Re: [ccp4bb] 3D stereo and pymol

[Jim Fairman]

Reporting in a setup that we just made: Quadro P4000 + 3 pin stereo bracket
+ 3d vision 2 kit + ASUS VG248QE.

Running System76's PoPOS Ubuntu 17.10 distro - you'll have to install a
desktop environment that supports non-compositing (ie: XFCE).

Works beautifully.



--
Jim Fairman
C: 1-240-479-6575

On Tue, Nov 28, 2017 at 6:40 AM, mesters 
wrote:

> Hi,
>
> yes, consumer cards do have OpenGL implemented on a chip but the Nvidia
> driver did not allow OpenGL 3D to work until February 2013. As of Nvidia
> driver version 314.07, Nvidia added OpenGL quad buffered 3D Stereo for
> GeForce cards (at least under MS Windows 7/8). However, this was never
> officially announced and officially supported and only works if the monitor
> is preset to run at 120 Hz and the software automatically switches into
> full-screen mode. Sadly, windowed applications will not work. Under MS
> Windows 10, it does not seem to work anymore.
>
> We have a monitor with a build in emitter and that one works with the
> smaller/cheaper Quadro cards without the 3-pin connector but, it is
> virtually impossible nowadays to get such a monitor in order to avoid
> needing to buy an expensive Nvidia card with a 3-pin connector.
>
> To enjoy OpenGL quad buffered 3D Stereo, you will at least need a Quadro
> K4000/P4000/4000 with separate 3-pin bracket (all-in-all very expensive
> solution) or you will need to buy an older FX model such as the FX3700 with
> build-in 3-pin connector.
>
> At the Bay in the USA, unused / brand-new FX3700s are being offered right
> now for about 90-110 US$. That's the cheapest way out and 512 MB memory is
> sufficient unless you are trying work with VERY big PDB files. If so, try
> to get your hands on a "new, see details" Quadro 4000 and a separate PNY
> 3-pin mini DIN stereo bracket (930-50764--000 C for about 20 US$) or a
> "new, see details" Quadro 5000 with build-in emitter.
>
> Good luck
>
> Jeroen.
>
>
> Am 28.11.17 um 10:50 schrieb Johannes Cramer:
>
> Hi Christine,
>
> as far as I know, it does not work at all with Geforce cards. The Nvidia
> drivers do not support windowed quad buffered GL, which you need for
> coot/pymol. It does not matter whether you use Windows or Linux.
> But this is based on my personal experience from around Oct. 2016. Maybe
> something changed quietly since then. Again, as far as I know, you need a
> Quadro card.
>
> Cheers,
> Johannes
>
> 2017-11-06 21:24 GMT+01:00 Christine Gee :
>
>> Hi,
>>
>> I have looked in the archive for posts about this, but there hasn't been
>> one for about a year. Can anyone comment on whether they have managed to
>> get a linux flavor and GeForce cards to work with pymol and/or coot 3D
>> stereo? Geforce cards supposedly support openGL, but posts from October
>> last year on the BB suggests that it only works in windows unless you have
>> a monitor with a built in emitter. I would appreciate any feedback.
>>
>> Regards
>> Christine
>>
>>
>
> --
> 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 <+49%20451%2031013105> (secretariate -31013101)
> fax: +49-451-31013104 <+49%20451%2031013104>
>
> [image: http://jobs.zeit.de/image-upload/logo_10564.jpg]
> 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 
>
> Visiting Professorship in Biophysics, University of South Bohemia (CZ)
> President of the International Organization for Biological Crystallization
> (IOBCr)
> --
> 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)
> --
> "Aujourd'hui je sais qu'il n'y a pas de limites à la bêtise humaine -
> qu'elle est infinie." (Gustave Flaubert, French novelist, 1821-1880)
> --
> It is invariably the case that high resolution X-ray structures show
> significantly better agreement with solution observables such as coupling
> constants, 13C chemical shifts, and proton chemical shifts, than the
> corresponding NMR structures, including the very best ones. Hence, in most
> cases, a high-resolution crystal structure (< 2.0 Å) will provide a
> better description of the structure in solution than the corresponding NMR
> structure  (Kuszewski, Gronenborn & Clore, 1996, Protein Science 5
> :1067-80)
> --
> 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.

[ccp4bb] PyMol question

[Cygler, Miroslaw]

Hi,
When I loaded the ed map into PyMol v1.8.4.1 and used iso mesh around part of 
the protein all is well until I use the RAY command. In the ray traced image I 
see the unit cell box that does not show on the image in the normal view. How 
can I remove the box from the ray traced image?
Thanks for your help,

Mirek

[ccp4bb] Positions available in an EU training network

[Goldman, Adrian]

15 positions for PhD students in various aspects of structural and adhesion 
biology for VIral and BacteRial Adhesins (ViBrANT) are available.  This is an 
EU ITN (innovative Training Network), with positions in both academia and 
industry, and spanning all the way from Portugal to Finland,   The closing date 
for applications is January 4th.  Information about the network and the 
application forms are available at http://www.vibrant-itn.eu/

These are well-funded positions in leading labs around Europe, and available to 
students worldwide.  The only major stipulations are: (1) you must move country 
and (2) you may not have been working as a researcher for more than four years 
after your first degree.

Adrian Goldman

[ccp4bb] postdoc position available

[Zheng, Hongjin]

Dear Colleagues,

We are currently seeking a postdoctoral fellow in the laboratory of Dr. Hongjin 
Zheng at the University of Colorado, Anschutz Medical Campus, Denver, CO, USA. 
The successful candidate will join an energetic group investigating the 
structural and functional mechanisms of various disease-related membrane 
proteins and protein complexes, using primarily cryo-EM and X-ray 
crystallography. Our laboratory is well supported by the department and school 
of medicine, equipped with state-of-art cryo electron microscope with direct 
detector, in-home X-ray machine, NMR, and a great biophysics core.
The ideal candidate should hold a Ph.D. degree in the areas related to 
biological sciences, with experiences in molecular biology, protein 
biochemistry and structural biology. Interested applicants please send your CV 
to hongjin.zh...@ucdenver.edu.

Best,
Hongjin Zheng

-
Hongjin Zheng, Ph.D.
Assistant Professor
Biochemistry & Molecular Genetics
Anschutz Medical Campus
University of Colorado, Denver
12801 East 17th Ave
MS 8101, Rm L18-9111A
Aurora, CO 80045
Phone: 303-724-9374
Email: hongjin.zh...@ucdenver.edu

[ccp4bb] AW: Re: [ccp4bb] Van der waals force

[Herman . Schreuder]

Hi Jiri,

A low-tech solution that will certainly work, is just to manually show the 
relevant distances. In coot under measure there is an option to show distances, 
just by clicking on the two atoms involved.

Good luck!
Herman



Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von chemocev 
marker
Gesendet: Samstag, 9. Dezember 2017 16:57
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Van der waals force

Hi
Thanks for your good help and I am wondering is there clear way to show these 
forces like H-bond. I tried KING and can see the VDW radii but not the visual 
representation. Does coot has any option for this.
best
Jiri

On Fri, Dec 8, 2017 at 8:57 AM, HERMAN VAN TILBEURGH 
mailto:herman.van-tilbeu...@u-psud.fr>> wrote:
jiri, VDW forces are always acting and between any pair of atoms
the optimal distance (most favourable interaction energy) depends on the pair 
of atoms involved in the interaction, but is a big bitter than the sum of 
atomic radii
all the best
herman
Herman van Tilbeurgh
Professor structural biology
Directeur Adjoint Ecole Doctorale Innovation Thérapeutique: du fondamental à 
l'appliqué

Institut de Biologie Intégrative de la Cellule - I2BC
UMR 9198 CNRS- Université Paris Sud
Team: Fonction et Architecture des Assemblages MacroMoléculaires
http://www.i2bc.paris-saclay.fr/spip.php?article256

Batiment 430
91405 Orsay
France

Tel: 33 1 69 15 31 55
fax: 33 1 69 85 37 15
herman.van-tilbeu...@u-psud.fr





Le 8 déc. 2017 à 08:52, KLAHOLZ bruno 
mailto:klah...@igbmc.fr>> a écrit :


Hello,

van der Waals interactions are very weak, this is why we usually speak about 
van der Waals contacts rather than interactions.
These are usually in the range of 3.5-3.8/4 Å (smaller than that may indicate a 
close contact or steric clash of an atomic model under refinement), 
corresponding to the packing of the van der Waals spheres of the individual 
atoms.
In hydrogen bond interactions, the term “interaction” normally implies sharing 
a hydrogen atom between two polar residues, for example between the hydroxyl 
group of a threonine side chain with a carbonyl group of the main chain peptide 
backbone; in there one should take into account the geometry as well (e.g. 
~120°-180° is favorable, 90° is not). Note that some positions such as Calpha-H 
can be slightly polarized (these contribute to bifurcated H-bonds in beta 
sheets for example, see e.g. 
https://www.ncbi.nlm.nih.gov/pubmed/12220491
 ).
In the context of series of van der Waals contacts between hydrophobic residues 
there can be additive effects of the weak interactions with then sum up, but in 
this context one should also consider entropic effects such as de-solvatation 
which becomes favorable energetically.

Hope this helps.

Best regards,

Bruno


###
Bruno P. Klaholz
Centre for Integrative Biology
Institute of Genetics and of Molecular and Cellular Biology
67404 ILLKIRCH
FRANCE
http://igbmc.fr/Klaholz




From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of chemocev 
marker
Sent: 08 December 2017 07:55
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Van der waals force

Hi
I just have a basic question if the Van der waals interaction will exist 
between the hydrophobic residues or it can also be contributed by the polar 
residues as well. What distance is required for the Van der waals interaction.
best
Jiri

[ccp4bb] Call for access to Synchrotron Beamline Facilities, 2017 - EMBL Hamburg, Germany

[Sarah Marshall-Bensch]

*Call for access to Synchrotron Beamline Facilities, 2018 - EMBL 
Hamburg, Germany


*We announce a call for synchrotron beam time applications in biological 
small-angle X-ray scattering (SAXS) and macromolecular crystallography 
(MX) for the period April - December 2018. The following EMBL/DESY 
beamlines at PETRA III are available: P12 (SAXS), P13 (MX), and P14 
(MX). The deadline for submission of proposals is on _Friday 12th 
January 2018_ after which the proposals will be evaluated by an external 
Project Evaluation Committee. The users will be informed about the 
results of their application by 5th March 2018.


Groups applying for beam time to work on several projects in MX and SAXS 
are strongly encouraged to submit BAG (Block Allocation Group) 
proposals. If you wish to renew an existing BAG proposal, you will be 
requested to complete a progress report or a full two-year report before 
submitting your proposal. Mail-in proposals for the use of robotic 
sample changer are encouraged for SAXS.


A detailed description of the three beamlines and links to the 
electronic proposal forms can be found at:


SAXS: http://www.embl-hamburg.de/services/saxs/index.html
MX: http://www.embl-hamburg.de/services/mx/index.html

Submit 
a proposal via the EMBL Hamburg user portal: 
https://smis.embl-hamburg.de/misapps/SMISWebClient/protected/welcome.do


Access to the EMBL Hamburg facilities also includes assistance with 
crystallisation, sample preparation and, in combination with an EMBL 
beamline visit, with sample characterisation and optimisation.
Usage of the beamlines and biophysical facilities for translational 
research can in part be supported by the iNEXT project 
(http://www.inext-eu.org/access/) of the Horizon 2020 programme of the 
European Union.


For further general information, please contact the EMBL Hamburg user 
office:

Tel.: +49 40-89902-111 / 183
Email: useroffice (at) embl-hamburg.de

For specific information:
saxs (at) embl-hamburg.de (small-angle X-ray scattering)
mx (at) embl-hamburg.de (macromolecular crystallography)
spc (at) embl-hamburg.de (sample preparation and characterisation)

Re: [ccp4bb] domain prediction of a membrane protein

[Robert Stroud]

If the protein is eukaryotic you may need to express it in eukaryotic cells, 
probably with a tag for later identification / purification of the fragments. 
This might work for a plasma membrane protein, -but if the protein is from an 
internal organelle then to find the correct topology you may need to purify the 
organelle. Proteolysis is easy to apply, -several proteases from the outside of 
the cell followed by mass spec of the species with the tag. mutagenesis and 
chemical labelling is another approach.  If the protein has a cleaved signal 
sequence that would give a strong experimental clue to sidelines also. 
Robert Stroud
str...@msg.ucsf.edu




> On Dec 10, 2017, at 6:33 PM, Firdous Tarique  
> wrote:
> 
> Hello everyone
> 
> I am trying to clone some domains of a transmembrane protein. I have used an 
> online server "Phobius" for the prediction of sequences which is showing it 
> to be a membrane protein with cytoplasmic, non cytoplasmic and transmembrane 
> regions. Attached is the image of that prediction. Regions from 100-200 amino 
> acid residues which I am more concerned about is predicted to be cytoplasmic 
> in nature while other servers have predicted it to be non cytoplasmic in 
> nature. I am having problems in expressing this domain. Sometimes the 
> prediction may go wrong for such a short stretch of amino acid residues.
> 
> My question is to know about any technique or any classical experiment which 
> can actually tell me the exact location of this domain across the membrane. I 
> mean real experiments not predictions.
> 
> Regards
> 
> Firdous
> Graduate student
> Delhi University
> India  
> 

[ccp4bb] BCA BSG Winter Meeting

[Mark Roe]

Dear All,

Registration (https://registrations.hg3conferences.co.uk/bcabsg17) is open for 
the BSG Winter Meeting next Monday (18th) at the Cavendish Labs, Cambridge.

The meeting is aimed at giving the audience an insight into the "joy and pain" 
of protein crystallographic/structural biology research. Speakers have been 
asked to choose a particular piece of published work from any stage of their 
career and speak about the "real" story behind it - the people, the chance 
meeting, the experimental process, the 100's of failed trials that eventually 
led to "perfect" experiments, etc. The aim here is to give the audience a 
deeper insight into the processes that lead to the wonderful science that 
structural biology reveals.


Programme:

Professor Malcolm Longair, Cavendish Laboratory, “Decline and Regeneration: the 
Cavendish Laboratory 1932 to 1953 and the Development of Molecular Biology”

Professor Judith Howard, Durham University, “Early diffraction experiment at 
low temperature - with reference to a PRS paper on unstable Pt species”

Sir Tom Blundell, University of Cambridge, ”Joy and Pain in Nature and Science: 
Structural biology of DNA-PK and DNA Double-strand-break Repair"

Professor Randy Read, University of Cambridge, ”The road to ab initio phasing 
by molecular replacement"

Dr. Pamela Williams, Astex Pharmaceuticals, “Crystal structure of human 
cytochrome P450 2C9 with bound warfarin”

Dr. Ben Bax, York Structural Biology Laboratory“Structural studies in support 
of the development of new antibiotics targeting DNA gyrase and the development 
of oligonucleotide topoisomerase inhibitors (OTIs)”

Professor Janet Thornton, European Bioinformatics Institute, “Of Exploration 
and Errors - PROCHECK - an 'accidental' paper”

Dr. Richard Henderson, MRC Laboratory of Molecular Biology, “The struggle to 
get high resolution phases for 2D crystals of bacteriorhodopsin - pain, joy, 
more pain, more joy”