Re: [ccp4bb] Ubuntu and Coot

[Tom Peat]

And yet another quick update- I rebooted the machine again and now the ccp4 
version of Coot is working, but the standalone version is not (and the Phenix 
version continues to work). Just thought I would throw this out there for 
others...
cheers, tom

From: CCP4 bulletin board  on behalf of Tom Peat 

Sent: Thursday, May 9, 2024 9:29 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Ubuntu and Coot

You don't often get email from b7e4a7a8af49-dmarc-requ...@jiscmail.ac.uk. 
Learn why this is important
Just an update- I tested using Coot through the Phenix package and that seems 
to work (version 1.21-5207-000 and version 0.9.8.93 of Coot). Maybe a version 
issue? Or Phenix just comes with libraries that ccp4 doesn't? Not sure yet.
cheers, tom

From: CCP4 bulletin board  on behalf of Martin Malý 

Sent: Wednesday, May 8, 2024 5:31 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Ubuntu and Coot

Dear Tom,
I am using basically the same setup (Linux Mint 21.3 Xfce based on Ubuntu 
22.04, CCP4 8.0.019 including Coot 0.9.8.93). Everything works well on my 
computer. I did not have any issues with Coot even in CCP4 8.0.017. I am sorry 
I don't know the reason of the error...
Cheers,
Martin

On 08/05/2024 06:59, Tom Peat wrote:
Hello All,

I'm not sure if this is specific to me or whether I missed the fix, but I'm 
currently running Ubuntu 22.04.1 and updated to the latest ccp4 version 8.0.019 
and Coot crashes. I tested to see whether it was just the ccp4 version by 
downloading coot separately into my bin directory 
(coot-Linux-x86_64-ubuntu-20.04.3-pre-release-gtk2-python as this was the 
latest version I could find) and that gave the same outcome: core: #f
No core file found. No debugging

Coot crashed in the previous version of ccp4 8.0.017, which is one reason I 
upgraded to 8.0.019. I'm not sure if there was an update to Ubuntu that may 
have started this whole debacle, but everything seemed to work last month...

Has anyone else encountered this? Was there a fix? I googled several times and 
got some potential issues with libraries (libssl, etc), but none of these 
potential fixes helped.
cheers, tom



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Re: [ccp4bb] Ubuntu and Coot

[Tom Peat]

Just an update- I tested using Coot through the Phenix package and that seems 
to work (version 1.21-5207-000 and version 0.9.8.93 of Coot). Maybe a version 
issue? Or Phenix just comes with libraries that ccp4 doesn't? Not sure yet.
cheers, tom

From: CCP4 bulletin board  on behalf of Martin Malý 

Sent: Wednesday, May 8, 2024 5:31 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Ubuntu and Coot

Dear Tom,
I am using basically the same setup (Linux Mint 21.3 Xfce based on Ubuntu 
22.04, CCP4 8.0.019 including Coot 0.9.8.93). Everything works well on my 
computer. I did not have any issues with Coot even in CCP4 8.0.017. I am sorry 
I don't know the reason of the error...
Cheers,
Martin

On 08/05/2024 06:59, Tom Peat wrote:
Hello All,

I'm not sure if this is specific to me or whether I missed the fix, but I'm 
currently running Ubuntu 22.04.1 and updated to the latest ccp4 version 8.0.019 
and Coot crashes. I tested to see whether it was just the ccp4 version by 
downloading coot separately into my bin directory 
(coot-Linux-x86_64-ubuntu-20.04.3-pre-release-gtk2-python as this was the 
latest version I could find) and that gave the same outcome: core: #f
No core file found. No debugging

Coot crashed in the previous version of ccp4 8.0.017, which is one reason I 
upgraded to 8.0.019. I'm not sure if there was an update to Ubuntu that may 
have started this whole debacle, but everything seemed to work last month...

Has anyone else encountered this? Was there a fix? I googled several times and 
got some potential issues with libraries (libssl, etc), but none of these 
potential fixes helped.
cheers, tom



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[ccp4bb] CryoEM Research Assistant position at MSKCC

[de la Cruz, M. Jason]

Dear Colleagues,

The Memorial Sloan Kettering Cancer Center in New York City has recently 
expanded its CryoEM Facility, and has an opening for a CryoEM Research 
Assistant.  The CryoEM Facility specializes in macromolecular structure 
determination of proteins via single particle analysis.  The facility operates 
a Titan Krios G2 microscope with a Gatan K3 camera and a newly-installed Krios 
G4 microscope with Selectris X energy filter and Falcon 4i camera.

The CryoEM Research Assistant will assist the facility manager to perform 
research activities central to an efficient cryoEM imaging operation, including 
TEM grid preparation, microscope loading, and providing training and support to 
facility users.  The candidate must have good communication skills, the ability 
to teach users from diverse backgrounds, and be an excellent team player.

Candidates should have a bachelor’s degree in science, particularly in the 
fields of biology, biophysics, biochemistry, or engineering.  A Master’s degree 
is preferred, but not essential for candidates with appropriate background in 
electron microscopy/cryoEM.

The salary range for this position is $66,500 - $103,100.

The formal application link is here: 
https://externaltalent-mskcc.icims.com/jobs/77801/cryoem-research-assistant/job?mode=view=false=755=500=true=false=-300=-240

Interested candidates should contact:

M. Jason de la Cruz
Manager, CryoEM Facility
Associate Laboratory Member, Structural Biology Program
Sloan Kettering Institute
Memorial Sloan Kettering Cancer Center
delac...@mskcc.org

=

Please note that this e-mail and any files transmitted from
Memorial Sloan Kettering Cancer Center may be privileged, confidential,
and protected from disclosure under applicable law. If the reader of
this message is not the intended recipient, or an employee or agent
responsible for delivering this message to the intended recipient,
you are hereby notified that any reading, dissemination, distribution,
copying, or other use of this communication or any of its attachments
is strictly prohibited. If you have received this communication in
error, please notify the sender immediately by replying to this message
and deleting this message, any attachments, and all copies and backups
from your computer.

Disclaimer ID:MSKCC



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Re: [ccp4bb] [EXTERNAL]Re: [ccp4bb] Modeling Disulfide Bond Occupancies

[Liliana Margent]

Thank you so much

From: Eleanor Dodson 
Date: Monday, May 6, 2024 at 3:30 PM
To: Liliana Margent 
Cc: CCP4BB@jiscmail.ac.uk 
Subject: [EXTERNAL]Re: [ccp4bb] Modeling Disulfide Bond Occupancies
***ATTENTION: This email came from an external source. Do not open attachments 
or click on links from unknown senders or unexpected emails.***

Well - I turn off occupancy refinement once there is a sort of consensus..
Disulphides often break after long exposures and you see the positive and 
negative blobs clearly. I must admit I usually just set 0.5 as occ , fix the 
surviving disulphide link and let the B values suggest a better ratio than 
o.5:0.5..
Eleanor

On Mon, 6 May 2024 at 20:20, Liliana Margent 
mailto:lmarg...@gradcenter.cuny.edu>> wrote:
Greetings everyone,

I'm currently in the process of modeling a disulfide bond in two structures. 
However, when I attempt to model single occupancy for the cysteines involved in 
the bond, negative density blobs emerge within the disulfide bond. This 
suggests the possibility of alternate conformations for the cysteines.

Yet, when I endeavor to model alternate conformations for both cysteines, their 
occupancies do not align despite running refinement with a bond parameter file 
that specifies the link. To illustrate, I initiate the refinement with 
occupancies for Cys472 as A0.75/B0.25 and for C384 as A0.75/B0.25, but 
post-refinement, the output occupancies appear as Cys472 A0.84/B0.16 and for 
C384 A0.97/B0.03. Where A confs participate in the s-s bond.

Has anyone else encountered this issue before, or does anyone have suggestions 
on how to refine these cysteines to achieve coherent occupancies?

Thank you for any insights you can provide.

Best,
Liliana



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[ccp4bb] 3 cryo-EM facility positions at Scottish Centre for Macromolecular Imaging, Glasgow, UK

[Mads Gabrielsen]

On behalf of Dr James Streetley. Please pass all enquiries to him.

Dear colleagues,

The Scottish Centre for Macromolecular 
Imaging (SCMI) is 
Scotland’s national cryo-EM facility, based at the University of Glasgow. Using 
our JEOL CRYO ARM 300 with Direct Electron Apollo and DE-64 detectors, we 
provide cryo-EM access to consortium members and external partners across 
Scotland. We also run a sample preparation lab and microscopes for specimen 
screening for local use.

Thanks to additional investment in the facility by the University of Glasgow, 
we are looking to recruit three support scientists to work with our users and 
develop the facility.

Glasgow is often listed as one of the top cities in the 
world
 and is especially known for its friendliness. In addition to the benefits of 
living in a vibrant city with rich heritage, our location on the west coast of 
Scotland gives great access to the Scottish countryside including the highlands 
and islands.

Senior Cryo-EM Support Scientist
Grade 7 (£39,347-£44,263), open-ended contract

These roles will focus on user training and support, setting up data 
collections and further development and optimisation of the facility.
This post is eligible for visa sponsorship.
Full details and application portal: 
https://my.corehr.com/pls/uogrecruit/erq_jobspec_version_4.jobspec?p_id=145750

Senior Cryo-EM Data Scientist
Grade 7 (£39,347-£44,263), open-ended contract

This role will be to provide expert assistance to users with their data 
processing tasks and manage the user experience post-acquisition: 
pre-processing, data delivery and eventual archiving.
This post is eligible for visa sponsorship.
Full details and application portal: 
https://my.corehr.com/pls/uogrecruit/erq_jobspec_version_4.jobspec?p_id=145749

Cryo-EM Support Scientist
Grade 6 (£32,332 - £36,024), open-ended contract

This role will manage operations in our sample preparation lab with a view to 
providing imaging support as the postholder’s experience grows.
This post may be eligible for sponsorship under the skilled worker visa, if the 
applicant can use the new entrant tradeable points scheme.
Full details and application portal: 
https://my.corehr.com/pls/uogrecruit/erq_jobspec_version_4.jobspec?p_id=145751

All positions are eligible for relocation assistance where appropriate.
The closing date is 4th June, 23:45.

I am happy to take any questions via email but please note applications must go 
through the University’s portal to be considered.

Best wishes,
James

Dr James Streetley

SCMI Facility Manager
Scottish Centre for Macromolecular Imaging
Sir Michael Stoker Building
464 Bearsden Road
Glasgow
G61 1QH
United Kingdom

+44 141 330 2161 (office)
+44 141 330 7495 (microscope suite)
https://www.gla.ac.uk/researchinstitutes/iii/cvr/facilities/scmi/







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Re: [ccp4bb] ccp4i2 stopped working (no startup) - advice?

[Renato Weiße]

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" :


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  

[ccp4bb] ccp4i2 stopped working (no startup) - advice?

[Thorn, Dr. Andrea]

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

Re: [ccp4bb] Ubuntu and Coot

[Martin Malý]

Dear Tom,
I am using basically the same setup (Linux Mint 21.3 Xfce based on 
Ubuntu 22.04, CCP4 8.0.019 including Coot 0.9.8.93). Everything works 
well on my computer. I did not have any issues with Coot even in CCP4 
8.0.017. I am sorry I don't know the reason of the error...

Cheers,
Martin

On 08/05/2024 06:59, Tom Peat wrote:

Hello All,

I'm not sure if this is specific to me or whether I missed the fix, 
but I'm currently running Ubuntu 22.04.1 and updated to the latest 
ccp4 version 8.0.019 and Coot crashes. I tested to see whether it was 
just the ccp4 version by downloading coot separately into my bin 
directory (coot-Linux-x86_64-ubuntu-20.04.3-pre-release-gtk2-python as 
this was the latest version I could find) and that gave the same 
outcome: core: #f

No core file found. No debugging

Coot crashed in the previous version of ccp4 8.0.017, which is one 
reason I upgraded to 8.0.019. I'm not sure if there was an update to 
Ubuntu that may have started this whole debacle, but everything seemed 
to work last month...


Has anyone else encountered this? Was there a fix? I googled several 
times and got some potential issues with libraries (libssl, etc), but 
none of these potential fixes helped.

cheers, tom



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