[ccp4bb] Final reminder: 2008 Crystallographic Computing School

[Ralf W. Grosse-Kunstleve]

The registration deadline for the 2008 Crystallographic Computing
School is in two days: *** July 25 ***

The schedule of the program including abstracts from all speakers is
available here:

  http://www.iucr.org/iucr-top/comm/ccom/kyoto2008/program.html

This program puts a strong weight on fostering one-on-one
interactions. There will be only 16 lectures of 45 minutes
each (12 hours total) but more than 20 hours of tutorials and
demonstrations. Don't miss this unique opportunity for close
interaction with the developer community!

On behalf of the organizing committee:
A. L. Spek (Utrecht University , Netherlands)
R. Grosse-Kunstleve (LBNL, USA)
M. Yao (Hokkaido University, Japan)
A. Nakagawa (Osaka Institute of Protein, Japan)
H. Powell (MRC, UK)
L. Cranswick (NRC , Canada)

[ccp4bb] Using multiple crystals for structure solution in P1 using MAD/SAS/SAD

[hari jayaram]

We are faced  with phasing a structure for a protein that refuses to
crystallize in any spacegroup but P1.
To add to the fun , the resolution for most selenomethionine  and heavy atom
soak datasets ranges from 3.8 to 4.2 A .

In order to increase the redundancy we have been taking many inverse beam
datasets from each crystal  by making sure the beam is significantly
attenuated.
We now have 360 times 6, ( i.e 6 passes) and in some case 8 passes, datasets
for a few crystals collected at the peak wavelength in the case of
Selenomethionine crystals. In some cases we even managed an inflection
dataset . Needless to say the anomolous signal seems quite week at these
resolutions and low redundancies for any single crystal dataset.

I was wondering if anyone could comment on combining datasets from multiple
P1 crystals to increase the redundancy even further for such heavy atom (
SAS / SAD ) or MAD experiments.

Thanks a lot for your help and suggestions in advance
hari

[ccp4bb] Resuming creat 3D small molecules

[Ariel Talavera]

HI again,

Thanks for your very quick answer. I will compile all the suggestions. 
Just in case some one else need it.


http://davapc1.bioch.dundee.ac.uk/prodrg/
https://www.phenix-online.org/documentation/elbow.htm
http://davapc1.bioch.dundee.ac.uk/prodrg/
http://www.msg.ucsf.edu/local/programs/coot/user-manual.html#SEC112

Best,
Ariel

Ariel Talavera wrote:


Hi all,

I need to create the coordinates of a small molecule with no structure 
yet. Could any one tell me what program can I use to build small 
molecules?


Thanks in advamced.

Ariel



--
Ariel Talavera, Lic.
Dept. of Computational and Structural Biology
Center of Molecular Immunology
P.O.Box 16040, Havana 11600
Cuba
tel: (53-7) 271 7933, ext. 219
fax: (53-7) 272 0644
email: [EMAIL PROTECTED] 

Re: [ccp4bb] creat 3D small molecules

[Jayashankar]

DearAriel,

http://davapc1.bioch.dundee.ac.uk/prodrg/

try this and see,


On Tue, Jul 22, 2008 at 9:42 PM, Ariel Talavera <[EMAIL PROTECTED]> wrote:

>
> Hi all,
>
> I need to create the coordinates of a small molecule with no structure yet.
> Could any one tell me what program can I use to build small molecules?
>
> Thanks in advamced.
>
> Ariel
>
> --
> Ariel Talavera, Lic.
> Dept. of Computational and Structural Biology
> Center of Molecular Immunology
> P.O.Box 16040, Havana 11600
> Cuba
> tel: (53-7) 271 7933, ext. 219
> fax: (53-7) 272 0644
> email: [EMAIL PROTECTED]
>



-- 
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany

Re: [ccp4bb] creat 3D small molecules

[William Scott]

My favorite is the elbow builder in phenix.  You give it a "smiles"  
string and it will build (and optionally, optimize either classically  
or quantum-mechanically) your small molecule structure.



http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification

http://www.phenix-online.org/documentation/elbow.htm

You can also build one using a "smiles" string in coot.


http://www.msg.ucsf.edu/local/programs/coot/user-manual.html#SEC112





On Jul 22, 2008, at 1:42 PM, Ariel Talavera wrote:


Hi all,

I need to create the coordinates of a small molecule with no  
structure yet. Could any one tell me what program can I use to build  
small molecules?


Thanks in advamced.

Ariel

--
Ariel Talavera, Lic.
Dept. of Computational and Structural Biology
Center of Molecular Immunology
P.O.Box 16040, Havana 11600
Cuba
tel: (53-7) 271 7933, ext. 219
fax: (53-7) 272 0644
email: [EMAIL PROTECTED]

[ccp4bb] creat 3D small molecules

[Ariel Talavera]

Hi all,

I need to create the coordinates of a small molecule with no structure 
yet. Could any one tell me what program can I use to build small molecules?


Thanks in advamced.

Ariel

--
Ariel Talavera, Lic.
Dept. of Computational and Structural Biology
Center of Molecular Immunology
P.O.Box 16040, Havana 11600
Cuba
tel: (53-7) 271 7933, ext. 219
fax: (53-7) 272 0644
email: [EMAIL PROTECTED] 

[ccp4bb] Auto Sharp - problem

[sajid akthar]

Hi all

I am trying to run autoSHARP. When I submit the job I got following message and 
the job is not running. Does any one have got error like this when you start 
autoSHARP

Any advice please

Sajid


**
(In case of remotely submitted jobs, the "go to log file" will not work until 
the job is actually started)

 
 USAGE: /home/sajid/sharp/sushi/submit/interactive/start.sh -h $BDG_home -u 
$BDG_user -p $BDG_project -j $BDG_job
-t $BDG_type -l $BDG_log -e $BDG_err -v "$BDG_var" -b -a
 
 -h $BDG_home= Home directory of BDG installation 
 -u $BDG_user= user name 
 -p $BDG_project = project name 
 -j $BDG_job = job ID (name + number) 
 -t $BDG_type= (buster|sharp|denmod) 
 -l $BDG_log = log file 
 -e $BDG_err = standard error file 
 -v "$BDG_var"   = variable setting 
 -b  = flag for backgrounding job
 -a  = flag to do everything apart from actually running the job
 
 
 Maybe you are using the old syntax (Sushi < 3.0.16) in your
 
$BDG_home/submit.local/*/
 
 subdirectories? Have a look at the new syntax in
 
$BDG_home/submit/*/
 
 
 Your actual command was:
 
   /home/sajid/sharp/sushi/submit/interactive/start.sh -h /home/sajid/sharp -u 
syed -j MIRAS_with se.0 -p None -t detect -l LISTautoSHARP -e STDERR -b
**




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

Re: [ccp4bb] Na Acetate Buffer

[David Briggs]

Hi y'all.

One nice cheat is to get a groovy little web server to do the work for you:

http://www.liv.ac.uk/buffers/

Enter your requirements and you'll get a nice little recipe given back.

Dave

2008/7/22 Nadir T. Mrabet <[EMAIL PROTECTED]>:
> I bet it is more difficult to adjust a pH-meter than to use the
> Henderson-Hasselbalch equation
> and still get the expected pH with a pretty good accuracy especially if your
> work near the pKa.
>
> There are actually two ways to prepare this 25 mM buffer, pH 4.5.
>
> The pKa of acetate is 4.76 at 25 °C (with dpKa/° C = +0.0002, so don't worry
> too much about this).
> Reference is "Buffers for pH and Metal Ion Control", Perrin & Dempsey,
> Chapman & Hall, NY, ISBN 0 412 21890 9.
>
> High-grade glacial acetic acid (99-100%) is 18 N.
> Make a stock solution of 250 mM (eg 3.472 mL for 1.0 L final). Keep is a
> dark, tightly closed bottle.
>
> Make a stock solution of 250 mM sodium acetate (if you use FW, not MW, to
> calculate mass to use, then no worry about anhydrous or not since water is
> also taken into account if present)
>
> or
>
> make a stock solution of 5N NaOH. Keep is a dark, tightly closed bottle.
>
> Use then the Henderson-Hasselbalch equation (HH), pH = pKa + log
> ([A-]/[AH]).
>
> In the first case, you write it : 4.5 = 4.76 + log ([sodium acetate]/[acetic
> acid])
> Second equation is [sodium acetate] + [acetic acid] = 25 mM
> which gives [sodium acetate] = 8.886 mM and [acetic acid] = 16.134 mM.
> For 1.0 L buffer, mix adequate volumes of stock solutions of sodium acetate
> and acetic acid and complete with water (add acid after un first fill with
> water to ~ 800 mL).
>
> In the second case, the HH is written 4.5 = 4.76 + log([NaOH])/(25 -
> [NaOH]),
> which gives [NaOH] = 8.886 mM (same result as above for sodium acetate which
> was then the base).
>
> The added advantage of using HH and stock solutions is that even if your pH
> is not exactly 4.5, say 4.55, if you make a new buffer the next day or even
> the next month,
> your buffer will have the same pH value. I don't expect you can ever achieve
> such a repeatability using a pH-meter.
>
> HTH,
>
> Nadir Mrabet
>
> --
>
> Pr. Nadir T. Mrabet
>   Cellular & Molecular Biochemistry
>   INSERM U-724
>   Nancy University, School of Medicine
>   9, Avenue de la Foret de Haye, BP 184
>   54505 Vandoeuvre-les-Nancy Cedex
>   France
>   Phone: +33 (0)3.83.68.32.73
>   Fax:   +33 (0)3.83.68.32.79
>   E-mail: [EMAIL PROTECTED]
>
>
>
>
> William G. Scott wrote:
>>
>> So what, then, will be the concentration of the acetate ion in your stock
>> solution when you have finished?
>>
>> (Disclaimer:  I get to teach this stuff periodically in remedial chemistry
>> as a punishment for deployment of excessive sarcasm during faculty
>> meetings.)
>>
>> On Jul 22, 2008, at 6:10 AM, Santosh wrote:
>>
>>> Hi,
>>> Make a  1M Na-Acetate do not make up to the 1 Ltr volume. Leave some
>>> extra
>>> volume and now start adding Acetic acid till you get pH 4.5 (Glacial
>>> Acetic
>>> Acid).
>>> Now make up the volume to 1ltr or how much ever you are deciding to make
>>> the
>>> 50X stock solution.
>>> Best,
>>> Santosh
>>>
>>> On Mon, Jul 21, 2008 at 11:20 PM, William G. Scott <
>>> [EMAIL PROTECTED]> wrote:
>>>
 This is a job for the trusty Henderson-Hasselbalch equation:

 http://en.wikipedia.org/wiki/Henderson-Hasselbalch_equation



 On Jul 21, 2008, at 8:12 PM, Meg wrote:

 Dear All,
>
> I want to prepare 25 mM sodium acetate buffer pH 4.5. can anyone give
> the
> exact composition of how to prepare it. we prepare it using sodium
> acetate
> and acetic acid combination. i am not able to arrive at the
> calculatation
> correctly, so if anyone can  explain me with the above buffer how to
> calculate. and what sodium acetate [Anhydrous / trihydrate] and acetic
> acid
> [glacial/ plain] to use.
>
> thanks n regards
>
> Meg goyal,
> M.SC Biotechnology [Research]
> Institute of science,
> Fort
> Mumbai, INDIA
>

>>
>>
>



-- 

David C. Briggs PhD
Father & Crystallographer
http://www.dbriggs.talktalk.net
AIM ID: dbassophile

Re: [ccp4bb] SUMMARY: synchrotron remote data collection

[Green, Todd]

SER-CAT at APS has their own puck design. The layout is different than the 
unipuck and uses the ALS style pins.


-Original Message-
From: CCP4 bulletin board on behalf of Juergen Bosch
Sent: Tue 7/22/2008 1:52 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] SUMMARY: synchrotron remote data collection
 
Hi all,

now that we know who does remote data collection, how many different  
systems are our there which are incompatible with each other in terms  
of sending crystals in pucks or SSRl types of cassettes for robot  
remote data collection ?

-
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


This email was scanned with Mcafee's Anti-Virus appliance, but this 
is no guarantee that no virus exists. You are asked to make sure you
have virus protection and that it is up to date.

Re: [ccp4bb] SUMMARY: synchrotron remote data collection

[Juergen Bosch]

Hi all,

now that we know who does remote data collection, how many different  
systems are our there which are incompatible with each other in terms  
of sending crystals in pucks or SSRl types of cassettes for robot  
remote data collection ?


-
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

[ccp4bb] mail-in data collection

[Henry Bellamy]

The PX beamline at CAMD (Baton Rouge LA) does mail-in data collection,  
but not remote data collection.

For details see:  www.camd.lsu.edu/gcpcc/GCPCChome.htm

Henry Bellamy
Associate Professor - Research
Center for Advanced Microstructures and Devices
Louisiana State University
6980 Jefferson Hwy.
Baton Rouge LA 70806
225-578-9342 (voice)
225-578-6954 (fax)
[EMAIL PROTECTED]

Re: [ccp4bb] microfluidics in protein crystallography

[Daniel Pomeranz Krummel]

Dear Isabel,

It worked for a complex that I tested, but crystals were grown in similar
conditions by vapour diffusion using Limbro plates. Advantage was that
small amount of sample was needed. However, one can screen 96 conditions
with as little as ~10 ul of sample using a drop dispensing robot.

Daniel

> Dear CCP4ers,
>
>   I would like to have more info about microfluidics in protein
> xtallography: has anyone out there used it with success?.
> Thanks,
>
> Isabel
>
>
>
>
> Isabel Garcia-Saez PhD
> Institut de Biologie Structurale Jean-Pierre Ebel
> Laboratoire des Protéines du Cytosquelette
> 41, rue Jules Horowitz
> F-38027 Grenoble CEDEX 1
> France
> tel.: 00-33-438 789615
> FAX:  00-33-438 785494
> e-mail: [EMAIL PROTECTED]
> http://www.ibs.fr
>
>
>
>
>

Re: [ccp4bb] SUMMARY: synchrotron remote data collection

[Kay Diederichs]

Thanks to Christina,
the CCP4 wiki 
(http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Synchrotrons 
 ) now has the list which may be easily updated.


HTH,
Kay


smime.p7s
Description: S/MIME Cryptographic Signature

[ccp4bb] problem with ccp4 : local host definition on Kubuntu

[Gustavo Arruda]

Dear all,


Suddenly the following error appeared:

ERROR running script can not connect to server port
(RunNotification)
SERVER_HOST localhost SERVER_PORT 4441
Message: "couldn't open socket: host is unreachable"

and the process stays always on "starting".

I already know that this is a problem with the definition of localhost.
I tried to add the line:

 127.0.0.1  localhost.localdomain localhost

However, the problem never go away.

My system is Kubuntu. Someone could please give me a hand???

Thanks in advance,
Gustavo Arruda




  Novos endereços, o Yahoo! que você conhece. Crie um email novo com a sua 
cara @ymail.com ou @rocketmail.com.
http://br.new.mail.yahoo.com/addresses

Re: [ccp4bb] Na Acetate Buffer

[Nadir T. Mrabet]

I bet it is more difficult to adjust a pH-meter than to use the 
Henderson-Hasselbalch equation
and still get the expected pH with a pretty good accuracy especially if 
your work near the pKa.


There are actually two ways to prepare this 25 mM buffer, pH 4.5.

The pKa of acetate is 4.76 at 25 °C (with dpKa/° C = +0.0002, so don't 
worry too much about this).
Reference is "Buffers for pH and Metal Ion Control", Perrin & Dempsey, 
Chapman & Hall, NY, ISBN 0 412 21890 9.


High-grade glacial acetic acid (99-100%) is 18 N.
Make a stock solution of 250 mM (eg 3.472 mL for 1.0 L final). Keep is a 
dark, tightly closed bottle.


Make a stock solution of 250 mM sodium acetate (if you use FW, not MW, 
to calculate mass to use, then no worry about anhydrous or not since 
water is also taken into account if present)


or

make a stock solution of 5N NaOH. Keep is a dark, tightly closed bottle.

Use then the Henderson-Hasselbalch equation (HH), pH = pKa + log 
([A-]/[AH]).


In the first case, you write it : 4.5 = 4.76 + log ([sodium 
acetate]/[acetic acid])

Second equation is [sodium acetate] + [acetic acid] = 25 mM
which gives [sodium acetate] = 8.886 mM and [acetic acid] = 16.134 mM.
For 1.0 L buffer, mix adequate volumes of stock solutions of sodium 
acetate and acetic acid and complete with water (add acid after un first 
fill with water to ~ 800 mL).


In the second case, the HH is written 4.5 = 4.76 + log([NaOH])/(25 - 
[NaOH]),
which gives [NaOH] = 8.886 mM (same result as above for sodium acetate 
which was then the base).


The added advantage of using HH and stock solutions is that even if your 
pH is not exactly 4.5, say 4.55, if you make a new buffer the next day 
or even the next month,
your buffer will have the same pH value. I don't expect you can ever 
achieve such a repeatability using a pH-meter.


HTH,

Nadir Mrabet

--

Pr. Nadir T. Mrabet
   Cellular & Molecular Biochemistry
   INSERM U-724
   Nancy University, School of Medicine
   9, Avenue de la Foret de Haye, BP 184
   54505 Vandoeuvre-les-Nancy Cedex
   France
   Phone: +33 (0)3.83.68.32.73
   Fax:   +33 (0)3.83.68.32.79
   E-mail: [EMAIL PROTECTED]




William G. Scott wrote:
So what, then, will be the concentration of the acetate ion in your 
stock solution when you have finished?


(Disclaimer:  I get to teach this stuff periodically in remedial 
chemistry as a punishment for deployment of excessive sarcasm during 
faculty meetings.)


On Jul 22, 2008, at 6:10 AM, Santosh wrote:


Hi,
Make a  1M Na-Acetate do not make up to the 1 Ltr volume. Leave some 
extra
volume and now start adding Acetic acid till you get pH 4.5 (Glacial 
Acetic

Acid).
Now make up the volume to 1ltr or how much ever you are deciding to 
make the

50X stock solution.
Best,
Santosh

On Mon, Jul 21, 2008 at 11:20 PM, William G. Scott <
[EMAIL PROTECTED]> wrote:


This is a job for the trusty Henderson-Hasselbalch equation:

http://en.wikipedia.org/wiki/Henderson-Hasselbalch_equation



On Jul 21, 2008, at 8:12 PM, Meg wrote:

Dear All,


I want to prepare 25 mM sodium acetate buffer pH 4.5. can anyone 
give the
exact composition of how to prepare it. we prepare it using sodium 
acetate
and acetic acid combination. i am not able to arrive at the 
calculatation

correctly, so if anyone can  explain me with the above buffer how to
calculate. and what sodium acetate [Anhydrous / trihydrate] and acetic
acid
[glacial/ plain] to use.

thanks n regards

Meg goyal,
M.SC Biotechnology [Research]
Institute of science,
Fort
Mumbai, INDIA

Re: [ccp4bb] Cryo with succinate

[Alastair McEwen]

I have recently been working with crystals grown 
from 1M sodium succinate at pH 7.5 and I have 
found that 20% ethylene glycol worked well as a 
cryoprotectant. At concentrations below this we 
had ice formation. We did not do an exhaustive 
search for a cryo but found that we had very poor 
diffraction with glycerol, parrafin oil and various Fomblin oils.


Hope this helps,

Alastair


Le 14:41 22/07/2008,Tjaard Pijning écrit:
I have crystals grown from 1 M sodium succinate 
pH 7 and have been searching for suitable cryo conditions.
Is succinate in itself already a cryoprotectant 
(maybe at somewhat higher concentration) or should I

add e.g. glycerol ? Any experience or ideas are welcome.

Thanks in advance,


[]
   Ing. Tjaard Pijning

Protein Crystallography Group
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands
Tel. (31)(0)50 363 4385





Dr. Alastair McEwen
Département de Biologie et Génomique Structurales
IGBMC, 1 rue Laurent Fries, BP10142
67404 ILLKIRCH, France
Tel:  +33 (0)3 88 65 57 73
Fax: +33 (0)3 88 65 32 76
email: [EMAIL PROTECTED] <>

Dr. Alastair McEwen
Département de Biologie et Génomique Structurales
IGBMC, 1 rue Laurent Fries, BP10142
67404 ILLKIRCH, France
Tel:  +33 (0)3 88 65 57 73
Fax: +33 (0)3 88 65 32 76
email: [EMAIL PROTECTED]

Re: [ccp4bb] Na Acetate Buffer

[William G. Scott]

So what, then, will be the concentration of the acetate ion in your  
stock solution when you have finished?


(Disclaimer:  I get to teach this stuff periodically in remedial  
chemistry as a punishment for deployment of excessive sarcasm during  
faculty meetings.)


On Jul 22, 2008, at 6:10 AM, Santosh wrote:


Hi,
Make a  1M Na-Acetate do not make up to the 1 Ltr volume. Leave some  
extra
volume and now start adding Acetic acid till you get pH 4.5 (Glacial  
Acetic

Acid).
Now make up the volume to 1ltr or how much ever you are deciding to  
make the

50X stock solution.
Best,
Santosh

On Mon, Jul 21, 2008 at 11:20 PM, William G. Scott <
[EMAIL PROTECTED]> wrote:


This is a job for the trusty Henderson-Hasselbalch equation:

http://en.wikipedia.org/wiki/Henderson-Hasselbalch_equation



On Jul 21, 2008, at 8:12 PM, Meg wrote:

Dear All,


I want to prepare 25 mM sodium acetate buffer pH 4.5. can anyone  
give the
exact composition of how to prepare it. we prepare it using sodium  
acetate
and acetic acid combination. i am not able to arrive at the  
calculatation

correctly, so if anyone can  explain me with the above buffer how to
calculate. and what sodium acetate [Anhydrous / trihydrate] and  
acetic

acid
[glacial/ plain] to use.

thanks n regards

Meg goyal,
M.SC Biotechnology [Research]
Institute of science,
Fort
Mumbai, INDIA

Re: [ccp4bb] Na Acetate Buffer

[Roger Rowlett]

Meg wrote:

Dear All,

I want to prepare 25 mM sodium acetate buffer pH 4.5. can anyone give the
exact composition of how to prepare it. we prepare it using sodium acetate
and acetic acid combination. i am not able to arrive at the calculatation
correctly, so if anyone can  explain me with the above buffer how to
calculate. and what sodium acetate [Anhydrous / trihydrate] and acetic acid
[glacial/ plain] to use.

thanks n regards

Meg goyal,
M.SC Biotechnology [Research]
Institute of science,
Fort
Mumbai, INDIA
  
If you want to get the pH exactly right, the only proper way to do this 
is to make a solution of 25 mM acetic acid in water (leaving out about 
20% of the water temporarily), then titrate with NaOH until you reach a 
pH of 4.50. Then make up to the final volume with water and mix. You can 
get the proportions approximately right by using the 
Henderson-Hasselbalch equation, but in practice the pH may not come out 
exactly right.


--

Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [EMAIL PROTECTED]

Re: [ccp4bb] Cryo with succinate

[Roger Rowlett]

Tjaard Pijning wrote:
I have crystals grown from 1 M sodium succinate pH 7 and have 
been searching for suitable cryo conditions.
Is succinate in itself already a cryoprotectant (maybe at somewhat 
higher concentration) or should I

add e.g. glycerol ? Any experience or ideas are welcome.
 
Thanks in advance,
 


***   **Ing. Tjaard Pijning*

Protein Crystallography Group
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands
Tel. (31)(0)50 363 4385

 

Adding 25-30% glucose is sufficient to cryoprotect almost any 
crystallization solution from ice formation. If your crystals can't 
tolerate transfer to M.L. + glucose without cracking, you can try adding 
the cryoprotectant solution gradually to the drop the crystals are in. I 
usually add M.L. + cryoprotectant at 125% of the final concentration in 
0.25, 0.25, 0.5, 1.0, and 2.0 drop volumes a few minutes apart to allow 
for mixing and equilibration. (You can do this over the original well to 
avoid excessive evaporation.)


Alternatively, you can freeze empty drops with various amounts of 
glycerol and examine the frozen loops. If your solutions freeze clear, 
you probably have enough glycerol to prevent ice formation.


Cheers,


--

Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [EMAIL PROTECTED]

Re: [ccp4bb] Cryo with succinate

[Van Den Berg, Bert]

It should be pretty straightforward to figure that out by freezing and shooting 
loops with mother liquor only. You can easily fine-tune by including any 
additional buffer components you may have.
 
Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Biotech II, 373 Plantation Street, Suite 115
Worcester MA 01605
Phone: 508 856 1201 (office); 508 856 1211 (lab)
e-mail: [EMAIL PROTECTED]
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm



From: CCP4 bulletin board on behalf of Tjaard Pijning
Sent: Tue 7/22/2008 8:41 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Cryo with succinate


I have crystals grown from 1 M sodium succinate pH 7 and have been searching 
for suitable cryo conditions.
Is succinate in itself already a cryoprotectant (maybe at somewhat higher 
concentration) or should I
add e.g. glycerol ? Any experience or ideas are welcome.
 
Thanks in advance,
  

 

Ing. Tjaard Pijning

Protein Crystallography Group
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands
Tel. (31)(0)50 363 4385

 

<><>

[ccp4bb] Cryo with succinate

[Tjaard Pijning]

I have crystals grown from 1 M sodium succinate pH 7 and have been searching 
for suitable cryo conditions.
Is succinate in itself already a cryoprotectant (maybe at somewhat higher 
concentration) or should I
add e.g. glycerol ? Any experience or ideas are welcome.

Thanks in advance,
  
   Ing. Tjaard Pijning

Protein Crystallography Group
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands
Tel. (31)(0)50 363 4385


<><>

[ccp4bb] weak protein complexes

[amit sharma]

Dear CCP4BBers,
I am trying to crystallize a protein-protein complex with Kd in the range of
~40uM. I think that if I hike the concentration of the complex by
10-fold(~400uM), I would still have ~25%of uncomplexed material present. Is
it possible that I add some crowding agent such as PEG to bring down the Kd
value?
Any suggestions or strategies would be very helpful.

Thanks,
Amit

Re: [ccp4bb] SUMMARY: synchrotron remote data collection

[Robert Sweet]

You also missed the link for the BNL / NSLS Mail-in program, where three 
scientists spend about one full-time equivalent of effort, employing about 
one full-time beamline among the six PXRR beamlines. 


http://www.px.nsls.bnl.gov/ -->

Access to Beam Time http://www.px.nsls.bnl.gov/beamtime_requests.html -->

Mail-in Program http://www.px.nsls.bnl.gov/Mailin.html

It's a very busy and successful program:
http://journals.iucr.org/d/issues/2006/11/00/dz5083/index.html


On Tue, 22 Jul 2008, Chavas Leo wrote:


Dear all --
On 22 Jul 2008, at 00:45, Tom Caradoc-Davies wrote:
  Beamline 3BM1 at the Australian Synchrotron


I believe in Japan as well there is a remote control available, at SPring8. It 
is called Mail-in
system. You can probably find more informations there:
http://www.spring8.or.jp/en/about_us/organization/research_utilization/biology

HTH
Kind regards.

-- Leo --

Chavas Leonard, Ph.D. @ home
Research Associate

Faculty of Life Sciences
The University of Manchester
The Michael Smith Building
Oxford Road
Manchester Lancashire
M13 9PT

Tel: +44(0)161-275-1586
e-mail: [EMAIL PROTECTED]
http://personalpages.manchester.ac.uk/staff/leonard.chavas/






--
=
Robert M. Sweet E-Dress: [EMAIL PROTECTED]
Group Leader, PXRR: Macromolecular   ^ (that's L
  Crystallography Research Resource at NSLSnot 1)
  http://px.nsls.bnl.gov/
Biology Dept
Brookhaven Nat'l Lab.   Phones:
Upton, NY  11973631 344 3401  (Office)
U.S.A.  631 344 2741  (Facsimile)
=

[ccp4bb] Summary moving crystals

[Mark J. van Raaij]

Thanks for all helpful replies, below a summary of different moving  
crystal scenarios.
For our particular case, I am quite convinced it was the glue  
continuing to set/react after mounting. We had to glue some pins at  
the last moment, without having time to leave them to set a few hours  
as we do normally, and these were all litholoops if I remember  
correctly.
After the moving, extending, away from the goniometer head, the  
crystals stayed stable. This rules out ice between the head and base,  
or loosening of the pin in the base. Other crystals were also stable,  
ruling out something wrong with the goniometer setup, etc.


Summary of other possible moving events pointed out:
- ice crystals at the bottom of the base which slowly thaw
- loose pins in the base
- too weak magnets (too heavy base)
- too strong magnet, leading to whiplash effect, catapulting crystals  
(this presumably only occurs when directly freezing crystals on the  
beamline, not when mounting prefrozen crystals)

- incorrectly fastened goniometer, magnet etc.

PS new email address (forwarding will only work for a limited time):
[EMAIL PROTECTED]

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

[ccp4bb] microfluidics in protein crystallography

[Isabel Garcia-Saez]

Dear CCP4ers,

	I would like to have more info about microfluidics in protein  
xtallography: has anyone out there used it with success?.

Thanks,

Isabel




Isabel Garcia-Saez PhD
Institut de Biologie Structurale Jean-Pierre Ebel
Laboratoire des Protéines du Cytosquelette
41, rue Jules Horowitz
F-38027 Grenoble CEDEX 1
France
tel.: 00-33-438 789615
FAX:  00-33-438 785494
e-mail: [EMAIL PROTECTED]
http://www.ibs.fr

[ccp4bb] 6th NCCR Symposium New Trends in Structural Biology - Program online

[Patrick Sticher]

Dear colleagues,

6th International NCCR Symposium on New Trends in Structural Biology
8 + 9 September 2008, University of Zürich, Lecture Hall KOH-B10, 
Zürich, Switzerland

www.structuralbiology.uzh.ch/symposium2008.asp

The lecture program is available online at:
http://www.structuralbiology.uzh.ch/symposium2008_lectures.asp

Plenary lecturers:
Markus G. Grütter, Stephen C. Kowalczykowski, Kaspar Locher, Keiichi 
Namba, Poul Nissen, Andrej Sali, Ilme Schlichting, Titia Sixma, Jeffrey 
Skolnick, A. Joshua Wand


The meeting will be held together with the Annual Meeting of the Swiss 
Crystallography Society.

Society lectures will be given by Clemens Schulze-Briese and Colin Nave

Online registration to this event is still possible through the 
symposium homepage or directly at:

http://www.structuralbiology.uzh.ch/registration08.asp

Please do not hesitate to contact me anytime if you need further 
information ([EMAIL PROTECTED]).


With best regards,
Patrick Sticher

The NCCR Structural Biology is a research initiative of the Swiss 
Science Foundation. Its research encompasses the fields of recombinant 
protein technologies, macromolecular structure determination and 
computational biomolecular sciences with a special focus on membrane 
proteins and supramolecular assemblies/interactions. 19 research groups 
from Swiss Universities and Research Institutions participate in this 
network. www.structuralbiology.uzh.ch/


_
Dr. Patrick Sticher Moser
NCCR Scientific Officer
Institute of Biochemistry
University of Zürich
Winterthurerstrasse 190
CH - 8057 Zürich