Re: [ccp4bb] Wincoot stereo display on Windows 10

[Trevor Sewell]

We continue to use Nvidia 3D vision with coot under Windows 7 and Linux with 
the old Nvidia drivers and Quadro M5000 graphics cards

The Nvidia statement on their 3D vision product is here:

https://nvidia.custhelp.com/app/answers/detail/a_id/4845/~/3d-vision-end-of-life---faq

They have separated the graphics driver and the hub driver - which is now 
available separately for Windows 10

https://www.nvidia.com/en-us/drivers/nv3dvisionusb/390_41/nv3dvisionusb-driver/

Replacement  IR hub and glasses are being made by XINSAITE in China and are 
available on eBay https://www.ebay.com/itm/283651885707 at an exploitative 
price!

An alternative - mentioned in the Nvidia FAQ may be worth trying - It would be 
good to hear if anyone has experience with this

http://volfoni.com/en/edge-rf/

All the best

Trevor


On 23 Mar 2020, at 17:46, EchelonIV . 
mailto:arne.raasa...@gmail.com>> wrote:


CAUTION: This email originated outside the UCT network. Do not click any links 
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Hello,

stereo display works completely fine for me on Windows 10 (WinCoot version 
0.8.6.1) - go ahead and try an older version if you have the 
option. Have you tried re-installing WinCoot?

Stay healthy,
Arne

On Mon, Mar 23, 2020 at 4:42 PM Yong Wang 
<3c4fc05cc53b-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Hello,

Wincoot stereo display works on Windows 7 but not on Windows 10 (program 
crashes as soon as stereo is enabled).  It has been a while since Windows 10 
became the main Windows platform.  Has anyone found a way to get Wincoot stereo 
display to work on Windows 10?

Thanks,

Yong

Research Advisor
Global Structural Biology
Lilly Research Laboratories
A Division of Eli Lilly and Company
Lilly Coporate Center
Indianapolis, Indiana 46285 U.S.A.

Phone: 1-317-655-9145




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--
--
Arne Raasakka
PhD Biochemistry
Department of Biomedicine, University of Bergen
Norway



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[ccp4bb] Professor and director of the Electron Microscope Unit, University of Cape Town

[Trevor Sewell]

The University of Cape Town is seeking to recruit a Professor and Director to 
lead the Electron Microscope Unit within the Aaron Klug Centre for Imaging and 
Analysis.  This world-class facility serves the nanoscale imaging needs of both 
the physical and life sciences, across Science, Engineering and Health Sciences 
at UCT, with a wide user base beyond UCT. The Unit is located in a modern 
building that is purpose-built to house high resolution electron microscopes. 
The resources of the Unit include transmission and scanning electron 
microscopes, other related imaging tools, specialized preparative equipment and 
six scientific and technical officers capable of operating and maintaining the 
equipment. 

The main purpose of the position is to lead, develop, maintain, market and 
manage the Unit to ensure that it is at the cutting edge of imaging and 
analysis techniques.  The Director is expected to lead the Unit as an 
internationally recognized multi-disciplinary facility in the interests of the 
users of the facility, primarily researchers from the University of Cape Town 
and their post-graduate students. 

Up to fifty percent of the Director’s time should be spent on self-initiated 
research in imaging and analysis or a field which uses modern imaging 
techniques extensively. 

Requirements:

•   Possession of a PhD and an academic track record to qualify for 
appointment at Professorial level; 
•   An active, funded, research programme;
•   At least ten years’ experience in an academic and/or applied research 
environment, with demonstrated leadership achievements;
•   Substantial experience in the use of electron microscopy and other 
imaging and analysis techniques in research, as evidenced by a publication 
record and a track record; 
•   Demonstrated leadership and managerial skills;
•   Excellent track record of raising funds for research as lead 
investigator and/or as co-investigator on grant applications; and
•   Experience in managing the professional development activities of young 
scientists.
Responsibilities:

The successful candidate will be responsible for: 

•   Providing strategic direction to the Unit;
•   Directing, managing and leading the activities and development of the 
Unit; 
•   Marketing and the promotion of the Unit in the interests of the users 
of the facility; 
•   Conduct high quality scholarly research in an area that is closely 
related to nanoscale imaging and supervise postgraduate students;
•   Educate researchers and postgraduate students in the application and 
use of advanced electron microscopy and other imaging and analysis techniques;
•   Formulate grant proposals for new equipment and major long-term 
research projects;
•   Forge synergies between the Unit, the academic departments and other 
entities within and outside the University;
•   Providing scientific leadership within the Unit; and
•   Managing research teams. 

The annual remuneration packages for 2018, including benefits, at Professor 
level is R1 167 756.

To apply, please e-mail the below documents in a single pdf file to Ms Tracy 
Moore at recruitmen...@uct.ac.za:
-   UCT Application Form (download at http://forms.uct.ac.za/hr201.doc)  
-   A covering letter of motivation which addresses the above criteria, 
including a statement on your potential contribution as the Director for the 
Unit, and 
-   Curriculum Vitae (CV)   

Please ensure the title and reference number are indicated in the subject line.

An application which does not comply with the above requirements will be 
regarded as incomplete. 

Telephone:  021 650 5405Website:
www.uct.ac.za 

Reference number:   E18350  Closing date:   
31 October 2018 

UCT is committed to the pursuit of excellence, diversity and redress in 
achieving its equity targets. Our Employment Equity Policy is available at 
http://www.uct.ac.za/downloads/uct.ac.za/about/policies/eepolicy.pdf. 

UCT reserves the right not to appoint.



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[ccp4bb] Incorrect Structure in the PDB

[Trevor Sewell]

I have come across a key paper in my field that describes an enzyme mechanism. 
Their work is based on a deposited structure – by other authors - that is 
incorrectly interpreted.

Is there a process for removing a demonstrably wrong structure (deposited by 
others) from the PDB and replacing it with a correctly interpreted structure 
based on the original data? Or is there an alternative, and generally 
recognized, way of getting the correct structure in the public domain?

Many thanks for your advice on this matter.

Trevor Sewell

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[ccp4bb] Refmac5 and Coot for refining cryo-EM structures

[Trevor Sewell]

I have a 3.4 A (enzyme – protein only) map that I have fitted manually using 
Coot and automatically with Rapper. It all looks very nice – I can fit all but 
13 of the 330 residues. I have the following questions:

Does refmac5 have a way of refining the scale of the map? – I did my best to 
calibrate the microscope – but it would be nice to have the scale as a 
refinable parameter.

Is there a way of having Coot know that it is an electron map and not an x-ray 
map? The main issue is that carboxyls seem to be invisible and Coot tries to 
fit them as though the map had them there – which results in some pretty dopey 
stuff. The problem doesn’t seem to apply in refmac5 if you use the source EM as 
described in the instructions.

What is a reasonable starting weight for vdwrestraints ? Is there a rule of 
thumb for choosing this?

What are acceptable values for the Rfactor produced by Refmac5? The fit looks 
pretty good with an Rfactor of .39. What is the experience of the community in 
this regard?

Many thanks

Trevor Sewell


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