[phenixbb] Crashing Phenix

Billy Poon bkpoon at lbl.gov
Tue Nov 22 15:04:52 PST 2016


Hi Reza,

What is the linux distribution and version that you are using?

--
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 Tue, Nov 22, 2016 at 5:22 PM, Reza Khayat <rkhayat at ccny.cuny.edu> wrote:

> Hi,
>
>
> Typing locale generates:
>
> LANG=en_US.UTF-8
>
> ...
>
> LC_ALL=
>
>
> Running
>
> sudo locale-gen "en_US.UTF-8"
>
> does not change anything
>
>
> modifying /etc/environment to include
>
> LC_ALL=en_US.UTF-8
> LANG=en_US.UTF-8​
>
> Then Running locale indicates that LC_ALL=en_US.UTF-8. However, the
> problem persists.
>
>
> Reza
>
>
>
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
> ------------------------------
> *From:* Billy Poon <bkpoon at lbl.gov>
> *Sent:* Tuesday, November 22, 2016 4:57 PM
> *To:* Reza Khayat
> *Cc:* phenixbb at phenix-online.org
> *Subject:* Re: [phenixbb] Crashing Phenix
>
> Hi Reza,
>
> Do you have the LANG or LC_ALL environment variables set? If you have LANG
> can you try setting LC_ALL to the same value? Also, make sure that there is
> a "UTF-8" somewhere. So for English (U.S.), LC_ALL should be set to
> en_US.UTF-8.
>
> --
> 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 Tue, Nov 22, 2016 at 3:38 PM, Reza Khayat <rkhayat at ccny.cuny.edu>
> wrote:
>
>> Hi,
>>
>>
>> I recently installed phenix-1.11.1-2575 (CentOS 5 flavor) and am getting
>> the following crashes when trying to launch the GUI.
>>
>> 15:31:23: Cannot set locale to language "English".
>> 15:31:23: locale 'en_GB' cannot be set.
>>
>> phenix-1.10.1-2155 (on the same system) also gives me a locale 'en_GB'
>> error but the GUI launches and I can run programs.
>>
>>
>> Any suggestions on how to fix this problem? Thanks.
>>
>>
>> Best wishes,
>> Reza
>>
>> Reza Khayat, PhD
>> Assistant Professor
>> City College of New York
>> Department of Chemistry
>> New York, NY 10031
>> ------------------------------
>> *From:* phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-onlin
>> e.org> on behalf of Pavel Afonine <pafonine at lbl.gov>
>> *Sent:* Wednesday, August 3, 2016 7:39 AM
>> *To:* phenixbb at phenix-online.org
>> *Subject:* Re: [phenixbb] Realspace refinement
>>
>>
>> Hi Reza,
>> yes, it does.
>>
>> Pavel
>>
>> On 8/1/16 04:16, Reza Khayat wrote:
>>
>> Hi,
>>
>>
>>
>> Does realspace refinement consider temperature factors during refinement?
>> Thanks.
>>
>>
>>
>> Best wishes,
>> Reza
>>
>>
>>
>> Reza Khayat, PhD
>>
>> Assistant Professor
>>
>> Department of Chemistry
>>
>> City College of New York
>>
>> 85 Saint Nicholas Terrace, CDI 2.318
>>
>> New York, NY 10031
>>
>> http://www.khayatlab.org/
>>
>> 212-650-6070
>>
>>
>>
>>
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>>
>>
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>
>
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