Re: [ccp4bb] ccp4i2 stopped working (no startup) - advice?
Renato and Stuart McNicholls wrote exactly the right thing: deleting this file
resolved the issue. Thank you very much!
-Original Message-
From: CCP4 bulletin board On Behalf Of Renato Weiße
Sent: 08 May 2024 16:44
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ccp4i2 stopped working (no startup) - advice?
Hi Andrea,
concerning Log #1: there is a log file
/home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml, which is
probably empty. If it is, then deleting it should resolve the error. I have
seen this problem from time to time on students laptops, but could not figure
out, for what reason it occurs.
Cheers,
Renato
Zitat von "Thorn, Dr. Andrea" <d000cdf57279-dmarc-requ...@jiscmail.ac.uk>:
> Dear all,
> My ccp4i2 installation stopped working - it does not start up
> properly anymore (see Log #1 below for the output).
> I started ccp4i which brought up the update manager and ran
> outstanding updates. This did not fix the issue. I also sourced the
> source file manually, just to make sure.
> Then I ran ./find-missing-libs.sh and fixed some issues, but got
> stuck (see Log #2 below).
> Deleting the ccp4 folder and re-install also did not help.
> The system is Ubuntu in a virtual box.
> I would be grateful for any advice.
> Best wishes,
>
> Andrea.
>
> __
>
> LOG #1:
>
> Running CCP4i2 browser from:
> /opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2
> Python 3.7.12 (default, Jan 6 2022, 21:30:12)
> [GCC 8.2.1 20180905 (Red Hat 8.2.1-3)]
> Qt version 5.15.2
>
> Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use
> QT_QPA_PLATFORM=wayland to run on Wayland anyway.
> Sandboxing disabled by user.
> Installed Qt WebEngine locales directory not found at location
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying
> application directory...
> Qt WebEngine locales directory not found at location
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback
> directory... Translations MAY NOT not be correct.
> Path override failed for key ui::DIR_LOCALES and path
> '/home/athorn/.browser.py'
> [0508/160512.882309:WARNING:resource_bundle_qt.cpp(115)]
> locale_file_path.empty() for locale
> Installed Qt WebEngine locales directory not found at location
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying
> application directory...
> Installed Qt WebEngine locales directory not found at location
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying
> application directory...
> Qt WebEngine locales directory not found at location
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback
> directory... Translations MAY NOT not be correct.
> Qt WebEngine locales directory not found at location
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback
> directory... Translations MAY NOT not be correct.
> Path override failed for key ui::DIR_LOCALES and path
> '/home/athorn/.QtWebEngineProcess'
> Path override failed for key ui::DIR_LOCALES and path
> '/home/athorn/.QtWebEngineProcess'
> [0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)]
> locale_file_path.empty() for locale
> [0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)]
> locale_file_path.empty() for locale
> Installed Qt WebEngine locales directory not found at location
> /opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying
> application directory...
> Qt WebEngine locales directory not found at location
> /opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback
> directory... Translations MAY NOT not be correct.
> Path override failed for key ui::DIR_LOCALES and path
> '/home/athorn/.QtWebEngineProcess'
> [0508/160512.925233:WARNING:resource_bundle_qt.cpp(115)]
> locale_file_path.empty() for locale
> ccp4i2 version 1.1.0
> ccp4i2 source revision 6539
> CPrintHandler saving print output to directory:
> /home/athorn/.CCP4I2/logs/started_1715177113
> None
> None
> Starting Project Manager
> Current schema version: ('0.1.22', '23-09-2016')
> CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
> updateDbSchema 0.1.22 23-09-2016
> Starting Project Manager - DONE
> Starting Job Controller
> Starting Job Controller - DONE
>
> isDarkMode? False
>
> Starting 0.00048089027404785156
> StyleSheet screen size: 1920 1089
> Current schema version: ('0.1.22', '23-09-2016')
> CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
> updateDbSchema 0.1.22 23-09-2016
> CCP4i2 starting HTTP server on 127.0.0.1 port 43434
>
> Retrieving status
> file:/
[ccp4bb] ccp4i2 stopped working (no startup) - advice?
Dear all,
My ccp4i2 installation stopped working - it does not start up properly anymore
(see Log #1 below for the output).
I started ccp4i which brought up the update manager and ran outstanding
updates. This did not fix the issue. I also sourced the source file manually,
just to make sure.
Then I ran ./find-missing-libs.sh and fixed some issues, but got stuck (see Log
#2 below).
Deleting the ccp4 folder and re-install also did not help.
The system is Ubuntu in a virtual box.
I would be grateful for any advice.
Best wishes,
Andrea.
__
LOG #1:
Running CCP4i2 browser from:
/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2
Python 3.7.12 (default, Jan 6 2022, 21:30:12)
[GCC 8.2.1 20180905 (Red Hat 8.2.1-3)]
Qt version 5.15.2
Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use
QT_QPA_PLATFORM=wayland to run on Wayland anyway.
Sandboxing disabled by user.
Installed Qt WebEngine locales directory not found at location
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying application
directory...
Qt WebEngine locales directory not found at location
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback directory...
Translations MAY NOT not be correct.
Path override failed for key ui::DIR_LOCALES and path '/home/athorn/.browser.py'
[0508/160512.882309:WARNING:resource_bundle_qt.cpp(115)]
locale_file_path.empty() for locale
Installed Qt WebEngine locales directory not found at location
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying application
directory...
Installed Qt WebEngine locales directory not found at location
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying application
directory...
Qt WebEngine locales directory not found at location
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback directory...
Translations MAY NOT not be correct.
Qt WebEngine locales directory not found at location
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback directory...
Translations MAY NOT not be correct.
Path override failed for key ui::DIR_LOCALES and path
'/home/athorn/.QtWebEngineProcess'
Path override failed for key ui::DIR_LOCALES and path
'/home/athorn/.QtWebEngineProcess'
[0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)]
locale_file_path.empty() for locale
[0508/160512.894852:WARNING:resource_bundle_qt.cpp(115)]
locale_file_path.empty() for locale
Installed Qt WebEngine locales directory not found at location
/opt/xtal/ccp4-8.0/translations/qtwebengine_locales. Trying application
directory...
Qt WebEngine locales directory not found at location
/opt/xtal/ccp4-8.0/libexec/qtwebengine_locales. Trying fallback directory...
Translations MAY NOT not be correct.
Path override failed for key ui::DIR_LOCALES and path
'/home/athorn/.QtWebEngineProcess'
[0508/160512.925233:WARNING:resource_bundle_qt.cpp(115)]
locale_file_path.empty() for locale
ccp4i2 version 1.1.0
ccp4i2 source revision 6539
CPrintHandler saving print output to directory:
/home/athorn/.CCP4I2/logs/started_1715177113
None
None
Starting Project Manager
Current schema version: ('0.1.22', '23-09-2016')
CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
updateDbSchema 0.1.22 23-09-2016
Starting Project Manager - DONE
Starting Job Controller
Starting Job Controller - DONE
isDarkMode? False
Starting 0.00048089027404785156
StyleSheet screen size: 1920 1089
Current schema version: ('0.1.22', '23-09-2016')
CCP4i2 opening database file /home/athorn/.CCP4I2/db/database.sqlite
updateDbSchema 0.1.22 23-09-2016
CCP4i2 starting HTTP server on 127.0.0.1 port 43434
Retrieving status
file:/home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml
Traceback (most recent call last):
File
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4Utils.py", line
266, in openFileToEtree
tree = parse_from_unicode(s,useLXML=useLXML)
File
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4Utils.py", line
255, in parse_from_unicode
return etree.fromstring(s, parser=utf8_parser)
File "src/lxml/etree.pyx", line 3211, in lxml.etree.fromstring
File "src/lxml/parser.pxi", line 1877, in lxml.etree._parseMemoryDocument
File "src/lxml/parser.pxi", line 1765, in lxml.etree._parseDoc
File "src/lxml/parser.pxi", line 1127, in lxml.etree._BaseParser._parseDoc
File "src/lxml/parser.pxi", line 601, in
lxml.etree._ParserContext._handleParseResultDoc
File "src/lxml/parser.pxi", line 711, in lxml.etree._handleParseResult
File "src/lxml/parser.pxi", line 640, in lxml.etree._raiseParseError
File "", line 1
lxml.etree.XMLSyntaxError: Document is empty, line 1, column 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/opt/xtal/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4File.py", line
1263, in getEtreeRoot
[ccp4bb] AI papers in experimental macromolecular structure determination
Dear colleagues, I have compiled a list of papers that cover the application of AI/machine learning methods in single-crystal structure determination (mostly macromolecular crystallography) and single-particle Cryo-EM. The draft list is attached below. If I missed any papers, please let me know. I will send the final list back here, for the benefit of all who are interested in the topic. Best wishes, Andrea. __ General: - Gopalakrishnan, V., Livingston, G., Hennessy, D., Buchanan, B. & Rosenberg, J. M. (2004). Acta Cryst D. 60, 1705–1716. - Morris, R. J. (2004). Acta Cryst D. 60, 2133–2143. Micrograph preparation: - (2020). Journal of Structural Biology. 210, 107498. Particle Picking: - Sanchez-Garcia, R., Segura, J., Maluenda, D., Carazo, J. M. & Sorzano, C. O. S. (2018). IUCrJ. 5, 854–865. - Al-Azzawi, A., Ouadou, A., Tanner, J. J. & Cheng, J. (2019). BMC Bioinformatics. 20, 1–26. - George, B., Assaiya, A., Roy, R. J., Kembhavi, A., Chauhan, R., Paul, G., Kumar, J. & Philip, N. S. (2021). Commun Biol. 4, 1–12. - Lata, K. R., Penczek, P. & Frank, J. (1995). Ultramicroscopy. 58, 381–391. - Nguyen, N. P., Ersoy, I., Gotberg, J., Bunyak, F. & White, T. A. (2021). BMC Bioinformatics. 22, 1–28. - Wang, F., Gong, H., Liu, G., Li, M., Yan, C., Xia, T., Li, X. & Zeng, J. (2016). Journal of Structural Biology. 195, 325–336. - Wong, H. C., Chen, J., Mouche, F., Rouiller, I. & Bern, M. (2004). Journal of Structural Biology. 145, 157–167. Motion description in Cryo-EM: - Matsumoto, S., Ishida, S., Araki, M., Kato, T., Terayama, K. & Okuno, Y. (2021). Nat Mach Intell. 3, 153–160. - Zhong, E. D., Bepler, T., Berger, B. & Davis, J. H. (2021). Nat Methods. 18, 176–185. Local resolution: - Avramov, T. K., Vyenielo, D., Gomez-Blanco, J., Adinarayanan, S., Vargas, J. & Si, D. (2019). Molecules. 24, 1181. - Ramírez-Aportela, E., Mota, J., Conesa, P., Carazo, J. M. & Sorzano, C. O. S. (2019). IUCrJ. 6, 1054–1063. - (2021). QAEmap: A Novel Local Quality Assessment Method for Protein Crystal Structures Using Machine Learning. Map post-processing: - Sanchez-Garcia, R., Gomez-Blanco, J., Cuervo, A., Carazo, J. M., Sorzano, C. O. S. & Vargas, J. (2020). BioRxiv. 2020.06.12.148296. Secondary structure assignment in map: - Subramaniya, S. R. M. V., Terashi, G. & Kihara, D. (2019). Nat Methods. 16, 911–917. - Li, R., Si, D., Zeng, T., Ji, S. & He, J. (2016). 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Vol. pp. 41–46. - Si, D., Ji, S., Nasr, K. A. & He, J. (2012). Biopolymers. 97, 698–708. - He, J. & Huang, S.-Y. Brief Bioinform. - Lyu, Z., Wang, Z., Luo, F., Shuai, J. & Huang, Y. (2021). Frontiers in Bioengineering and Biotechnology. 9,. - Mostosi, P., Schindelin, H., Kollmannsberger, P. & Thorn, A. (2020). Angewandte Chemie International Edition. Automatic structure building: - Alnabati, E. & Kihara, D. (2020). Molecules. 25, 82. - Si, D., Moritz, S. A., Pfab, J., Hou, J., Cao, R., Wang, L., Wu, T. & Cheng, J. (2020). Sci Rep. 10, 1–22. - Moritz, S. A., Pfab, J., Wu, T., Hou, J., Cheng, J., Cao, R., Wang, L. & Si, D. (2019). - Chojnowski, G., Pereira, J. & Lamzin, V. S. (2019). Acta Cryst D. 75, 753–763. Crystallization: - Liu, R., Freund, Y. & Spraggon, G. (2008). Acta Cryst D. 64, 1187–1195. - (2004). Methods. 34, 390–407. - Bruno, A. E., Charbonneau, P., Newman, J., Snell, E. H., So, D. R., Vanhoucke, V., Watkins, C. J., Williams, S. & Wilson, J. (2018). PLOS ONE. 13, e0198883. Crystal centering: - Ito, S., Ueno, G. & Yamamoto, M. (2019). J Synchrotron Rad. 26, 1361–1366. - Crystal centering using deep learning in X-ray crystallography. - Elbasir, A., Moovarkumudalvan, B., Kunji, K., Kolatkar, P. R., Mall, R. & Bensmail, H. (2019). Bioinformatics. 35, 2216–2225. Diffraction image analysis: - Czyzewski, A., Krawiec, F., Brzezinski, D., Porebski, P. J. & Minor, W. (2021). Expert Systems with Applications. 174, 114740. Peak search in serial crystallography: Ke, T.-W., Brewster, A. S., Yu, S. X., Ushizima, D., Yang, C. & Sauter, N. K. (2018). J Synchrotron Rad. 25, 655–670. Space group assignment from diffraction image (small molecules): Aguiar, J. A., Gong, M. L., Unocic, R. R., Tasdizen, T. & Miller, B. D. (2019). Science Advances. 5, eaaw1949. Data quality assessment in MX: - Vollmar, M., Parkhurst, J. M., Jaques, D., Baslé, A., Murshudov, G. N., Waterman, D. G. & Evans, G. (2020). IUCrJ. 7, 342–354. Ligand recognition: Kowiel, M., Brzezinski, D., Porebski, P. J., Shabalin, I. G., Jaskolski, M. & Minor, W. (2019). Bioinformatics. 35, 452–461. Prediction of missing atoms in small molecular structures: Thomas, N., Smidt, T., Kearnes, S., Yang, L., Li, L., Kohlhoff, K. & Riley, P. (2018). ADP estimation (small molecules): Gagner, V. A., Jensen, M. & Katona, G. (2021). Mach. Learn.: Sci. Technol. 2, 035033. -- Dr. Andrea Thorn | group leader andrea.th...@uni-hamburg.de Institute for Nanostructure and Solid State Physics, Universität Hamburg
