Re: [ccp4bb] analytical ultracentrifugation

[weikai]

Hi:

Just a related question.  To measure MW of membrane proteins, the density
of detergents needs to be matched by D2O/H2O and should be within 1.0 to
1.1.  Anyone knows some literature that gives a list of detergents having
suitable density?  Unfornatatedly, the common ones like Foscholine 12(DPC)
and C12E9 do not work with my protein.

Regards,

Weikai




> Hi Mike,
>
> try the National Analytical Ultracentrifugation Facility in Connecticut.
>
> http://www.biotech.uconn.edu/auf/
>
> Cheers, Petra
>
>
>> Dear colleagues,
>>
>> does anyone know of a faciltiy for analytical ultracentrifugation?
>>
>> Thanks.
>>
>> Mike Colaneri
>>
>
>
> --
> Petra Verdino, PhD
> Research Associate
> The Scripps Research Institute, BCC206
> 10550 North Torrey Pines Road
> CA 92037 La Jolla, USA
> tel:1-858-784-2945
> fax:1-858-784-2980
> http://www.scripps.edu/~verdino/homepage.htm
>

Re: [ccp4bb] 3D model building without CRT monitor

[James M. Vergis]

Has anyone tried a 3D DLP-TV?  They have the input for a stereographics
emitter.  Probably too big for a desktop but at 50-72" they would work in a
conference room.  They range in price from $1900-3500.  Here is the link for
the SAMSUNG website http://product.samsung.com/dlp3d/index.html.  Mitsubishi
also sells 3D TVs... I'm not sure about other manufacturers.

James


James M. Vergis, Ph.D.
University of Virginia Molecular Physiology and Biological Physics
MKWEINR 438 Jordan Hall
1340 Jefferson Park Ave
Charlottesville, VA 22908-0736
phone: 434-243-2730   FAX: 434-982-1616
[EMAIL PROTECTED]



-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Vangelis Christodoulou
Sent: Thursday, June 05, 2008 2:02 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3D model building without CRT monitor

There is a 20-inch (20-3D2W04) display that costs around $6000. For  
$13000 you get a 42-inch, so I guess the 52-inch that was introduced  
today will cost  a lot.

Vangelis

On Jun 5, 2008, at 7:30 PM, Juergen Bosch wrote:

>> Interesting!  Their PDF says it works with OpenGL:
>>
http://www.business-sites.philips.com/assets/Downloadablefile//2006-05-30-Te
chnology-backgrounder-13560.pdf
>>
>> Does it mean it will work in Coot as is?
>>
>> Dima
>>
> If you don't mind the 12K price tag, maybe.
>
> Juergen
>
> -- 
> Jürgen Bosch
> University of Washington
> Dept. of Biochemistry, K-426
> 1705 NE Pacific Street
> Seattle, WA 98195
> Box 357742
> Phone: +1-206-616-4510
> FAX:   +1-206-685-7002
> Web: http://faculty.washington.edu/jbosch

Re: [ccp4bb] 3D model building without CRT monitor

[PhilEvans]

We now have a Planar system, which works very nicely with coot, O ,  
ccp4mg etc. Rather expensive though


Phil Evans

On 2 Jun 2008, at 17:06, Mike Latchem wrote:


These "new" TFT monitors do seem like a really good idea, but, it is
well worth doing in depth research as most of the accessible (Cheap)
ones designed for gaming currently only operate with directX. As I
understand it there are plans to make these work with openGL as well  
as
directX so they should work with programs like coot etc. Just be  
careful

and confirm with the people supplying the TFT that it will work with
your software package of choice.

P.S. a colleague of mine who is interested in tomography suggested the
planar TFTs work well (they are also very expensive and bulky) - but  
be
sure to confirm they work with your software of choice before paying  
for

one

http://www.planar3d.com/

Regards

Mike


On Mon, 2008-06-02 at 11:51 -0400, Jim Fairman wrote:

Hello all,

There is a new company around that makes a 3D capable 22 inch flat
screen LCD monitor (http://www.iz3d.com) capable of a maximum
resolution of 1680x1050.  It is originally designed for the purpose  
of

playing video games in 3D, but looks promising for ridding ourselves
of the huge bulky CRTs.

Cheers

On Mon, Jun 2, 2008 at 11:08 AM, Warren DeLano <[EMAIL PROTECTED]>
wrote:

   For used-stereo-3D-capable-CRT seekers, our stereo 3D page may
   be of some use.  A number of target monitors are listed.

   http://pymol.sourceforge.net/stereo3d.html

   -Original Message-
   From: CCP4 bulletin board on behalf of Krojer,Tobias
   Sent: Mon 6/2/2008 5:24 AM
   To: CCP4BB@JISCMAIL.AC.UK
   Subject: [ccp4bb] 3D model building without CRT monitor

   Dear all,

   recently some of our CRT monitors broke down and we realized
   that these
   monitors are no longer produced. However, we would still like
   to
   continue model building in 3D which is apparently not possible
   with
   current TFT displays. Beside the possibility of getting old
   CRT monitors
   at ebay, I was wondering how other groups solved this problem.

   Thank you very much for suggestions!
   best wishes,
   Tobias




   Tobias Krojer, PhD
   IMP (Research Institute of Molecular Pathology)
   Dr. Bohr-Gasse 7
   1030 Vienna
   Austria
   Tel.: +43-1-797303358
   Fax.: +43-1-7987153








--
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 [EMAIL PROTECTED] [EMAIL PROTECTED]
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Re: [ccp4bb] Fwd: [ccp4bb] crystallisation and mosaicity

[Tommi Kajander]

according to literature,see below and references 
http://www.px.nsls.bnl.gov/courses/papers/ZD_EG_papers.html,
it is not clear that liq. propane plunged item would cool 
faster. (whilst i havent tested this)...  

Would anyone have actual experimental data with protein crystals
on the hyperquenching suggested by 
Warkentin, V. Berejnov, and R. E. Thorne, J. Appl. Cryst. (2006) 39,
805-811. (no diffraction data in the paper). in particular with 
small samples.

thanks,
Tommi

Quoting Petr Leiman <[EMAIL PROTECTED]>:

> >> yes you are right, but I assumed if people see a cloud of condensed
> >> fog over their LN2 bath they should remove that by
> >> a) filling up the bowl completely e.g. some LN2 drips out of the bowl
> >> b) blow the fog away before you dip
> 
> I think the original poster meant the relatively low heat conduction of 
> liquid N2, which causes boiling around the crystal immediately after 
> plunging.
> 
> The best way to freeze things is to put a small container of liquid
> ethane 
> or propane into a liquid N2 bowl, and plunge into the ethane/propane
> (this 
> methods was suggested earlier).
> 
> Petr
> 
> 


-- 
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
P.O. Box 65 (Street address: Viikinkaari 1, 4th floor)
University of Helsinki
FIN-00014 Helsinki, Finland
Tel. +358-9-191 58903
Fax  +358-9-191 59940

Re: [ccp4bb] analytical ultracentrifugation

[verdino]

Hi Mike,

try the National Analytical Ultracentrifugation Facility in Connecticut.

http://www.biotech.uconn.edu/auf/

Cheers, Petra


> Dear colleagues,
>
> does anyone know of a faciltiy for analytical ultracentrifugation?
>
> Thanks.
>
> Mike Colaneri
>


-- 
Petra Verdino, PhD
Research Associate
The Scripps Research Institute, BCC206
10550 North Torrey Pines Road
CA 92037 La Jolla, USA
tel:1-858-784-2945
fax:1-858-784-2980
http://www.scripps.edu/~verdino/homepage.htm

[ccp4bb] AstraZeneca US permanent PX position

[Read, Jon]

I would like to draw your attention to a protein crystallography position 
advertised on the AstraZeneca jobs web pages. This is a permanent position in a 
young structural biology team being established at our site in Boston, 
Massachussets. The position would suit an all-round, hands-on crystallographer. 
The work will support predominantly local Cancer and Infection projects. 
Interested and qualified individuals should apply online at 
www.astrazeneca-us.com/careers. Please use requisition number 1784496 to apply 
for this role. Interviews will begin in August.  

Jon Read, 
AstraZeneca, 
35 Gatehouse Drive, 
Waltham, MA 02451 USA

email: [EMAIL PROTECTED]
Tel: +1 781 839 4536

[ccp4bb] analytical ultracentrifugation

[Michael Colaneri]

Dear colleagues,

does anyone know of a faciltiy for analytical ultracentrifugation?

Thanks.

Mike Colaneri

Re: [ccp4bb] 3D model building without CRT monitor

[Vangelis Christodoulou]

There is a 20-inch (20-3D2W04) display that costs around $6000. For  
$13000 you get a 42-inch, so I guess the 52-inch that was introduced  
today will cost  a lot.


Vangelis

On Jun 5, 2008, at 7:30 PM, Juergen Bosch wrote:


Interesting!  Their PDF says it works with OpenGL:
http://www.business-sites.philips.com/assets/Downloadablefile//2006-05-30-Technology-backgrounder-13560.pdf

Does it mean it will work in Coot as is?

Dima


If you don't mind the 12K price tag, maybe.

Juergen

--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone:   +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation and mosaicity

[Edward Berry]

I think the important thing here is that liquid nitrogen in the lab
tends to be exactly at its boiling point, since the temperature is
maintained by continuously boiling off some of the N2.

This means the only mechanism for heat absorption is through vaporization,
depending on the latent heat of vaporization rather than the heat
capacity. So as soon as any heat is removed from the object, some gas
is formed, and the gas layer insulates.

Propane is chilled with LN2 to near its freezing point, so it can absorb
quite a lot of heat before any vapor is formed. If you spill some on your
hand you will have a nasty burn immediately, whereas you can usually get
away unscathed with splashing LN2 on your hand briefly.

Petr Leiman wrote:

yes you are right, but I assumed if people see a cloud of condensed
fog over their LN2 bath they should remove that by
a) filling up the bowl completely e.g. some LN2 drips out of the bowl
b) blow the fog away before you dip


I think the original poster meant the relatively low heat conduction of 
liquid N2, which causes boiling around the crystal immediately after 
plunging.


The best way to freeze things is to put a small container of liquid 
ethane or propane into a liquid N2 bowl, and plunge into the 
ethane/propane (this methods was suggested earlier).


Petr

Re: [ccp4bb] crystallisation and mosaicity

[Lokesh Gakhar]

Charlie,

The insulating gas cushion is due to the Leidenfrost effect (
http://en.wikipedia.org/wiki/Leidenfrost_effect). We discussed this somewhat
in:

J. Appl. Cryst. (2005). 38, 945-950

-Lokesh

On Wed, Jun 4, 2008 at 8:11 PM, Charlie Bond <[EMAIL PROTECTED]>
wrote:

> I seem to recall an explanation a few years ago that a problem with dunking
> into liquid nitrogen is that a cushion of nitrogen gas persists around the
> crystal/loop so that 'freezing' is not so reproducible (hopefully an expert
> will elaborate on this). The same problem doesn't exist with liquid propane,
> but it has other issues...
>
> I generally default to using the cryostream unless I know by experiment
> that dunking works.
>
> Cheers,
> Charlie
>
> Ohren, Jeffrey wrote:
>
>> Could it be that evaporation on the way from the microscope to the cold
>> stream increases the effective cryo concentration as well as causing a
>> beneficial dehydration effect?
>> There are quite a few publications that have carefully evaluated
>> optimizing cryo cooling. Check out Elspeth Garman's many excellent
>> papers on the subject as well as J. Appl. Cryst. (2006). 39, 244-251;
>> Methods 34 (2004) 415-423 and Acta Cryst. (2002). D58, 459-471, to name
>> a few.
>> Jeff
>>
>> -Original Message-
>> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
>> Paul Paukstelis
>> Sent: Tuesday, June 03, 2008 11:59 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] crystallisation and mosaicity
>>
>> I have also observed this. In my cases I have also been able to get away
>>
>> with using less cryoprotectant when freezing in the cryostream.
>>
>> --paul
>>
>> Daniel Pomeranz Krummel wrote:
>>
>>> Dear Sajid,
>>>
>>> I have observed a consistent reduction in mosaicity (from approx. 0.95
>>>
>> to
>>
>>> 0.45) for one case by freezing the crystals in a cryostream (N2
>>>
>> vapour) as
>>
>>> opposed to submerging in liquid nitrogen.
>>>
>>> Have others observed this?
>>>
>>> Daniel
>>>
>>>
 Dear All

 My protein size is ~30kD and crystallizes with
 19%Peg3350, 0.2M Nacl, and 0.1M Na Cacodylate buffer.

 Please refer the attached crystal image with this. The
 crystal looks like good enough for home source. These
 crystals appears in 4-5 days at room temp.

 Sometimes I'm getting crystals like this, but very few
 in 24 well tray. Most of the time, I found the drop
 contains needles. If I reduce the precipitant little
 bit, I wont find any change in the drop even after
 long time. Changing pH (or temp)of the buffer does not
 help me any better. The crystal appears only around
 5.5pH.

 The problem is mosaicity. This crystal diffracted in
 home source upto 3.2A and the mosaicity is 2.5degree.
 Almost all the good crystal like this having same
 mosaicity.

 Good cryo condition so far that I found was
 10%Glycerol with mother liquor. Other conditions
 weekens the diffraction quality or increase mosaicity.

 In many crystal I could see some crack in the middle
 of the crystal, it looks like twin crystal. Or the
 crystal appears with some sattelite crystals.

 Can anyone suggest me some good way to overcome these
 problems.

 Thankz

 Sajid



  From Chandigarh to Chennai - find friends all over India. Go to
 http://in.promos.yahoo.com/groups/citygroups/


>>>
>>>
>>
>>
>> .
>>
>>
> --
> Charlie Bond
> Professorial Fellow
> University of Western Australia
> School of Biomedical, Biomolecular and Chemical Sciences
> M310
> 35 Stirling Highway
> Crawley WA 6009
> Australia
> [EMAIL PROTECTED]
> +61 8 6488 4406
>

Re: [ccp4bb] 3D model building without CRT monitor

[Juergen Bosch]

Dima Klenchin wrote:


Vangelis Christodoulou wrote:


Philips is offering an interesting solution:
http://www.business-sites.philips.com/3dsolutions/products/3dscreens/index.html 




Interesting!  Their PDF says it works with OpenGL:
http://www.business-sites.philips.com/assets/Downloadablefile//2006-05-30-Technology-backgrounder-13560.pdf 



Does it mean it will work in Coot as is?

Dima


If you don't mind the 12K price tag, maybe.

Juergen

--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone:   +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation and mosaicity

[Petr Leiman]

yes you are right, but I assumed if people see a cloud of condensed
fog over their LN2 bath they should remove that by
a) filling up the bowl completely e.g. some LN2 drips out of the bowl
b) blow the fog away before you dip


I think the original poster meant the relatively low heat conduction of 
liquid N2, which causes boiling around the crystal immediately after 
plunging.


The best way to freeze things is to put a small container of liquid ethane 
or propane into a liquid N2 bowl, and plunge into the ethane/propane (this 
methods was suggested earlier).


Petr

Re: [ccp4bb] 3D model building without CRT monitor

[Dima Klenchin]

Vangelis Christodoulou wrote:

Philips is offering an interesting solution:
http://www.business-sites.philips.com/3dsolutions/products/3dscreens/index.html


Interesting!  Their PDF says it works with OpenGL:
http://www.business-sites.philips.com/assets/Downloadablefile//2006-05-30-Technology-backgrounder-13560.pdf 



Does it mean it will work in Coot as is?

Dima

Re: [ccp4bb] 3D model building without CRT monitor

[Vangelis Christodoulou]

Philips is offering an interesting solution:
http://www.business-sites.philips.com/3dsolutions/products/3dscreens/index.html

Vangelis

On Jun 2, 2008, at 2:10 PM, Krojer,Tobias wrote:


Dear all,

recently some of our CRT monitors broke down and we realized that  
these monitors are no longer produced. However, we would still like  
to continue model building in 3D which is apparently not possible  
with current TFT displays. Beside the possibility of getting old CRT  
monitors at ebay, I was wondering how other groups solved this  
problem.


Thank you very much for suggestions!
best wishes,
Tobias




Tobias Krojer, PhD
IMP (Research Institute of Molecular Pathology)
Dr. Bohr-Gasse 7
1030 Vienna
Austria
Tel.: +43-1-797303358
Fax.: +43-1-7987153

[ccp4bb] Fwd: [ccp4bb] crystallisation and mosaicity

[Patrick Loll]

Hi Charlie,

yes you are right, but I assumed if people see a cloud of condensed  
fog over their LN2 bath they should remove that by

a) filling up the bowl completely e.g. some LN2 drips out of the bowl
b) blow the fog away before you dip


True; this has been demonstrated quite rigorously:

A general method for hyperquenching protein crystals
Journal Journal of Structural and Functional Genomics
Volume 8, Number 4 / December, 2007
DOI 10.1007/s10969-007-9029-0
Pages   141-144

AND

J. Appl. Cryst. (2006). 39, 805-811[ doi:10.1107/S0021889806037484 ]
Hyperquenching for protein cryocrystallography
M. Warkentin, V. Berejnov, N. S. Husseini and R. E. Thorne






 
---

Patrick J. Loll, Ph. D. 
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
[EMAIL PROTECTED]

Re: [ccp4bb] crystallisation and mosaicity

[Juergen Bosch]

Hi Charlie,

yes you are right, but I assumed if people see a cloud of condensed fog 
over their LN2 bath they should remove that by

a) filling up the bowl completely e.g. some LN2 drips out of the bowl
b) blow the fog away before you dip
c) ask someone for advice

In general I have observed much better results with cryo-cooling 
crystals by plunging  them into LN2 versus mounting them on a blocked 
cryostream and then unblock it. Some tend also just to swing the crysal 
onto the goniometer head without worrying about the cryostream, so the 
crystal is cooled while it is mounted. Unless you have a very good cryo, 
this procedure will result in bad reproducibility and most likely very 
often in badly frozen crystals.


Just my 3 eurocents,

Juergen

Charlie Bond wrote:

I seem to recall an explanation a few years ago that a problem with 
dunking into liquid nitrogen is that a cushion of nitrogen gas 
persists around the crystal/loop so that 'freezing' is not so 
reproducible (hopefully an expert will elaborate on this). The same 
problem doesn't exist with liquid propane, but it has other issues...


I generally default to using the cryostream unless I know by 
experiment that dunking works.


Cheers,
Charlie

Ohren, Jeffrey wrote:


Could it be that evaporation on the way from the microscope to the cold
stream increases the effective cryo concentration as well as causing a
beneficial dehydration effect?
There are quite a few publications that have carefully evaluated
optimizing cryo cooling. Check out Elspeth Garman's many excellent
papers on the subject as well as J. Appl. Cryst. (2006). 39, 244-251;
Methods 34 (2004) 415-423 and Acta Cryst. (2002). D58, 459-471, to name
a few.
Jeff

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Paul Paukstelis
Sent: Tuesday, June 03, 2008 11:59 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] crystallisation and mosaicity

I have also observed this. In my cases I have also been able to get away

with using less cryoprotectant when freezing in the cryostream.

--paul

Daniel Pomeranz Krummel wrote:


Dear Sajid,

I have observed a consistent reduction in mosaicity (from approx. 0.95


to


0.45) for one case by freezing the crystals in a cryostream (N2


vapour) as


opposed to submerging in liquid nitrogen.

Have others observed this?

Daniel
 


Dear All

My protein size is ~30kD and crystallizes with
19%Peg3350, 0.2M Nacl, and 0.1M Na Cacodylate buffer.

Please refer the attached crystal image with this. The
crystal looks like good enough for home source. These
crystals appears in 4-5 days at room temp.

Sometimes I'm getting crystals like this, but very few
in 24 well tray. Most of the time, I found the drop
contains needles. If I reduce the precipitant little
bit, I wont find any change in the drop even after
long time. Changing pH (or temp)of the buffer does not
help me any better. The crystal appears only around
5.5pH.

The problem is mosaicity. This crystal diffracted in
home source upto 3.2A and the mosaicity is 2.5degree.
Almost all the good crystal like this having same
mosaicity.

Good cryo condition so far that I found was
10%Glycerol with mother liquor. Other conditions
weekens the diffraction quality or increase mosaicity.

In many crystal I could see some crack in the middle
of the crystal, it looks like twin crystal. Or the
crystal appears with some sattelite crystals.

Can anyone suggest me some good way to overcome these
problems.

Thankz

Sajid



  From Chandigarh to Chennai - find friends all over India. Go to
http://in.promos.yahoo.com/groups/citygroups/



  




.






--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone:   +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch

Re: [ccp4bb] B factor calculation

[Mark J. van Raaij]

in ccp4, "baverage" does the job.
Mark

Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/



On 4 Jun 2008, at 21:40, xu zhen wrote:


Hi, everyone,

I am preparing the table of data collection and refinement statics.   
In this table, I need to list the average B factor of protein,  
ligand and water seperately, can you tell me how to calculate thoes  
numbers?


Zhen
_
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