Re: [ccp4bb] Validity of Ion Sites in PDB

[Robbie Joosten]

Dear Jacob,

There are a lot of potential problems with ion validation, that make obtaining 
a reliable answer difficult. If you want to datamine ion validation results, 
you can use the ready-made WHAT_CHECK files in the PDBREPORT databank for 
original PDB files or in the PDB_REDO databank for their re-refined or rebuilt 
counterparts (note that PDB_REDO does not explicitly do anything with ions,  
yet).
WHAT_CHECK uses the bond valence method to check for waters that should be ions 
and ions that should be other ions or water and mines the crystallisation 
conditions for hints of what could be there.

HTH,
Robbie

Sent from my Windows Phone

Van: Keller, Jacob
Verzonden: 6-3-2014 20:45
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] Validity of Ion Sites in PDB

Dear Crystallographers,

I was curious whether there has been a rigorous evaluation of ion binding sites 
in the structures in the pdb, by PDB-REDO or otherwise. I imagine that there is 
a considerably broad spectrum of habits and rigor in assigning solute blobs to 
ion X or water, and in fact it would be difficult in many cases to determine 
which ion a given blob really is, but there should be at least some fraction of 
ions/waters which can be shown from the x-ray data and known geometry to be X 
and not Y. This could be by small anomalous signals (Cl and H2O for example), 
geometric considerations, or something else. Maybe this does not even matter in 
most cases, but it might be important in others...

All the best,

Jacob Keller


***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Farms Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

[Sabuj Pattanayek]

Thanks! we're gonna test one of the lg's from b&h, one of our zalman's just
died today.


On Thu, Mar 6, 2014 at 6:06 PM, Shaun Lott  wrote:

> Thanks to everyone who responded, on and off the list. I thought I'd post
> a quick summary.
>
> To clarify my question slightly (if belatedly) I'm specifically looking
> for a passive 3D solution to plug into my MacBook Pro whilst on sabbatical
> in the USA. I'll be using it for a mixture of 2D and 3D viewing, not for
> many hours of dedicated hand building of my 3.5A maps. Well, I hope not! ;)
>
> The LG D2343PB-BN gets honourably mentioned, and is available in several
> places:
>
> http://www.adorama.com/LOCD2343PBBN.html
> $273.50 including shipping
>
>
> http://www.bhphotovideo.com/c/product/1002116-REG/lg_electronics_d2343pb_bn_23_mon_led_lcd.html
> $273.50 + shipping
>
> Another candidate is this from AOC:
>
> http://www.amazon.com/AOC-E2352PHZ-23-Widescreen-Flicker/dp/B005LORQGG
> $250 including shipping
>
> The Asus VG27AH also got good reports, but is listed as either 'out of
> stock' or 'unavailable'.
>
> However, its kid brother, the VG23AH is available:
>
> http://www.pinnaclemicro.com/computer/dsku.php?g=VG23AH&m=ASUS
> $251 including shipping (you need to enter the promo code SAS10 to get $10
> off!)
>
> This monitor got a poor review on cnet (
> http://reviews.cnet.com/lcd-monitors/asus-vg23ah/4505-3174_7-35306085.html)
> but much better and more thoughtful reviews elsewhere (
> http://3dvision-blog.com/7861-review-of-the-23-inch-asus-vg23ah-passive-3d-ips-display)
> so I'm going to go with the Asus for the following very scientific reasons:
>
> 1) It's $20 cheaper than the LG
> 2) The colours felt a bit washed out on the only AOC monitor I've used
> previously
> 3) It has built in speakers and I don't have any on my desk
>
> My feeling is that these will all perform in a very similar fashion - I'll
> report back once I've plugged it in!
>
> cheers
>
> Shaun
>

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

[Shaun Lott]

Thanks to everyone who responded, on and off the list. I thought I'd post a 
quick summary.

To clarify my question slightly (if belatedly) I'm specifically looking for a 
passive 3D solution to plug into my MacBook Pro whilst on sabbatical in the 
USA. I'll be using it for a mixture of 2D and 3D viewing, not for many hours of 
dedicated hand building of my 3.5A maps. Well, I hope not! ;)

The LG D2343PB-BN gets honourably mentioned, and is available in several places:

http://www.adorama.com/LOCD2343PBBN.html 
$273.50 including shipping 

http://www.bhphotovideo.com/c/product/1002116-REG/lg_electronics_d2343pb_bn_23_mon_led_lcd.html
 
$273.50 + shipping 

Another candidate is this from AOC:

http://www.amazon.com/AOC-E2352PHZ-23-Widescreen-Flicker/dp/B005LORQGG
$250 including shipping

The Asus VG27AH also got good reports, but is listed as either 'out of stock' 
or 'unavailable'.

However, its kid brother, the VG23AH is available:

http://www.pinnaclemicro.com/computer/dsku.php?g=VG23AH&m=ASUS 
$251 including shipping (you need to enter the promo code SAS10 to get $10 off!)

This monitor got a poor review on cnet 
(http://reviews.cnet.com/lcd-monitors/asus-vg23ah/4505-3174_7-35306085.html) 
but much better and more thoughtful reviews elsewhere 
(http://3dvision-blog.com/7861-review-of-the-23-inch-asus-vg23ah-passive-3d-ips-display)
 so I'm going to go with the Asus for the following very scientific reasons:

1) It's $20 cheaper than the LG
2) The colours felt a bit washed out on the only AOC monitor I've used 
previously
3) It has built in speakers and I don't have any on my desk

My feeling is that these will all perform in a very similar fashion - I'll 
report back once I've plugged it in!

cheers

Shaun

Re: [ccp4bb] Validity of Ion Sites in PDB

[Talon Romain]

Dear Jacob Keller,

As you say, there is a number of methods used to assign, as correctly as 
possible, ions and water molecules:
> depending of everything you know about the purification protocol of 
the molecule (every ions and compound which could have been seen by the 
target protein),

> depending of the composition of the crystallization drop,
> according to the residual map you observe for the "suspicious" blobs 
during the refinement,
> according to the coordinating residues, the coordination number of 
the suspected ion, its theorical coordination distances and angles,
> according to the structure factor imaginary part value which can be 
increased by choosing the right wavelength for the data collection (see 
also the ANODE program, Thorn and Sheldrick, 2011).


But, to my knowledge, there is no automatic evaluation of ion binding 
sites during the pdb deposition procedure or in the automated structure 
solutions currently proposed in the common refinement programs suites.
Important ion binding sites determination methods could be discussed in 
the matching publications...


Best regards.

Romain.

Le 06/03/2014 20:56, Nat Echols a écrit :
On Thu, Mar 6, 2014 at 11:45 AM, Keller, Jacob 
mailto:kell...@janelia.hhmi.org>> wrote:


I was curious whether there has been a rigorous evaluation of ion
binding sites in the structures in the pdb, by PDB-REDO or
otherwise. I imagine that there is a considerably broad spectrum
of habits and rigor in assigning solute blobs to ion X or water,
and in fact it would be difficult in many cases to determine which
ion a given blob really is, but there should be at least some
fraction of ions/waters which can be shown from the x-ray data and
known geometry to be X and not Y. This could be by small anomalous
signals (Cl and H2O for example), geometric considerations, or
something else. Maybe this does not even matter in most cases, but
it might be important in others...


A couple of references:

http://www.ncbi.nlm.nih.gov/pubmed/18614239
http://www.ncbi.nlm.nih.gov/pubmed/24356774

Anecdotally, it is not difficult to find incorrect structures; in 
fact, one of mine has "magnesium" ions at crystal contacts with big 
Fo-Fc and anomalous map peaks, and I know it's not the only such 
structure in the PDB. However, while there are plenty of examples that 
are clearly wrong, it is difficult to come up with strict rules that 
apply to typical MX data - at 3Å resolution (or even better), a native 
Zn-binding site might have bond valences that are just awful.  This 
doesn't mean the metal assignment is wrong.  The placement of waters 
alone has a huge impact on such calculations.


-Nat

Re: [ccp4bb] Validity of Ion Sites in PDB

[Nat Echols]

On Thu, Mar 6, 2014 at 11:45 AM, Keller, Jacob wrote:

> I was curious whether there has been a rigorous evaluation of ion binding
> sites in the structures in the pdb, by PDB-REDO or otherwise. I imagine
> that there is a considerably broad spectrum of habits and rigor in
> assigning solute blobs to ion X or water, and in fact it would be difficult
> in many cases to determine which ion a given blob really is, but there
> should be at least some fraction of ions/waters which can be shown from the
> x-ray data and known geometry to be X and not Y. This could be by small
> anomalous signals (Cl and H2O for example), geometric considerations, or
> something else. Maybe this does not even matter in most cases, but it might
> be important in others...
>

A couple of references:

http://www.ncbi.nlm.nih.gov/pubmed/18614239
http://www.ncbi.nlm.nih.gov/pubmed/24356774

Anecdotally, it is not difficult to find incorrect structures; in fact, one
of mine has "magnesium" ions at crystal contacts with big Fo-Fc and
anomalous map peaks, and I know it's not the only such structure in the
PDB.  However, while there are plenty of examples that are clearly wrong,
it is difficult to come up with strict rules that apply to typical MX data
- at 3Å resolution (or even better), a native Zn-binding site might have
bond valences that are just awful.  This doesn't mean the metal assignment
is wrong.  The placement of waters alone has a huge impact on such
calculations.

-Nat

Re: [ccp4bb] Validity of Ion Sites in PDB

[David Schuller]

Certainly some sites will be defined better than others by such 
criteria. I would hope that they are discussed in the publications 
relevant to the PDB submission.




On 03/06/14 14:45, Keller, Jacob wrote:

Dear Crystallographers,

I was curious whether there has been a rigorous evaluation of ion binding sites 
in the structures in the pdb, by PDB-REDO or otherwise. I imagine that there is 
a considerably broad spectrum of habits and rigor in assigning solute blobs to 
ion X or water, and in fact it would be difficult in many cases to determine 
which ion a given blob really is, but there should be at least some fraction of 
ions/waters which can be shown from the x-ray data and known geometry to be X 
and not Y. This could be by small anomalous signals (Cl and H2O for example), 
geometric considerations, or something else. Maybe this does not even matter in 
most cases, but it might be important in others...

All the best,

Jacob Keller


***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Farms Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***



--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

[ccp4bb] Validity of Ion Sites in PDB

[Keller, Jacob]

Dear Crystallographers,

I was curious whether there has been a rigorous evaluation of ion binding sites 
in the structures in the pdb, by PDB-REDO or otherwise. I imagine that there is 
a considerably broad spectrum of habits and rigor in assigning solute blobs to 
ion X or water, and in fact it would be difficult in many cases to determine 
which ion a given blob really is, but there should be at least some fraction of 
ions/waters which can be shown from the x-ray data and known geometry to be X 
and not Y. This could be by small anomalous signals (Cl and H2O for example), 
geometric considerations, or something else. Maybe this does not even matter in 
most cases, but it might be important in others...

All the best,

Jacob Keller


***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Farms Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

[David Roberts]

Every now and then I pipe on this as well.  We have Zalman monitors here - I 
bought them about 4 years ago - when you could not buy them any more in the 
states.  I just bought them on Ebay - they came new in the box directly from 
China.  The person did fed-ex shipping - did not cost any extra, and at the 
time it was a very cheap way to get these models that were not available in the 
US.  I don’t know if they still sell this way or not - but for me it worked 
great.

The monitors still work, and I agree with Zhijie, the 2D applications look 
perfect on them.  Maybe it’s because I was so used to old, dim, CRT displays.  
In any event - they are great monitors for normal work, and it’s nice on 
occasion to use 3D with them.  The 3D is OK - not perfect - but I don’t think 
any are as good as old CRT displays.  The 3D does show what you need.  What I 
really do find with modeling (myself included) is the following:  I came from a 
situation where I used 3D exclusively (SGI’s, CRT’s, blah blah blah).  Going to 
the newer, brighter, faster LCD displays means that 3D isn’t as important to me 
anymore, and I find that I typically use 2D almost exclusively.  Occasionally I 
do 3D, and when I do, the Zalman is fine for that.

Hope that helps

Dave


On Mar 6, 2014, at 7:50 AM, Zhijie Li  wrote:

> I beg to differ on this:
>   "Also, passive screens have a pol-filter in place, the fine lines of which 
> you will observe on a white background, the more disturbing the closer the 
> viewing distance to the screen is. So, for general office applications 
> (writing text), the screens are less useful. "
>  
> Our LG D2342P has no issue with office work. I never noticed any thin lines 
> on the screen. In fact I think its 2D display is excellent. I wonder if the 
> issue you have is related to the screen size: the pixels of 27 in screens are 
> bigger than our 22 in screens.
>  
> Zhijie
>  
> From: mesters
> Sent: Thursday, March 06, 2014 3:55 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Stereo monitors for use with Pymol and Coot
>  
> Hi,
> 
> this is probaly due to the transition from old TFT style to new IPS panel 
> based monitors... Several new passive 3d monitors are hitting the market such 
> as AOC d2769Vh and the Philips Gioco 278G4. Both are based on 27" IPS Monitor 
> panels. 
> 
> A list of possible monitors can be found at Tridef (many are old but new 
> models are listed),  https://www.tridef.com/products/pc-licensed-products.
> 
> Problem with passive stereo is, you will half the resolution in the vertical 
> direction. It is a problem if you are looking at wire-models of structures in 
> pymol and especially fine-wire electron density mesh and models in coot as 
> those noticably loose resolution compared to active stereo screens. Also, 
> passive screens have a pol-filter in place, the fine lines of which you will 
> observe on a white background, the more disturbing the closer the viewing 
> distance to the screen is. So, for general office applications (writing 
> text), the screens are less useful. This is not to big a problem for viewing 
> full screen pictures, games and movies (increased distance to the screen...).
> 
> Moreover, with passive monitors, as the stereo effect increases with the 
> screen size, the picture looks more "pixeled" compared to active stereo 
> screens. I personally own a AOC d2769Vh and for 3D movies it is great, for 
> coot not that useful if you plan longer sessions. At work, we operate an ASUS 
> VG278HR (active stereo and build in emitter for glasses). Many hardware 
> testers consider this screen the best one available on  the market.
> 
> If you mainly need it for coot, I recommend to change your priorities and buy 
> an active stereo screen such as Asus VG248QE or Asus VG278HR.
> You do not need an expensive quadro card (600 will do fine) as the VG278HR 
> has build-in emitter for operation with cheap nvidia glasses.
> It pays off in the long run to invest a few more dollars as you (I assume) 
> will spend a lot of time in front of the this device (so buy the best as you 
> only have one pair of eyes).
> 
> - J. -
> 
> 
> 
> 
> Am 05.03.14 23:46, schrieb Shaun Lott:
>> A rather US-centric question on passive 3D monitors...
>> 
>> I'm just getting set up in the US, and I'm surprised on how few passive 3D 
>> monitors seem to be around - many models seem listed as 'out of stock' when 
>> looking in the usual places (Amazon, NewEgg, BestBuys, Walmart etc.)
>> 
>> The best deal I have found is for an LG D2343PB-BN 
>> (http://www.lg.com/us/commercial/lcd-computer-monitors/lg-D2343PB-BN) at 
>> US$274
>> 
>> Does anyone have any experience with this model, or any suggestion about 
>> where best to buy 3D monitors in the US?
>> 
>> many thanks in advance
>> 
>> Shaun
> 
> 
> -- 
> Dr. Jeroen R. Mesters
> Deputy, Senior Researcher & Lecturer
> 
> Institute of Biochemistry, University of Lübeck
> Ratzeburger Allee 160, 23538 Lübeck, Germany
> 
> phone: +49-

Re: [ccp4bb] Efforts been made to solve protein (soluble) aggregation

[Bosch, Juergen]

Co expression of binding partner perhaps ? And then tagging the other protein 
partner ?
Jürgen 

..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://lupo.jhsph.edu

On Mar 6, 2014, at 2:13, "WENHE ZHONG"  wrote:

> Dear CCP4 friends,
> 
> I have been searching around the CCP4 mails for the discussion of soluble 
> protein aggregations, as I have the same problem recently. Many efforts I 
> have tried but without success. Here, I would like to summarise what I have 
> done and maybe any of you come across some ideas.
> 
> 1. My protein (not membrane protein) is around 35kDa with a pI of 8.6. It was 
> expressed in E.coli as a fusion protein where its N-ter was fused by MBP-tag 
> with a flexible linker (Factor Xa cleavage site available). The whole fusion 
> protein is ~77kDa (pI 6.1). 
> 2. After MBPTrap affinity purification, the protein was run through 
> gel-filtration column it came out at void volume. The aggregation was also 
> confirmed by DLS. The buffer condition is: 20 mM HEPES, pH7.4, 125 mM KCl, 
> 20% glycerol, 40 mM maltose, 5 mM DTT.
> 3. I made several truncations and only one gave me a monomer (The other 
> truncations were all soluble aggregates). However, this monomeric truncation 
> is small (~5 kDa) and not important for the function (not interesting 
> fragment). At least, this monomeric truncation suggests that the aggregation 
> is not due to the aggregation of MBP. The truncations were designed in both 
> two versions: long linker (including TEV cleavage site) and short linker 
> (-Ser-Ser-Ser-).
> 4. Hampton detergent screens and high salt (1-2 M KCl or NaCl) were tried on 
> both truncations and full-length protein, but none of them work (DLS 
> confirm). Divalents and other ions should not bind to this protein. 
> 5. The full-length aggregated protein is still functional in Gel-shift assay, 
> which indicates the protein is corrected folding.
> 
> I guess "soluble aggregation" is a common problem for tough proteins. If 
> anyone has experience on it and can share with us, please drop an email.
> 
> Kind regards,
> Wenhe

[ccp4bb] WWTF-funded positions in the Life Sciences, hosted by the Max F. Perutz Laboratories (MFPL), Vienna

[Kristina Djinovic Carugo]

*WWTF-funded positions in the Life Sciences, hosted by the Max F. Perutz 
Laboratories (MFPL), Vienna, Austria*


The Vienna Science and Technology Fund (*WWTF*) has launched a call for 
applications in the Life Sciences.


The "Vienna Research Groups for Young Investigators" call by the City of 
Vienna and the WWTF will fund promising young scientists starting their 
first independent research group in Vienna. Two to three positions with 
up to 1,6 Mio. EUR funding per group are available, for 6-8 years, with 
the possibility during this time of conversion to a tenure track 
position. See: www.wwtf.at/programmes/ls/index 



The positions need to be hosted by a university or research institute in 
Vienna so the MFPL (http://www.mfpl.ac.at) is now seeking outstanding 
candidates to sponsor, particularly in the following areas:


*Structural Biology and Biophysics*

*Cell Signaling*

*RNA Biology*

*Chromosome Dynamics*

*Computational Biology/Bioinformatics*

*Immunology and Infection Biology*

This is a two-step procedure. Interested candidates should send their 
cv, brief career summary and research proposal, up to three 
publications, and the names of three referees, preferably as a single 
PDF, to Graham Warren (facultyopeni...@mfpl.ac.at). The deadline is the 
30^th April 2014.


Short-listed applicants will be invited to MFPL for interview in May and 
successful candidates will then be sponsored by the MFPL to apply for 
one of the WWTF positions, the deadline for which is the 24^th July 2014.


--
___

Kristina Djinovic-Carugo
Department of Structural and Computational Biology
Max F. Perutz Laboratories
University of Vienna
Campus Vienna Biocenter 5
A-1030 Vienna
Austria

e-mail: kristina.djino...@univie.ac.at
Phone: +43-1-4277-52203/52201
Mobile: +43-664-602 77-522 03
Fax: +43-1-4277-9522

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

[Zhijie Li]

I beg to differ on this:
"Also, passive screens have a pol-filter in place, the fine lines of which you 
will observe on a white background, the more disturbing the closer the viewing 
distance to the screen is. So, for general office applications (writing text), 
the screens are less useful. "
Our LG D2342P has no issue with office work. I never noticed any thin lines on 
the screen. In fact I think its 2D display is excellent. I wonder if the issue 
you have is related to the screen size: the pixels of 27 in screens are bigger 
than our 22 in screens.
Zhijie
From: mesters 
Sent: Thursday, March 06, 2014 3:55 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

Hi,

this is probaly due to the transition from old TFT style to new IPS panel based 
monitors... Several new passive 3d monitors are hitting the market such as AOC 
d2769Vh and the Philips Gioco 278G4. Both are based on 27" IPS Monitor panels. 

A list of possible monitors can be found at Tridef (many are old but new models 
are listed),  https://www.tridef.com/products/pc-licensed-products.

Problem with passive stereo is, you will half the resolution in the vertical 
direction. It is a problem if you are looking at wire-models of structures in 
pymol and especially fine-wire electron density mesh and models in coot as 
those noticably loose resolution compared to active stereo screens. Also, 
passive screens have a pol-filter in place, the fine lines of which you will 
observe on a white background, the more disturbing the closer the viewing 
distance to the screen is. So, for general office applications (writing text), 
the screens are less useful. This is not to big a problem for viewing full 
screen pictures, games and movies (increased distance to the screen...).

Moreover, with passive monitors, as the stereo effect increases with the screen 
size, the picture looks more "pixeled" compared to active stereo screens. I 
personally own a AOC d2769Vh and for 3D movies it is great, for coot not that 
useful if you plan longer sessions. At work, we operate an ASUS VG278HR (active 
stereo and build in emitter for glasses). Many hardware testers consider this 
screen the best one available on the market.

If you mainly need it for coot, I recommend to change your priorities and buy 
an active stereo screen such as Asus VG248QE or Asus VG278HR.
You do not need an expensive quadro card (600 will do fine) as the VG278HR has 
build-in emitter for operation with cheap nvidia glasses.
It pays off in the long run to invest a few more dollars as you (I assume) will 
spend a lot of time in front of the this device (so buy the best as you only 
have one pair of eyes).

- J. -




Am 05.03.14 23:46, schrieb Shaun Lott:

A rather US-centric question on passive 3D monitors...

I'm just getting set up in the US, and I'm surprised on how few passive 3D 
monitors seem to be around - many models seem listed as 'out of stock' when 
looking in the usual places (Amazon, NewEgg, BestBuys, Walmart etc.)

The best deal I have found is for an LG D2343PB-BN 
(http://www.lg.com/us/commercial/lcd-computer-monitors/lg-D2343PB-BN) at US$274

Does anyone have any experience with this model, or any suggestion about where 
best to buy 3D monitors in the US?

many thanks in advance

Shaun



-- 
Dr. Jeroen R. Mesters
Deputy, Senior Researcher & Lecturer

Institute of Biochemistry, University of Lübeck
Ratzeburger Allee 160, 23538 Lübeck, Germany

phone: +49-451-5004065 (secretariate 5004061)
fax: +49-451-5004068

http://www.biochem.uni-luebeck.de
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)
-- 
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Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

[mesters]

  
  
Hi,
  
  this is probaly due to the transition from old TFT style to new
  IPS panel based monitors... Several new passive 3d monitors are
  hitting the market such as AOC d2769Vh and the
  
  Philips
Gioco 278G4. Both are based on 27" IPS Monitor
  panels. 
  
  A list of
  possible monitors can be found at Tridef (many are old but new
  models are listed), 
  https://www.tridef.com/products/pc-licensed-products.
  
Problem with passive stereo is, you will half the
  resolution in the vertical direction. It is a problem if you are
  looking at wire-models of structures in pymol and especially
  fine-wire electron density mesh and models in coot as those
  noticably loose resolution compared to active stereo screens.
  Also, passive screens have a pol-filter in place, the fine lines
  of which you will observe on a white background, the more
  disturbing the closer the viewing distance to the screen is. So,
  for general office applications (writing text), the screens are
  less useful. This is not to big a problem for viewing full screen
  pictures, games and movies (increased distance to the screen...).
  
  Moreover, with passive monitors, as the stereo effect increases
  with the screen size, the picture looks more "pixeled" compared to
  active stereo screens. I personally own a AOC d2769Vh and for 3D
  movies it is great, for coot not that useful if you plan longer
  sessions. At work, we operate an ASUS VG278HR (active stereo and
  build in emitter for glasses). Many hardware testers consider this
  screen the best one available on the market.
  
  If you mainly need it for coot, I recommend to change your
  priorities and buy an active stereo screen such as Asus
VG248QE
  
  or Asus VG278HR.
  You do not need an expensive quadro card (600 will do fine) as the
  VG278HR has build-in emitter for operation with cheap nvidia
  glasses.
  It pays off in the long run to invest a few more dollars as you (I
  assume) will spend a lot of time in front of the this device (so
  buy the best as you only have one pair of eyes).
  
  - J. -
  
  
  
  
  Am 05.03.14 23:46, schrieb Shaun Lott:


  A rather US-centric question on passive 3D monitors...

I'm just getting set up in the US, and I'm surprised on how few passive 3D monitors seem to be around - many models seem listed as 'out of stock' when looking in the usual places (Amazon, NewEgg, BestBuys, Walmart etc.)

The best deal I have found is for an LG D2343PB-BN (http://www.lg.com/us/commercial/lcd-computer-monitors/lg-D2343PB-BN) at US$274

Does anyone have any experience with this model, or any suggestion about where best to buy 3D monitors in the US?

many thanks in advance

Shaun




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Re: [ccp4bb] Efforts been made to solve protein (soluble) aggregation

[Mark J van Raaij]

Dear Wenhe,

this sounds a bit like our struggles to solubly express and purify the 
dsRNA-binding avian reovirus sigmaA protein, please find the two papers here:
http://www.ncbi.nlm.nih.gov/pubmed/?term=van+Raaij+MJ%2C+sigmaA
The key to solving our problem was to realise the protein aggregated especially 
at 4 degrees, but was more stable at room temp., i.e. it appeared to be 
cold-sensitive. So we did all functional assays, including gel-shift assays, 
with protein always kept at room temp.
However, it was finally crystallised at 5 degrees.
MBP is "notorious" for pulling partially-folded proteins into solution, which 
then aggregate or precipitate upon cleavage. Although your protein is active in 
gel-shift assay, it may still be partially folded I guess. Perhaps you can 
isolate a well-folded population by using a nucleic-acid column? Perhaps some 
mild unfolding-refolding?

Greetings,

Mark

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij





On 6 Mar 2014, at 08:12, WENHE ZHONG wrote:

> Dear CCP4 friends,
> 
> I have been searching around the CCP4 mails for the discussion of soluble 
> protein aggregations, as I have the same problem recently. Many efforts I 
> have tried but without success. Here, I would like to summarise what I have 
> done and maybe any of you come across some ideas.
> 
> 1. My protein (not membrane protein) is around 35kDa with a pI of 8.6. It was 
> expressed in E.coli as a fusion protein where its N-ter was fused by MBP-tag 
> with a flexible linker (Factor Xa cleavage site available). The whole fusion 
> protein is ~77kDa (pI 6.1). 
> 2. After MBPTrap affinity purification, the protein was run through 
> gel-filtration column it came out at void volume. The aggregation was also 
> confirmed by DLS. The buffer condition is: 20 mM HEPES, pH7.4, 125 mM KCl, 
> 20% glycerol, 40 mM maltose, 5 mM DTT.
> 3. I made several truncations and only one gave me a monomer (The other 
> truncations were all soluble aggregates). However, this monomeric truncation 
> is small (~5 kDa) and not important for the function (not interesting 
> fragment). At least, this monomeric truncation suggests that the aggregation 
> is not due to the aggregation of MBP. The truncations were designed in both 
> two versions: long linker (including TEV cleavage site) and short linker 
> (-Ser-Ser-Ser-).
> 4. Hampton detergent screens and high salt (1-2 M KCl or NaCl) were tried on 
> both truncations and full-length protein, but none of them work (DLS 
> confirm). Divalents and other ions should not bind to this protein. 
> 5. The full-length aggregated protein is still functional in Gel-shift assay, 
> which indicates the protein is corrected folding.
> 
> I guess "soluble aggregation" is a common problem for tough proteins. If 
> anyone has experience on it and can share with us, please drop an email.
> 
> Kind regards,
> Wenhe