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 
or open attachments unless you know and trust the source.


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] Crystallization screening for COVID-19 research

[Sarah Bowman]

Hello everyone,

As we all work towards applying structural techniques in the scientific efforts 
geared towards resolving the COVID pandemic, I wanted the community to be aware 
that the HWI Crystallization Center is available for crystallization screening 
for COVID-19 related structural work (non-infectious samples).

We enable rapid, efficient, mail-in screening for crystallization conditions 
using minimal sample volumes.

We have a custom 1536 screening platform and robust imaging capabilities for 
remotely monitoring crystal growth experiments.

Learn more at www.getacrystal.com and contact me 
directly for urgent needs.

Be well,
Sarah


Sarah EJ Bowman, PhD

Associate Research Scientist, Hauptman-Woodward Medical Research Institute
Director, High-Throughput Crystallization Screening Center
Research Associate Professor, Department of Biochemistry, University at Buffalo

Research Webpage
www.getacrystal.org

sbow...@hwi.buffalo.edu
716-898-8623



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[ccp4bb] Covid-19: open science to harness synergies in structure prediction and structure solution

[Randy Read]

The Covid-19 crisis is bringing out the best in the communities we belong to, 
with many people giving deep thought to how we can use our skills to help.  On 
the crystallography bulletin boards we've seen offers to help in solving 
Covid-19-related structures that prove difficult, offers to help with improving 
protein stability, suggestions that the deposition of raw diffraction images 
would allow the community to help get the best possible version of any relevant 
structure, and requests to share bioinformatics analyses and predictions of 
what are the most interesting targets.

We're writing to suggest an additional way that the community can help to 
accelerate progress in the structural understanding of Covid-19.  The CASP 
(Critical Assessment of Structure Prediction) organisers have recently launched 
an initiative to mobilise the structure prediction community to predict and 
refine 3D structures of SARS-2-Covid proteins and relevant complexes that 
either have unknown structure or are non-trivial modelling targets: 
http://predictioncenter.org/caspcommons/index.cgi.
Note that the models will be refined much more extensively than typically done 
in a normal CASP round, which should make them even better than the impressive 
results seen in recent years. 

We would like to build on this initiative, and the enthusiasm this has revealed 
in the prediction community, to help to accelerate the determination of 
structures needed for a molecular-level understanding of Covid-19.  Structure 
prediction has reached a level of maturity where predicted ab initio models and 
distant homology models can be accurate enough to solve new structures by 
molecular replacement.  The best way to bring the prediction and experimental 
communities together to exploit these developments and accelerate progress is 
to embrace an open science approach.  To that end, we propose the following:

* If you have diffraction data involving a SARS-2-Covid protein, a host protein 
relevant to pathogenesis or a complex, but you are not immediately able to 
solve the structure, contact the CASP organisers (c...@predictioncenter.org) 
with the sequence(s) of the construct(s) that went into the crystallisation 
drop.  If relevant predictions have already been made, any unreleased models 
will be released at this point (along with predictions of local accuracy).  If 
proteins in your crystals are not already modelling targets, the CASP 
organisers will consider them as potential new targets for the modelling 
community.

* We all want the fastest possible progress on scientific understanding of 
Covid-19, and this can best be achieved by completely open science.  On a 
number of occasions at crystallographic computing schools and workshops, we 
have seen extremely difficult structures yield to the combined expertise of a 
number of developers and "power users" of the software, none of whom knew how 
to solve every problem that arose.  Even before CASP models are available, some 
other crystallographer may find a way to solve the structure!  So it would be 
ideal if the sequence information you provide to the CASP organisers was 
accompanied by a DOI or URL pointing at the diffraction data, preferably in the 
form of raw images as well as integrated data.  Data from different crystal 
forms or poorly isomorphous crystals can also be incredibly valuable.  Openness 
should go both ways, so people who wish to access these data will be asked to 
agree to immediately release any positive results, even if these fall short of 
a full structure solution, so that others can build on them.

Best wishes,

Randy Read (in cooperation with the CASP organisers)

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building   Fax: +44 1223 336827
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk



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Re: [ccp4bb] Wincoot stereo display on Windows 10

[Bruno KLAHOLZ]

Dear Yong, Arne, Eric and others,

this seems to be related with Windows 10 indeed, an upgrade of a machine in our 
lab from Windows 7 to 10 lost the 3D capability.
Same now for a laptop running with Windows 10, which is connected to a Zalman 
monitor (passive stereo with real3D glasses, i.e. Nvidia card and Linux not 
needed for that).
Zalman stereo starts fine in Wincoot, but there is no 3D effect. This is with 
the latest Wincoot version 0.8.9.2.
The graphic card on the laptop is an Intel (R) HD Graphics Family (PCI 
express), probably that’s an additional problem.
In any case, it seems that 3D stereo under Windows 10 is not possible at the 
moment. Or did anyone find a solution for that?

Thanks,

Bruno






From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yong Wang
Sent: 24 March 2020 15:24
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Wincoot stereo display on Windows 10

Hi Eric,

Yes.  Hardware stereo on Windows 10 is sorely needed considering Windows 10 has 
been out for nearly 5 years and Windows 7 has been dropped from support.

Regards,

Yong

From: ENNIFAR Eric (ARN) 
mailto:e.enni...@ibmc-cnrs.unistra.fr>>
Sent: Tuesday, March 24, 2020 4:46 AM
To: EchelonIV . mailto:arne.raasa...@gmail.com>>; Yong 
Wang mailto:wang_yon...@lilly.com>>
Cc: CCP4BB mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [EXTERNAL] Re: [ccp4bb] [ccp4bb] Wincoot stereo display on Windows 10


EXTERNAL EMAIL: Use caution before replying, clicking links, and opening 
attachments.

Hi Arne & Yong,
I tried all the latest Wincoot version, including the 64bit beta one, I tried 
many many different setups, and no way to make it...
The best way is likely to run a Win7 version and that's it, hoping that 
Bernhard will be able to fix this. Provided you have a 3D vision system still 
available... So far, I'm not really conviced about the VRCoot version. VR is 
not 3D.
Best,
Eric




De: "EchelonIV ." mailto:arne.raasa...@gmail.com>>
À: "CCP4BB" mailto:CCP4BB@JISCMAIL.AC.UK>>
Envoyé: Lundi 23 Mars 2020 22:57:03
Objet: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Wincoot stereo display on Windows 10

Alright, definitely a bit of a misconception then because I understood 
"enabling stereo" meant any stereo view and not hardware stereo specifically.
Arne

On Mon, Mar 23, 2020 at 10:32 PM Yong Wang 
mailto:wang_yon...@lilly.com>> wrote:
Arne,

Side-by-side (wall eye or cross eye) and Zalman options work though I am not 
set up to view Zalman stereo.  Only the hardware stereo option crashes.

On laptops without 3D graphics card, turning on hardware stereo won’t crash the 
program.  Of course, there is no 3D displayed either.

Thanks,

Yong

From: EchelonIV . mailto:arne.raasa...@gmail.com>>
Sent: Monday, March 23, 2020 2:53 PM
To: Yong Wang mailto:wang_yon...@lilly.com>>
Cc: CCP4BB@jiscmail.ac.uk
Subject: [EXTERNAL] Re: [ccp4bb] Wincoot stereo display on Windows 10


EXTERNAL EMAIL: Use caution before replying, clicking links, and opening 
attachments.

I tried all settings through on my laptop display and they work - I don't have 
a possibility to view true 3D, but the settings themselves work. Does wall eye 
or cross eye work for you or are all stereo options crashing the software?

Arne

On Mon, Mar 23, 2020 at 7:36 PM Yong Wang 
mailto:wang_yon...@lilly.com>> wrote:
Hi Arne,

Are you using Wincoot “hardware stereo” option on your laptop?  Are you viewing 
the stereo directly on your laptop display or through a 3D external monitor?

Thanks,

Yong

From: EchelonIV . mailto:arne.raasa...@gmail.com>>
Sent: Monday, March 23, 2020 2:12 PM
To: Yong Wang mailto:wang_yon...@lilly.com>>
Cc: CCP4BB@jiscmail.ac.uk
Subject: [EXTERNAL] Re: [ccp4bb] Wincoot stereo display on Windows 10


EXTERNAL EMAIL: Use caution before replying, clicking links, and opening 
attachments.

Hi Yong,

I'm running a Lenovo Legion Y520 laptop from ca. 2016/2017 with Win10. Quick 
specs: i5-7300HQ 2.5 GHz quadcore, NVIDIA GTX1050 2 GB (driver ver 
23.21.13.9125, 3/16/2018), Samsung 8GB SODIMM 2400MHz, Samsung 256GB SSD. I'm 
running Wincoot with all standard settings, I also tried to play with disabling 
and enabling antialiasing as I sometimes had issues with that on some setups, 
but seems to work as intended.

Cheers,
Arne

On Mon, Mar 23, 2020 at 6:55 PM Yong Wang 
mailto:wang_yon...@lilly.com>> wrote:
Hello Arne,

I still have the crash problem with wincoot 0.8.6.1.  I wonder if there is a 
compatibility problem with the graphics card or driver.  Could you describe 
your system (graphics card info, driver version, laptop or desktop)?

Thanks,

Yong

From: EchelonIV . mailto:arne.raasa...@gmail.com>>
Sent: Monday, March 23, 2020 11:46 AM
To: Yong Wang mailto:wang_yon...@lilly.com>>
Cc: CCP4BB@jiscmail.ac.uk
Subject: [EXTERNAL] Re: [ccp4bb] Wincoot stereo display on Windows 10


EXTERNAL EMAIL: Use caution before replying, clicking links, 

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Clemens Vonrhein]

Dear all,

as a follow-up to our initial message (and similar to other activities
from the MX community), we added some content to our BUSTER wiki at

  https://www.globalphasing.com/buster/wiki/index.cgi?Covid19

to show interested users how to (re-)refine existing PDB entries with
BUSTER and how to look at the results. For anyone wanting to
(re-)process deposited raw diffraction data, we've started a page on
the autoPROC wiki at

  https://www.globalphasing.com/autoproc/wiki/index.cgi?RevisitingExistingData

that might be useful.

We will keep adding and updating those pages over the next days,
especially if more raw diffraction data becomes available and/or more
PDB structures are deposited or becoming relevant. We are very
grateful to any researcher making their (raw) data available under
such pressure and stress!

If there are any questions, suggestions, requests or ideas: please let
us know.

Best regards

Clemens & Gerard



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[ccp4bb] Cryo-EM acces for Covid-19 projects at CBI / IGBMC, Strasbourg

[Bruno KLAHOLZ]

Dear all,

this is to announce that we are opening our cryo-EM facilities for Covid-19 
projects at the Centre for Integrative Biology, Illkirch/Strasbourg, France, 
which hosts the French and European Infrastructures for Integrated Structural 
Biology, FRISBI, Instruct-ERIC and iNext-Discovery.

This can include for example work on Covid-19 related enzyme targets, 
genome-free capsid, membrane receptor complexes, antibody complexes etc. (i.e. 
non-infectious samples).
Cryo-EM samples (on grids) should be sent in with dewars as no on-site visits 
by users are possible. We also offer freezing and screening of grids for 
purified samples.
To apply please see below.

With best regards,

Bruno Klaholz



Cryo-EM facilities:
The Centre for Integrative Biology (CBI) at IGBMC, Illkirch/Strasbourg, France, 
provides a cutting-edge scientific and technological environment in integrated 
structural biology to address the structure and function of biological systems, 
notably on gene expression, from the atomic, molecular to the tissue scales. 
The CBI http://www.igbmc.fr/grandesstructures/cbi/, hosts the French and 
European Infrastructures for Integrated Structural Biology, FRISBI 
http://frisbi.eu/, Instruct-ERIC https://www.structuralbiology.eu/ and 
iNext-Discovery 
https://instruct-eric.eu/news/eu-inext-discovery-grant-provides-technologies-for-key-research-in-structural-biology/,
 which comprises advanced electron microscopy facilities equipped with 
cutting-edge instrumentation, see 
http://frisbi.eu/centers/instruct-center-france-1-igbmc/cryo-electron-microscopy/.
 Nodes of FRISBI and Instruct-ERIC also provide access for sample production, 
characterisation and structural analysis, and for nanobody production.

For Covid-19 projects we specifically provide acces to our Titan Krios 
microscope, which is equipped with Cs corrector, Falcon 3 camera, GIF energy 
filter, K3 camera and phase plate.
For purified samples (not yet on cryo-EM grids) we offer freezing (Vitrobot 
system) and screening of grids.
The non-infectious character of the samples needs to be confirmed by the 
director of the applying institute.
Please include a short description of the project and the characterisation of 
the sample (biophysically characterisation and images / class averages of 
cryo-EM tests if available). Applications will be handled confidentially as for 
any applications.



The EM facility has a suite of associated equipments for sample preparation and 
dedicated computing resources for image processing and 3D reconstruction by 
single particle cryo-EM and cryo electron tomography (cryo-ET) and software 
developements including on-the-fly data processing.

Project applications should be sent via the FRISBI portal 
https://frisbi.eu/submit-a-proposal/ (contact 
pma...@igbmc.fr ) or Instruct-ERIC (click 
here)
 or via iNext-Discovery: https://inext-discovery.eu/network/inext-d/home 
(specific Covid-19 call to come out shortly). Please contact 
pma...@igbmc.fr or 
klah...@igbmc.fr if you have any questions.


###
Bruno P. Klaholz
Centre for Integrative Biology
Department of Integrated Structural Biology
Institute of Genetics and of Molecular and Cellular Biology
IGBMC - UMR 7104 - U 1258
1, rue Laurent Fries
BP 10142
67404 ILLKIRCH CEDEX
FRANCE
Tel. from abroad: 0033.369.48.52.78
Tel. inside France: 03.69.48.52.78
websites:
http://igbmc.fr/Klaholz
http://www.igbmc.fr/grandesstructures/cbi
http://frisbi.eu
http://instruct-eric.eu




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Re: [ccp4bb] Wincoot stereo display on Windows 10

[Yong Wang]

Hi Eric,

Yes.  Hardware stereo on Windows 10 is sorely needed considering Windows 10 has 
been out for nearly 5 years and Windows 7 has been dropped from support.

Regards,

Yong

From: ENNIFAR Eric (ARN) 
Sent: Tuesday, March 24, 2020 4:46 AM
To: EchelonIV . ; Yong Wang 
Cc: CCP4BB 
Subject: [EXTERNAL] Re: [ccp4bb] [ccp4bb] Wincoot stereo display on Windows 10


EXTERNAL EMAIL: Use caution before replying, clicking links, and opening 
attachments.

Hi Arne & Yong,
I tried all the latest Wincoot version, including the 64bit beta one, I tried 
many many different setups, and no way to make it...
The best way is likely to run a Win7 version and that's it, hoping that 
Bernhard will be able to fix this. Provided you have a 3D vision system still 
available... So far, I'm not really conviced about the VRCoot version. VR is 
not 3D.
Best,
Eric




De: "EchelonIV ." mailto:arne.raasa...@gmail.com>>
À: "CCP4BB" mailto:CCP4BB@JISCMAIL.AC.UK>>
Envoyé: Lundi 23 Mars 2020 22:57:03
Objet: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Wincoot stereo display on Windows 10

Alright, definitely a bit of a misconception then because I understood 
"enabling stereo" meant any stereo view and not hardware stereo specifically.
Arne

On Mon, Mar 23, 2020 at 10:32 PM Yong Wang 
mailto:wang_yon...@lilly.com>> wrote:
Arne,

Side-by-side (wall eye or cross eye) and Zalman options work though I am not 
set up to view Zalman stereo.  Only the hardware stereo option crashes.

On laptops without 3D graphics card, turning on hardware stereo won’t crash the 
program.  Of course, there is no 3D displayed either.

Thanks,

Yong

From: EchelonIV . mailto:arne.raasa...@gmail.com>>
Sent: Monday, March 23, 2020 2:53 PM
To: Yong Wang mailto:wang_yon...@lilly.com>>
Cc: CCP4BB@jiscmail.ac.uk
Subject: [EXTERNAL] Re: [ccp4bb] Wincoot stereo display on Windows 10


EXTERNAL EMAIL: Use caution before replying, clicking links, and opening 
attachments.

I tried all settings through on my laptop display and they work - I don't have 
a possibility to view true 3D, but the settings themselves work. Does wall eye 
or cross eye work for you or are all stereo options crashing the software?

Arne

On Mon, Mar 23, 2020 at 7:36 PM Yong Wang 
mailto:wang_yon...@lilly.com>> wrote:
Hi Arne,

Are you using Wincoot “hardware stereo” option on your laptop?  Are you viewing 
the stereo directly on your laptop display or through a 3D external monitor?

Thanks,

Yong

From: EchelonIV . mailto:arne.raasa...@gmail.com>>
Sent: Monday, March 23, 2020 2:12 PM
To: Yong Wang mailto:wang_yon...@lilly.com>>
Cc: CCP4BB@jiscmail.ac.uk
Subject: [EXTERNAL] Re: [ccp4bb] Wincoot stereo display on Windows 10


EXTERNAL EMAIL: Use caution before replying, clicking links, and opening 
attachments.

Hi Yong,

I'm running a Lenovo Legion Y520 laptop from ca. 2016/2017 with Win10. Quick 
specs: i5-7300HQ 2.5 GHz quadcore, NVIDIA GTX1050 2 GB (driver ver 
23.21.13.9125, 3/16/2018), Samsung 8GB SODIMM 2400MHz, Samsung 256GB SSD. I'm 
running Wincoot with all standard settings, I also tried to play with disabling 
and enabling antialiasing as I sometimes had issues with that on some setups, 
but seems to work as intended.

Cheers,
Arne

On Mon, Mar 23, 2020 at 6:55 PM Yong Wang 
mailto:wang_yon...@lilly.com>> wrote:
Hello Arne,

I still have the crash problem with wincoot 0.8.6.1.  I wonder if there is a 
compatibility problem with the graphics card or driver.  Could you describe 
your system (graphics card info, driver version, laptop or desktop)?

Thanks,

Yong

From: EchelonIV . mailto:arne.raasa...@gmail.com>>
Sent: Monday, March 23, 2020 11:46 AM
To: Yong Wang mailto:wang_yon...@lilly.com>>
Cc: CCP4BB@jiscmail.ac.uk
Subject: [EXTERNAL] Re: [ccp4bb] Wincoot stereo display on Windows 10


EXTERNAL EMAIL: Use caution before replying, clicking links, and opening 
attachments.

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

Re: [ccp4bb] Se SAD phasing map becomes worse after refinement

[Eleanor Dodson]

When something like this happens I always go back to the data. What do the
mages look like - are the spots ugly streaky ones, or quite tidy.
Then is the spacegroup right ? Did you integrate assuming C/mmm symmetry?
If so go back and do it again in P1!   Look carefully at the pointless
analysis; I have just struggled the a case which is probably P21 but with
two molecules related by a two fold parallel to a* ,  which masqueraded as
C/mmm.
What is the multiplicity - high enough to be sure?

Check the self rotation function - is there a clear non-crystallographic
match (doesnt have to be a two fold..) I like the MOLREP plots to see that.

And it is often hard to build at 2.8A - can you squeeze a higher
resolution?

All the best Eleanor

On Tue, 24 Mar 2020 at 08:55, Randy Read  wrote:

> Dear Zhu,
>
> Questions specific to Phenix should really go to the Phenix-BB, so I am
> cross-posting my reply there.  Here I’ll focus more on generic issues.
> There are also CCP4 tools that you could consider and presumably other
> people will offer advice on those.
>
> One point you raise comes up so much that we have an entry in our FAQ (
> https://www.phaser.cimr.cam.ac.uk/index.php/FAQ) about it: “Can I use
> Phaser to check the correctness of a model I have already built and
> refined?”  The answer is no, because once you’ve refined the model it
> becomes better than random at predicting the data and therefore achieves a
> high LLG score, regardless of whether or not it is correct.
>
> In this case, you might be able to use Phaser to help complete the model
> if one of the two copies of the complex is more completely modelled than
> the other.  If, say, you had a model for one copy you could fix that and
> search for a second copy: this should work because the refinement didn’t
> know anything about the second copy.
>
> Phenix.autosol attempts to determine the NCS operators, so you need to
> check whether that has succeeded.  If not, you might need to try some more
> manual approaches to defining the NCS, which would help a great deal in map
> improvement.  Tom Terwilliger might answer this in more detail (perhaps on
> the Phenix-BB), but I don’t think you can build protein and nucleic acid in
> the same job, so you should look at the documentation to see how to do that.
>
> Good luck!
>
> Randy Read
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 1223 336500
> The Keith Peters Building   Fax: +44 1223
> 336827
> Hills Road   E-mail:
> rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
> > On 24 Mar 2020, at 04:31, Zhu Qiao  wrote:
> >
> > Dear All
> >
> > I am sorry for the long context.
> >
> > I have one protein (252 AAs, 2 Met) bound to double-stranded DNA (24 bp)
> crystalized.  I collected the Se-Met data of the crystal in C222 up to 2.8
> angstrom. the space group is confirmed by running the pointless.
> >
> > I used the Phenix.Autosol to find the heavy atoms and get a quite nice
> map after the density modification.  It seems there are two proteins and
> two DNA duplex are in one ASU. Phenix.Autobuild can only build less than
> half of the protein sequence into the map and fill in the potential DNA map
> with amino acids. The Rwork/Rfree is 0.40 and 0.46, with the map CC=0.60.
> If I do the MR with the initial model built by Autobuild, the result
> TFZ=40, LLG=200+, which suggests the partial correction of the initial
> model.
> >
> > Here is the problem. From the map, I can see one of my protein domain
> and a clear feature of DNA double helix. But whatever I go further for
> manual build using coot, like building the DNA double-strand into the map
> and building the resolved domain, the refinement statistics go bad with R
> free ~0.50.
> >
> > I am wondering what's going wrong and how come the refinement can't
> improve the R factor.
> >
> > I have attached the relevant photos.
> >
> https://drive.google.com/drive/folders/1dJ4kn7CEHkCL3sMcCJtBqa5OsVFQngBx?usp=sharing
> >
> >
> > Sincerely
> > Zhu
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> 
>
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Re: [ccp4bb] Se SAD phasing map becomes worse after refinement

[Randy Read]

Dear Zhu,

Questions specific to Phenix should really go to the Phenix-BB, so I am 
cross-posting my reply there.  Here I’ll focus more on generic issues.  There 
are also CCP4 tools that you could consider and presumably other people will 
offer advice on those.

One point you raise comes up so much that we have an entry in our FAQ 
(https://www.phaser.cimr.cam.ac.uk/index.php/FAQ) about it: “Can I use Phaser 
to check the correctness of a model I have already built and refined?”  The 
answer is no, because once you’ve refined the model it becomes better than 
random at predicting the data and therefore achieves a high LLG score, 
regardless of whether or not it is correct.

In this case, you might be able to use Phaser to help complete the model if one 
of the two copies of the complex is more completely modelled than the other.  
If, say, you had a model for one copy you could fix that and search for a 
second copy: this should work because the refinement didn’t know anything about 
the second copy.

Phenix.autosol attempts to determine the NCS operators, so you need to check 
whether that has succeeded.  If not, you might need to try some more manual 
approaches to defining the NCS, which would help a great deal in map 
improvement.  Tom Terwilliger might answer this in more detail (perhaps on the 
Phenix-BB), but I don’t think you can build protein and nucleic acid in the 
same job, so you should look at the documentation to see how to do that.

Good luck!

Randy Read
-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building   Fax: +44 1223 336827
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk

> On 24 Mar 2020, at 04:31, Zhu Qiao  wrote:
> 
> Dear All
> 
> I am sorry for the long context. 
> 
> I have one protein (252 AAs, 2 Met) bound to double-stranded DNA (24 bp) 
> crystalized.  I collected the Se-Met data of the crystal in C222 up to 2.8 
> angstrom. the space group is confirmed by running the pointless. 
> 
> I used the Phenix.Autosol to find the heavy atoms and get a quite nice map 
> after the density modification.  It seems there are two proteins and two DNA 
> duplex are in one ASU. Phenix.Autobuild can only build less than half of the 
> protein sequence into the map and fill in the potential DNA map with amino 
> acids. The Rwork/Rfree is 0.40 and 0.46, with the map CC=0.60. If I do the MR 
> with the initial model built by Autobuild, the result TFZ=40, LLG=200+, which 
> suggests the partial correction of the initial model. 
> 
> Here is the problem. From the map, I can see one of my protein domain and a 
> clear feature of DNA double helix. But whatever I go further for manual build 
> using coot, like building the DNA double-strand into the map and building the 
> resolved domain, the refinement statistics go bad with R free ~0.50. 
> 
> I am wondering what's going wrong and how come the refinement can't improve 
> the R factor. 
> 
> I have attached the relevant photos. 
> https://drive.google.com/drive/folders/1dJ4kn7CEHkCL3sMcCJtBqa5OsVFQngBx?usp=sharing
> 
> 
> Sincerely
> Zhu 
> 
> 
> 
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[ccp4bb] Experienced Technician in membrane protein expression and purification

[Schertler Gebhard (PSI)]

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Structural Biology ETH Zürich D-BIOL

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Division
Paul Scherrer Institut
Laboratory of Biomolecular Research,
LBR
OSRA 007
CH-5232 Villigen PSI
gebhard.schert...@psi.ch
phone +41 56 310 4265







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