Re: [ccp4bb] 3D viewing room options

[Arnaud Hungler]

Hi all,

In Stefan Arold's group, we are currently developping a virtual reality plugin
for PyMol. It is based on the OSVR platform, and therefore should work with
OSX, Windows, Linux, Android (if you find a way to use PyMol on an Android
device !), and be compatible with any kind of 3D headset (Oculus Rift, HTC
Vive, Razor OSVR, and even the Google cardboard).

The project is available on github here :
https://github.com/StruBE-KAUST/pymolOSVR

The most annoying part is to make the OSVR server work on your system. The
next step is to launch PyMol, install this repo as a plugin, then click on
Plugin > OSVR Viewer

You may need to move your window into the headset display, if it stays on your
computer screen.

The plugin is still under development. Some features are missing, and some are
not as stable as it should be. But we keep going.

Arnaud Hungler
Software Engineer - KAUST


On Monday, 14 November 2016 02:11:43 AST Matthias Wolf wrote:
> Hi Xavier et al,
>
> I second Brian's opinion.
> We have used a 49" 4k TV, a Sony Bravia X8500B for more than a year now with
> good results. http://www.sony.jp/bravia/products/KD-49X8500B/
> There is probably an updated model of this around.
>
> Passive stereo 3D on this screen has better depth perception than the active
> stereo on the Asus VG278, although getting the parallax right is tricky. As
> Brian mentioned, the vertical position of the viewer is critical and there
> is a rather narrow sweet spot vertically, which might limit its use for a
> larger viewing room. It gives good stereo perception at a distance -
> sitting close to it can cause some eye strain in stereo if settings are not
> tweaked, but it is just a big screen! Despite the 4k resolution, the
> horizontal alternately polarized lines are still visible in stereo
> (resulting in half the vertical resolution), which is not a big deal, in
> particular from a distance. The nice thing is that there is absolutely no
> flicker or ghosting, since it does not use page-flipped stereo. But for
> modeling I still prefer the active stereo displays.
>
> In 2D mode it works great as a 4k monitor and text appears crisp - the
> exception is red, which appears blurry and at low resolution (in particular
> on blue background - this must be due to the dye matrix). It is a great
> monitor replacement with a lot of screen real estate and I would recommend
> it as such. It also comes with an integrated camera. It is connected via
> HDMI 2.0 or display port and I have tested it with both, using NVidia
> quadro K5000 and GTX980 - the surprise was that windowed stereo worked just
> fine with the (non-quadro) GTX card (this was on windows server 2012R2, I
> didn't try it on linux). I tested wincoot, pymol, chimera and Amira in
> stereo, which all worked.
>
>Matt





This message and its contents including attachments are intended solely for the 
original recipient. If you are not the intended recipient or have received this 
message in error, please notify me immediately and delete this message from 
your computer system. Any unauthorized use or distribution is prohibited. 
Please consider the environment before printing this email.

[ccp4bb] Early bird registration for CCP4 Study Weekend 2017 this Sunday!!

[Karen McIntyre]

Early bird registration for CCP4 Study Weekend taking place in Nottingham in 
January 2017 will end on 20th November - this Sunday!!!

This is also the closing date for standard student bursaries.

You will be able to register after this date if spaces remain (until 12th 
December) but the registration fee will go up to £285.  Also no student 
bursaries will be available.

Register at 
https://eventbooking.stfc.ac.uk/news-events/ccp4-study-weekend-2017-344 .

Regards

Karen McIntyre
CCP4 Study Weekend Local Organising Committee
Scientific Computing Department - CCP4
R92 1.22 RCaH

Science & Technology Facilities Council
Rutherford Appleton Laboratory
Harwell Campus
Didcot
Oxfordshire
OX11 0FA

Tel +44 (0) 1235 44 5790
Fax  +44 (0) 1235 56 7720

[cid:image001.png@01D23E6E.29E8E820]@ccp4_mx

**Please note that I only work part-time until 1.30pm**

Re: [ccp4bb] Nitrate versus Carbonate

[Keller, Jacob]

Yes, exactly, those two proteins. Were you involved?

JPK

From: Clement Angkawidjaja [mailto:clem...@evec.jp]
Sent: Monday, November 14, 2016 12:42 AM
To: Keller, Jacob ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Nitrate versus Carbonate

Maybe the Ca is just there as an additional binding site for carbonate.
Btw, are you looking at CmpA/NrtA?

Cheers,
Clement

From: Keller, Jacob
Sent: Friday, November 11, 2016 2:51 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Nitrate versus Carbonate

Well, I was looking at two periplasmic binding proteins, one for NO3 and one 
for CO3/HCO3, and was wondering whether the obligate cooperative Ca ion 
adjacent to the ligand only in the CO3 binder was necessary, and how in any 
case it would help distinguish the two if at all. Roger’s comments about CA are 
interesting in light of this, since there is no Ca ion involved (from what he 
said), and still CA binds so specifically to HCO3 and not NO3. I wonder whether 
the Ca ion protein I am looking at is specific for CO3 alone? I have seen this 
Ca ion phenomenon also in a lactate binding protein. Or maybe the Ca ion just 
makes the affinity much stronger than in CA’s?

Jacob Pearson Keller

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Clement 
Angkawidjaja
Sent: Friday, November 11, 2016 12:11 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Nitrate versus Carbonate

Dear JPK

What I know is we do not have much nitrate in the blood unlike 
carbonate/bicarbonate.
Nitrite, a nitrate byproduct can cause problems but it has a different 
structure and probably does not interfere with bicarbonate binding to relevant 
proteins.

Cheers,
Clement

From: Keller, Jacob
Sent: Friday, November 11, 2016 5:41 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Nitrate versus Carbonate

Dear Crystallographers,

I don’t think there is any feasible way crystallographically to distinguish 
between nitrate and carbonate or bicarbonate—correct? But that is not my main 
question.

My main question is: given that nitrate and carbonate are both very important 
and also very different physiologically, and therefore they must be 
distinguished/recognized by cells, how is this done, since the ions are so 
similar in structure? Is there some aspect of these ions that differs 
dramatically of which I am not aware? What kind of “handles” could a protein 
grab onto to distinguish between nitrate and carbonate/bicarbonate?

JPK


***
Jacob Pearson Keller, PhD
Research Scientist
HHMI Janelia Research Campus / Looger lab
Phone: (571)209-4000 x3159
Email: kell...@janelia.hhmi.org
***

[ccp4bb] Postdoc Heidelberg, Germany

[Grant Hansman]

Project:
We will use a multidisciplinary approach to develop Nanobodies against murine 
norovirus, including bioinformatics, X-ray crystallography, molecular biology 
techniques, cell culture, and an animal model. Nanobodies are gaining a lot of 
interest in therapeutics and basic research tools. Nanobodies were shown to 
block virus attachment to cellular receptors in HIV, influenza virus, and 
respiratory syncytial virus. In this project, we will develop several high 
affinity Nanobodies that are able to disassemble virus particles or block 
attachment to cells - hence reduce or inhibit infections. By targeting regions 
on these particles that it is highly conserved among genetically distinct 
strains and most likely important for the structural integrity of the particles 
we expect that drug resistance is unlikely to develop, making conserved regions 
an ideal target for antivirals.

Requirements:
•   2+ years of relevant experience in protein structural biology

•   Experience in protein expression and purification (e.g., affinity, 
size-exclusion, ion-exchange, etc.)

•   Biochemical/biophysical characterization techniques (e.g., Western 
blot, light scattering, calorimetry, DLS)

•   Excellent knowledge and expertise in protein structural biology

•   Participation in all stages of the structure determination process from 
target selection through to model interpretation

•   Demonstrated independent thought/creativity in science. 

•   Willingness to drive challenging scientific projects in an independent 
and creative manner

•   Excellent collaboration, communication (oral and written) and 
multitasking skills

•   Presenting results in international meetings and peer-reviewed Journals


Interested applicants should send CV and statement of interest to Grant 
Hansman: g.hans...@dkfz.de

www.hansman-lab.com

Re: [ccp4bb] 3D viewing room options

[mesters]

Perception of depth is strongly dependent on the width of the screen and 
accordingly, a 49" TV should do better than a 27" Monitor :-)


Anyway, if you goal is to try and accommodate more than 4 people (not 
all can sit on the sweet spot I guess), the 3D DLP stereo beamer setup 
offers a more viable option in my humble opinion.


Jeroen


Am 14.11.16 um 03:11 schrieb Matthias Wolf:

Hi Xavier et al,

I second Brian's opinion.
We have used a 49" 4k TV, a Sony Bravia X8500B for more than a year now with 
good results.
http://www.sony.jp/bravia/products/KD-49X8500B/
There is probably an updated model of this around.

Passive stereo 3D on this screen has better depth perception than the active 
stereo on the Asus VG278, although getting the parallax right is tricky. As 
Brian mentioned, the vertical position of the viewer is critical and there is a 
rather narrow sweet spot vertically, which might limit its use for a larger 
viewing room. It gives good stereo perception at a distance - sitting close to 
it can cause some eye strain in stereo if settings are not tweaked, but it is 
just a big screen! Despite the 4k resolution, the horizontal alternately 
polarized lines are still visible in stereo (resulting in half the vertical 
resolution), which is not a big deal, in particular from a distance. The nice 
thing is that there is absolutely no flicker or ghosting, since it does not use 
page-flipped stereo. But for modeling I still prefer the active stereo displays.

In 2D mode it works great as a 4k monitor and text appears crisp - the 
exception is red, which appears blurry and at low resolution (in particular on 
blue background - this must be due to the dye matrix). It is a great monitor 
replacement with a lot of screen real estate and I would recommend it as such. 
It also comes with an integrated camera. It is connected via HDMI 2.0 or 
display port and I have tested it with both, using NVidia quadro K5000 and 
GTX980 - the surprise was that windowed stereo worked just fine with the 
(non-quadro) GTX card (this was on windows server 2012R2, I didn't try it on 
linux). I tested wincoot, pymol, chimera and Amira in stereo, which all worked.

Matt



--
Dr.math. et dis. nat. Jeroen R. Mesters
Deputy, Senior Researcher & Lecturer
Program Coordinator /Infection Biology/ 



Institute of Biochemistry, University of Lübeck
Ratzeburger Allee 160, 23538 Lübeck, Germany
phone: +49-451-31013105 (secretariate -31013101)
fax: +49-451-31013104


http://www.biochem.uni-luebeck.de 
http://www.eine-stadt-sieht-gelb.de 
http://www.uni-luebeck.de/studium/studiengaenge/infection-biology
http://www.iobcr.org 
--

If you can look into the seeds of time and tell which grain will grow 
and which will not, speak then to me who neither beg nor fear 
(Shakespeare's Macbeth, Act I, Scene 3)

--
Two things are infinite, the universe and human stupidity, and I'm not 
about the Universe (Albert Einstein)

--
Disclaimer
* This message contains confidential information and is intended only 
for the individual named. If you are not the named addressee you should 
not disseminate, distribute or copy this e-mail. Please notify the 
sender immediately by e-mail if you have received this e-mail by mistake 
and delete this e-mail from your system.
* E-mail transmission cannot be guaranteed to be secure or error-free as 
information could be intercepted, corrupted, lost, destroyed, arrive 
late or incomplete, or contain viruses. The sender therefore does not 
accept liability for any errors or omissions in the contents of this 
message, which arise as a result of e-mail transmission. If verification 
is required please request a hard-copy version. Please send us by fax 
any message containing deadlines as incoming e-mails are not screened 
for response deadlines.
* Employees of the Institute are expressly required not to make 
defamatory statements and not to infringe or authorize any infringement 
of copyright or any other legal right by email communications. Any such 
communication is contrary to Institute policy and outside the scope of 
the employment of the individual concerned. The Institute will not 
accept any liability in respect of such communication, and the employee 
responsible will be personally liable for any damages or other liability 
arising. Employees who receive such an email must notify their 
supervisor immediately.

--

[ccp4bb] Verify 3D score

[Hammond, Robert Glenn]

Hi,


Does anyone know how to calculate a theoretical or expected Verify 3D score 
based on the amino acid sequence length? In the reference papers ( Bowi, et 
al., 1991 and Leuthy, et al., 1992) they describe several proteins and their 
expected score but do not supply a function for how to calculate an expected 
score. I look at example proteins and come up with a ballpark value. Also, I 
consult their first table and to get an idea, but I do not have an exact value 
for what my Verify 3D would be.


Any help is appreciated. Thank you.


Regards,

Robert Hammond

[ccp4bb] BCA Winter Meeting 2016 (1st reminder).

[Jonathan Cooper]

BCA Biological Structures Group Winter Meeting 2016: "Seeing the Wood for the 
Trees in Structural Biology." The meeting will be held on Monday 19th December 
2016 at Birkbeck College, London starting at 11.00 am. The aim of the meeting 
is to glimpse at some of the contemporary approaches for assembling individual 
molecular structures into a bigger picture of biological systems, be they 
structural, metabolic, functional, disease-related or such-like. The meeting 
doubles as a career celebration event for the many ex-students, colleagues and 
collaborators of Prof Steve Wood whose research in Sussex, Birkbeck, 
Southampton and more recently UCL spans at least some 5 decades. Speakers 
include:
Prof Tom Blundell FRS, Department of Biochemistry, University of Cambridge. 
"Increasing complexity to obtain selectivity in cell regulation: structural 
studies of multiprotein signalling systems."
Prof Liz Carpenter, Structural Genomics Consortium, University of Oxford.
Prof Jonas Emsley, School of Pharmacy, University of Nottingham. "Investigation 
of the contact system assembly and activation."
Dr Simon Kolstoe, School of Biological Sciences, University of Portsmouth. 
"Determining the molecular interactions of serum amyloid P component."
Prof Laurence Pearl FRS, School of Life Sciences, University of Sussex. 
"Phosphorylation dependent assembly of the DNA Damage Response."
Prof Helen Saibil FRS, Department of Biological Sciences, Birkbeck.
Patrick Shaw-Stewart, Douglas Instruments Ltd. "Microseed matrix-screening 
(rMMS): introduction, theory, practice and a new technique for membrane protein 
crystallization in LCP."
Prof Garry Taylor, School of Biology, University of St Andrews. "An engineered 
multivalent sialic acid binding biologic as a preventative of influenza."
Prof Martin Warren, School of Biosciences, University of Kent.
Dr Marcus Winter. "Rigaku Oxford Diffraction: Advances in Crystallography." The 
closing date for registration is Friday 9th December 2016. As usual, the 
registration fee will include one year's membership of the BCA. For more 
information and to register, please visit the meeting website:
http://bsg.crystallography.org.uk/wint16.html

[ccp4bb] postdoctoral position at Columbia University Medical Center

[Qing Fan]

A postdoctoral research scientist position is available at Columbia
University Medical Center. We study the structure and function of cell
surface receptors using a combination of x-ray crystallography, cryo EM and
biochemical methods. The successful candidate will focus on the expression
and purification of several receptors using recombinant systems for
structure determination. The candidate should have a strong background in
molecular biology and protein biochemistry. Prior research experience in
large-scale protein production, membrane protein expression and
purification, and cell-based functional analysis is preferred.

Please send cv and contact information for at least two references to:

Qing R. Fan, PhD

Department of Pharmacology

Columbia University Medical Center

P&S Room 7-430

630 West 168th Street

New York, NY 10032

Email: qingrong...@gmail.com

[ccp4bb] Post-doc position at UTMB to study structural basis of neurodegenerative disease

[Morais, Marc C.]

Post-doctoral position open immediately at UTMB to study the structural biology 
of neurodegenerative disease

A postdoctoral position in structural biology is available to study the role of 
protein tau in neurodegenerative diseases at the University of Texas Medical 
Branch, in Galveston, TX. This NIH-funded position will utilize a combination 
of cryo-electron microscopy, tomography, X-ray crystallography, SAXS, and 
biochemistry to investigate the structures of protein tau assemblies and the 
mechanism of tau-related neuropathies. The successful candidate will report to 
Dr. Marc Morais and Dr. Rakez Kayed, experts in structural biology and 
tau-related neurodegenerative diseases, respectively. Experience in either 
X-ray crystallography or cryo-electron microscopy is required.


Structural biology facilities at UTMB are outstanding (https://scsb.utmb.edu/). 
X-ray crystallography 
resources include two X-ray 
area detector systems, a Phoenix crystallization robot, a Minstrel crystal 
imaging robot, and an Alchemist liquid handling robot. CryoEM resources include 
a JEOL 2200FS cryo-EM microscope equipped with a DE20 direct electron detector 
for high-resolution imaging work, a cryo-capable JEOL 2100, an FEI vitrobot, 
and a BSL-3 room for viral and pathogen work. UTMB is also a member of high 
resolution cryoEM imaging consortia at the Baylor College of Medicine, and 
UCLA, which provide access to JEOL 3200 and Titan Krios microscopes, 
respectively.

Interested parties should send a CV, a brief statement of research interests, 
and a list of 2-3 references to both Dr. Marc Morais 
(mcmor...@utmb.edu) and Dr. Rakez Kayed 
(raka...@utmb.edu).





Marc Morais
Associate Professor
Dept. of Biochemistry & Molecular Biology University of Texas Medical Branch
6.614B Basic Science Building 301 University Boulevard, Galveston, TX
77555-0647