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] on behalf of Pavel Afonine 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/ 212-650-6070 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected]

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 On Tue, Nov 22, 2016 at 3:38 PM, Reza Khayat mailto:[email protected]> 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]mailto:[email protected] mailto:[email protected]> on behalf of Pavel Afonine mailto:[email protected]> Sent: Wednesday, August 3, 2016 7:39 AM To: [email protected]mailto:[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/ 212-650-6070tel:212-650-6070 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected] _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected]

?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 On Tue, Nov 22, 2016 at 5:22 PM, Reza Khayat mailto:[email protected]> 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 mailto:[email protected]> Sent: Tuesday, November 22, 2016 4:57 PM To: Reza Khayat Cc: [email protected]mailto:[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) 486-5709tel:%28510%29%20486-5709 Fax: (510) 486-5909tel:%28510%29%20486-5909 Web: https://phenix-online.org On Tue, Nov 22, 2016 at 3:38 PM, Reza Khayat mailto:[email protected]> 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]mailto:[email protected] mailto:[email protected]> on behalf of Pavel Afonine mailto:[email protected]> Sent: Wednesday, August 3, 2016 7:39 AM To: [email protected]mailto:[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/ 212-650-6070tel:212-650-6070 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected] _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected]

Dear professor Reza, Sorry for the problems you’re having with MRage. If it wasn’t for the issues you’re having installing the latest official phenix release I was gonna suggest you try running MRage with that. Much has changed in the underlying code. Have you tried the centos6 installer version instead? Regards, Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html From: Reza Khayat Sent: Wednesday, November 23, 2016 2:05 PM To: [email protected] Subject: [phenixbb] Crashing Phenix during MRage Hi, MRage stops running after sometime with the following error: =========================================== Process Process-1:29434: Traceback (most recent call last): File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run result = calculation.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run assert len( raw ) == 1 AssertionError Process Process-1:29436: Traceback (most recent call last): File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run result = calculation.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run assert len( raw ) == 1 AssertionError Process Process-1:29438: Traceback (most recent call last): File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run result = calculation.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run assert len( raw ) == 1 AssertionError Process Process-1:29440: Traceback (most recent call last): File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run result = calculation.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run assert len( raw ) == 1 AssertionError ** (gedit:5901): WARNING **: Couldn't connect to accessibility bus: Failed to connect to socket /tmp/dbus-pJCFNfwEtI: Connection refused (gedit:5901): GLib-GIO-ERROR **: No GSettings schemas are installed on the system ============================================================================== The system is a Debian 8 (Jessie), and I'm using 40 threads for the job. Also, I'm using X11 forwarding for the GUI. Any help is appreciated. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 -------------------------------------------------------------------------------- _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

Hi Rob, The download version of centos6 gives me the same problems. Can I run MRage from the command line if I have a PHIL file that was generated by the GUI? I successfully used phenix.10-2155 GUI to run the toxd tutorial with the MRage package. I retrieved the PHIL file (mr_pipeline_13.eff) used by MRage in the .phenix directory. However, the suggested syntax does not appear to start the program. phenix.mrage -i mr_pipeline_13.eff The program just sits there and using the top command does not indicate that anything is running. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ________________________________ From: [email protected] on behalf of Reza Khayat Sent: Wednesday, November 23, 2016 9:28 AM To: Dr. Robert Oeffner; [email protected] Subject: Re: [phenixbb] Crashing Phenix during MRage Hi Rob, I'll give it a try. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ________________________________ From: Dr. Robert Oeffner Sent: Wednesday, November 23, 2016 9:24 AM To: Reza Khayat; [email protected] Subject: Re: [phenixbb] Crashing Phenix during MRage Dear professor Reza, Sorry for the problems you’re having with MRage. If it wasn’t for the issues you’re having installing the latest official phenix release I was gonna suggest you try running MRage with that. Much has changed in the underlying code. Have you tried the centos6 installer version instead? Regards, Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html From: Reza Khayat Sent: Wednesday, November 23, 2016 2:05 PM To: [email protected] Subject: [phenixbb] Crashing Phenix during MRage Hi, MRage stops running after sometime with the following error: =========================================== Process Process-1:29434: Traceback (most recent call last): File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run result = calculation.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run assert len( raw ) == 1 AssertionError Process Process-1:29436: Traceback (most recent call last): File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run result = calculation.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run assert len( raw ) == 1 AssertionError Process Process-1:29438: Traceback (most recent call last): File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run result = calculation.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run assert len( raw ) == 1 AssertionError Process Process-1:29440: Traceback (most recent call last): File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run result = calculation.run() File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run assert len( raw ) == 1 AssertionError ** (gedit:5901): WARNING **: Couldn't connect to accessibility bus: Failed to connect to socket /tmp/dbus-pJCFNfwEtI: Connection refused (gedit:5901): GLib-GIO-ERROR **: No GSettings schemas are installed on the system ============================================================================== The system is a Debian 8 (Jessie), and I'm using 40 threads for the job. Also, I'm using X11 forwarding for the GUI. Any help is appreciated. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ________________________________ _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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 On Tue, Nov 22, 2016 at 6:07 PM, Reza Khayat mailto:[email protected]> wrote: ​Debian 8 (jessie) Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ________________________________ From: Billy Poon mailto:[email protected]> Sent: Tuesday, November 22, 2016 6:04 PM To: Reza Khayat Cc: [email protected]mailto:[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) 486-5709tel:%28510%29%20486-5709 Fax: (510) 486-5909tel:%28510%29%20486-5909 Web: https://phenix-online.org On Tue, Nov 22, 2016 at 5:22 PM, Reza Khayat mailto:[email protected]> 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 mailto:[email protected]> Sent: Tuesday, November 22, 2016 4:57 PM To: Reza Khayat Cc: [email protected]mailto:[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) 486-5709tel:%28510%29%20486-5709 Fax: (510) 486-5909tel:%28510%29%20486-5909 Web: https://phenix-online.org On Tue, Nov 22, 2016 at 3:38 PM, Reza Khayat mailto:[email protected]> 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]mailto:[email protected] mailto:[email protected]> on behalf of Pavel Afonine mailto:[email protected]> Sent: Wednesday, August 3, 2016 7:39 AM To: [email protected]mailto:[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/ 212-650-6070tel:212-650-6070 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected] _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected]

Hi Chen and Billy, Thank you, the problem has been alleviated! Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ________________________________ From: Chen Zhao Sent: Wednesday, November 23, 2016 10:48 AM To: Reza Khayat Cc: Billy Poon; [email protected] Subject: 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 mailto:[email protected]> 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 mailto:[email protected]> Sent: Wednesday, November 23, 2016 10:40 AM To: Reza Khayat Cc: [email protected]mailto:[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) 486-5709tel:%28510%29%20486-5709 Fax: (510) 486-5909tel:%28510%29%20486-5909 Web: https://phenix-online.orghttps://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 mailto:[email protected]> wrote: ​Debian 8 (jessie) Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ________________________________ From: Billy Poon mailto:[email protected]> Sent: Tuesday, November 22, 2016 6:04 PM To: Reza Khayat Cc: [email protected]mailto:[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) 486-5709tel:%28510%29%20486-5709 Fax: (510) 486-5909tel:%28510%29%20486-5909 Web: https://phenix-online.orghttps://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 mailto:[email protected]> 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 mailto:[email protected]> Sent: Tuesday, November 22, 2016 4:57 PM To: Reza Khayat Cc: [email protected]mailto:[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) 486-5709tel:%28510%29%20486-5709 Fax: (510) 486-5909tel:%28510%29%20486-5909 Web: https://phenix-online.orghttps://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 mailto:[email protected]> 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]mailto:[email protected] mailto:[email protected]> on behalf of Pavel Afonine mailto:[email protected]> Sent: Wednesday, August 3, 2016 7:39 AM To: [email protected]mailto:[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= 212-650-6070tel:212-650-6070 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbbhttps://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]mailto:[email protected] _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbbhttps://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]mailto:[email protected] _______________________________________________ phenixbb mailing list [email protected]mailto:[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]mailto:[email protected]