev-2666 phenix phaser solve_resolve labelit dials
>>> xia2 iota prime'
>>>
>>> That is the command that is failing.
>>>
>>> Also, which installer are you using? The CentOS 6 installer is generally
>>> more compatible with more recent versions.
>>>
>>> --
>>> 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 Thu, Feb 2, 2017 at 2:02 PM, Murpholino Peligro <
>>> murpholinox at gmail.com> wrote:
>>>
>>>> Dear all.
>>>> has anyone been lucky with the installation of phenix in manjaro or any
>>>> other archlinux-based distribution?
>>>>
>>>> Thanks
>>>> Ps. Error looks like http://pastebin.com/WzwrbK8W
>>>>
>>>> _______________________________________________
>>>> phenixbb mailing list
>>>> phenixbb at phenix-online.org
>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>>>
>>>
>>>
>>
>
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Message: 5
Date: Mon, 6 Feb 2017 18:43:51 -0600
From: Murpholino Peligro <murpholinox at gmail.com>
To: Billy Poon <bkpoon at lbl.gov>
Cc: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] Phenix installation on manjaro
Message-ID:
        <CAMdBu0VbrTeQVTOmx3i+Z_s-5fnLiYodQatqO1pLXsU0ae-ZUQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

I am very sorry .. I think I deleted the original pastebin links
here:
http://pastebin.com/cigkmmqF
http://pastebin.com/WHKMH9hx

2017-02-06 18:33 GMT-06:00 Murpholino Peligro <murpholinox at gmail.com>:

> Here is the output
> http://pastebin.com/tEimEaF2
>
> Thanks
>
>
> 2017-02-06 18:23 GMT-06:00 Billy Poon <bkpoon at lbl.gov>:
>
>> Sorry, can you try running that command again, but in the
>>
>> /usr/local/phenix-dev-2666/build
>>
>> directory? The command needs to run in the same directory specified by
>> the --current_working_directory 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 Mon, Feb 6, 2017 at 4:04 PM, Murpholino Peligro <murpholinox at gmail.com
>> > wrote:
>>
>>> [eva03 phenix-installer-dev-2666-intel-linux-2.6-x86_64-centos5]#
>>> /usr/local/phenix-dev-2666/base/bin/python
>>> /usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py
>>> --current_working_directory /usr/local/phenix-dev-2666/build
>>> --command_version_suffix dev-2666 phenix phaser solve_resolve labelit dials
>>> xia2 iota prime
>>> Traceback (most recent call last):
>>>   File "/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py",
>>> line 22, in <module>
>>>     if not run():
>>>   File "/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py",
>>> line 17, in run
>>>     libtbx.env_config.cold_start(sys.argv)
>>>   File "/usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/env_config.py",
>>> line 2294, in cold_start
>>>     " --current_working_directory %s" % show_string(build_path))
>>> RuntimeError: Not equivalent to the current working directory:
>>> --current_working_directory "/usr/local/phenix-dev-2666/build"
>>>
>>> I am trying the centos5 version. I'll try the centos6 ...
>>>
>>> 2017-02-03 15:39 GMT-06:00 Billy Poon <bkpoon at lbl.gov>:
>>>
>>>> Hi,
>>>>
>>>> Can you provide the output for
>>>>
>>>> '/usr/local/phenix-dev-2666/base/bin/python
>>>> /usr/local/phenix-dev-2666/modules/cctbx_project/libtbx/configure.py
>>>> --current_working_directory /usr/local/phenix-dev-2666/build
>>>> --command_version_suffix dev-2666 phenix phaser solve_resolve labelit dials
>>>> xia2 iota prime'
>>>>
>>>> That is the command that is failing.
>>>>
>>>> Also, which installer are you using? The CentOS 6 installer is
>>>> generally more compatible with more recent versions.
>>>>
>>>> --
>>>> 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 Thu, Feb 2, 2017 at 2:02 PM, Murpholino Peligro <
>>>> murpholinox at gmail.com> wrote:
>>>>
>>>>> Dear all.
>>>>> has anyone been lucky with the installation of phenix in manjaro or
>>>>> any other archlinux-based distribution?
>>>>>
>>>>> Thanks
>>>>> Ps. Error looks like http://pastebin.com/WzwrbK8W
>>>>>
>>>>> _______________________________________________
>>>>> phenixbb mailing list
>>>>> phenixbb at phenix-online.org
>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>>>>
>>>>
>>>>
>>>
>>
>
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Message: 6
Date: Tue, 7 Feb 2017 15:19:28 -0500
From: wtempel <wtempel at gmail.com>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: [phenixbb] pdbtools atom_selection behavior
Message-ID:
        <CAGjFzmBb-qOGd+6tpDXnPrBkU_Hd5GUMDLpm5hmJ-1CeDQd2Pw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello all,
suppose I would like to remove one alternate conformation B from residue 1
in chain A and set the occupancy of remaining atoms in that residue to 1.

phenix.pdbtools alts_minim.pdb occupancies.set=1 \
  occupancies.atom_selection=?chain A and resid 1? \
  keep=?not (chain A and altid B and resid 1)? \
  output.file_name=alts.out.pdb


There are better methods to achieve that, but I eventually would like to
expand this command to do other ?things? to my coordinates.
Well, so far I have failed to have the atom_selection to work the way *I*
expect. stdout reveals that the program fails to apply a common scope to
the command switches, and proceeds to reset occupancies of all atoms. Can
this be done on the command line? A minimal (not) working example is
attached, and your feedback appreciated.
Best regards.
Wolfram Tempel

?
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