Re: [phenixbb] Crashing Phenix

Hi Reza, Actually Billy helped me solve this problem before. (Below is his previous reply) You just need to enable en_GB for the system. To do so, 1) As root, open /etc/locale.gen and uncomment the entries with en_GB. On my fresh install, I uncommented 3 entries, en_GB.ISO-8859-1, en_GB.ISO-8859-15 ISO-8859-16, and en_GB.UTF-8 UTF-8. 2) Again as root, rebuild the locales with "locale-gen" 3) Try running the Phenix GUI normally. Good luck, Chen On Wed, Nov 23, 2016 at 10:44 AM, Reza Khayat wrote:

Hi Billy,

CentOS 6 installer is giving me the same error. I've got the CLI version running, which is what I prefer. Nonetheless I'd like to get the GUI working as well.

Best wishes,

Reza

Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ------------------------------ *From:* Billy Poon *Sent:* Wednesday, November 23, 2016 10:40 AM

*To:* Reza Khayat *Cc:* [email protected] *Subject:* Re: [phenixbb] Crashing Phenix

Hi Reza,

For Debian/Ubuntu, please try the CentOS 6 installer. That is more compatible with more recent linux distributions.

-- 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 https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=CwMGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=jrysqj80pOeXTSLseJNMrowB5CD05J12DnPWBeN8dcw&s=fFcd1sa5sv9wqvKImCCGltadANMuHn_KhVATvHangBc&e=

On Tue, Nov 22, 2016 at 6:07 PM, Reza Khayat wrote:

...

​Debian 8 (jessie)

Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ------------------------------ *From:* Billy Poon *Sent:* Tuesday, November 22, 2016 6:04 PM

*To:* Reza Khayat *Cc:* [email protected] *Subject:* Re: [phenixbb] Crashing Phenix

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 https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=CwMGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=jrysqj80pOeXTSLseJNMrowB5CD05J12DnPWBeN8dcw&s=fFcd1sa5sv9wqvKImCCGltadANMuHn_KhVATvHangBc&e=

On Tue, Nov 22, 2016 at 5:22 PM, Reza Khayat 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 *Sent:* Tuesday, November 22, 2016 4:57 PM *To:* Reza Khayat *Cc:* [email protected] *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 https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=CwMGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=jrysqj80pOeXTSLseJNMrowB5CD05J12DnPWBeN8dcw&s=fFcd1sa5sv9wqvKImCCGltadANMuHn_KhVATvHangBc&e=

On Tue, Nov 22, 2016 at 3:38 PM, Reza Khayat 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:* [email protected] < [email protected]> on behalf of Pavel Afonine < [email protected]> *Sent:* Wednesday, August 3, 2016 7:39 AM *To:* [email protected] *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/ https://urldefense.proofpoint.com/v2/url?u=http-3A__www.khayatlab.org_&d=CwMGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=jrysqj80pOeXTSLseJNMrowB5CD05J12DnPWBeN8dcw&s=6rOWtgyU_jNmxc8udCzO4Wip1A6_25yrlispGBENJiM&e=

212-650-6070

_______________________________________________ phenixbb mailing [email protected]http://phenix-online.org/mailman/listinfo/phenixbb https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_phenixbb&d=CwMGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=jrysqj80pOeXTSLseJNMrowB5CD05J12DnPWBeN8dcw&s=KYF0MaPq8D1oe8ZrSKAqrkI8OJucU--ZCG2ePkQJ9ik&e= Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_phenixbb&d=CwMGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=jrysqj80pOeXTSLseJNMrowB5CD05J12DnPWBeN8dcw&s=KYF0MaPq8D1oe8ZrSKAqrkI8OJucU--ZCG2ePkQJ9ik&e= Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing list [email protected] https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix- 2Donline.org_mailman_listinfo_phenixbb&d=CwICAg&c=- dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m= jrysqj80pOeXTSLseJNMrowB5CD05J12DnPWBeN8dcw&s= KYF0MaPq8D1oe8ZrSKAqrkI8OJucU--ZCG2ePkQJ9ik&e= Unsubscribe: [email protected]