Re: [ccp4bb] CCP4 / Ubuntu 9.04 64-bit

[Stephen Weeks]

Sankar,
All the executables you downloaded (including bltwish) from the CCP4
site are compiled on a 32bit machine. You just need to install the 32bit
shared library package via synaptic. The following terminal  command should
do.

sudo apt-get ia32-libs


As for coot for what platform is your version compiled for ? We've had
pretty good success with the Centos 64 bit version running on Ubuntu 9.04
(although you can't retrieve PDB files or maps from the EDS server from
within the program). You can also always build you own, this was brought up
on a another post on the BB. The coot version that comes with CCP4, if you
took that option, will not run on 64  bit ubuntu.

Stephen


2009/8/3 Sankar narayanan 

> hi
>
> I installed CCP4 with Coot downloaded as a binary from the CCP4 website on
> a 64bit Ubuntu 9.04.
>
> The installation was flawless and the setup scripts ran like a charm.
>
> however, when i type ccp4i to get the GUI.
>
> i get the following error message:
>
> exec: 4: /usr/local/xtal/tcltk++/bin/bltwish: not found
>
> bltwish is there in the specified directory, which i manually checked.
>
> for coot,
>
> i get the following error messages:.
>
> COOT_PREFIX is /usr/local/xtal/Coot-0.5.2
> /usr/local/xtal/Coot-0.5.2/bin/coot-real
> /usr/local/xtal/Coot-0.5.2/bin/coot: 123:
> /usr/local/xtal/Coot-0.5.2/bin/coot-real: not found
> /usr/local/xtal/Coot-0.5.2/bin/coot: 130:
> /usr/local/xtal/Coot-0.5.2/bin/guile: not found
>
> All these files are there in the specified directories, which i checked
> manually.
>
> But still i could not run.
> Am i doing some thing terribly wrong ?
>
> sincerely
> sankar
>
>
>
> On Sat, 04 Jul 2009 Thomas J Magliery PhD wrote :
> > Hi, I just installed the 64-bit version of Ubuntu 9.04
> > Desktop, and then
> > I installed CCP4 6.1.1 using the standard package and
> > installation
> > script.  I can run ccp4i successfully.  However, when I
> > try to run Coot,
> > I get a bunch of errors.  I think the problem is that
> > Coot was compiled
> > with 32-bit libraries, which I don't have.
> >
> > Is there some way to fix this without compiling Coot or
> > re-installing
> > with 32-bit Ubuntu?  Who knows how, but I have CCP4
> > (6.0.2) and Coot
> > (0.5-pre-1) working on my 64-bit FC8 laptop.
> >
> > Thanks,
> > Tom
> >
> > ===
> > COOT_PREFIX is /usr/local/CCP4/Coot-0.5.2
> > /usr/local/CCP4/Coot-0.5.2/bin/coot-real
> > Acquiring application resources from
> > /usr/local/CCP4/Coot-0.5.2/share/coot/cootrc
> > Gtk-Message: Failed to load module
> > "canberra-gtk-module":
> > /usr/lib/gtk-2.0/modules/libcanberra-gtk-module.so:
> > wrong ELF class:
> > ELFCLASS64
> > INFO:: splash_screen_pixmap_dir
> > /usr/local/CCP4/Coot-0.5.2/share/coot/pixmaps
> > INFO:: Colours file: /usr/local/CCP4/Coot-0.5.2/share/co-
> > ot/colours.def
> > loaded
> > INFO:: Using Standard CCP4 Refmac dictionary from
> > CLIBD_MON:
> > /usr/local/CCP4/ccp4-6.1.1/lib/data/monomers/
> > There are 118 data in
> > /usr/local/CCP4/ccp4-6.1.1/lib/data/monomers//list/mon_l-
> > ib_list.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//a/ALA.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//a/ASP.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//a/ASN.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//c/CYS.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//g/GLN.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//g/GLY.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//g/GLU.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//p/PHE.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//h/HIS.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//i/ILE.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//l/LYS.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//l/LEU.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//m/MET.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//m/MSE.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//p/PRO.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//a/ARG.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//s/SER.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//t/THR.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//v/VAL.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//t/TRP.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//t/TYR.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
> > monomers//p/PO4.cif
> > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/data/-
>

Re: [ccp4bb] Twinning

[Eleanor Dodson]

Try refinement with the newest REFMAC which will take twinning into  
account.


But if your integration has missed some spots, or the spots were 
streaky you may have more complex problems -  with what is termed 
Order-disorder in the lattice.

  eleanor


Rana Refaey wrote:

Hi all,
I have a few datasets that I think are twinned for several reasons. 
1)The Rfree and Rmerge are both stuck very high. 
2) The L-test for twinning in Scala shows twinning 
3) Also the centric and acentric movements suggest twinning.  
4) The spots do not match the predication from Mosflm (Non-merohedral

twinning ?)

The space group is p212121, and am able to solve the structure using MR. But
when its comes to refining the Rfact and Rfree are stuck at high values (for
one of them at a resolution of 1.65 A they are 0.32 and 0.36 respectively )

Any suggestions how i could deal with these datasets ?

Many thanks

Rana 




  

Re: [ccp4bb] resolution shells for each bin in scala?

[Eleanor Dodson]

Cant you read the shell limits off the loggraphs? The numbers in the 
tables are given as 4sin**2/Lamba**2 I think but that is converted to As 
in the loggraph.

Is that what you mean though?
Eleanor

Francis E Reyes wrote:

Hello ccp4'ers


Where is / how can I obtain the resolution shell for each resolution 
bin in scala? My eyes can't seem to find it.



Thanks


FR

-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

Re: [ccp4bb] resolution shells for each bin in scala?

[Phil Evans]

The table has 1/d^2 and Dmin for the outer edge of each bin (columns 2  
& 3)


Phil

By  4SINTH/LASQ bins (all statistics relative to Mn(I))
 __

codebase="/usr/local/CCP4versions/Clapham/ccp4-6.1.1/bin">name="table" value="

 $TABLE: Analysis against resolution , New :
 $GRAPHS: I/sigma, Mean Mn(I)/sd(Mn(I)):N:2,11,13:
: Rmerge v Resolution:N:2,4,5,7:
 : Average I,sd and Sigma :A:2,9,10,12: : Fractional bias :A:2,17: $$
 N 1/resol^2 Dmin(A) Rmrg  Rfull   Rcum  Ranom  NanomAv_I  SIGMA  
I/sigma   sd Mn(I/sd)  Nmeas  Nref  Ncent FRCBIAS  Nbias $$



   N 1/d^2 Dmin(A) Rmrg  Rfull   Rcum  Ranom  NanomAv_I  SIGMA I/ 
sigma   sd Mn(I/sd)  Nmeas   Nref  Ncent FRCBIAS  Nbias

 $$
  1 0.0248  6.36  0.049   - 0.049   - 0   171815  17806
9.6  42009   7.3 3085 84481  -0.059899
  2 0.0495  4.49  0.068   - 0.058   - 092604  11948
7.8  22958   7.1 5715150884  -0.044   1765
  3 0.0743  3.67  0.113   - 0.080   - 0   136756  35595
3.8  33538   6.9 5188144655  -0.062   1499
  4 0.0990  3.18  0.161   - 0.099   - 080572  34834
2.3  21356   5.9 6512183257  -0.103   1898
  5 0.1238  2.84  0.129   - 0.102   - 035017   7334
4.8   9786   5.5 8897248481  -0.038   2663
  6 0.1485  2.59  0.192   - 0.107   - 017780   5282
3.4   6082   4.2 7234206957   0.002   2061
  7 0.1733  2.40  0.268   - 0.112   - 011018   4436
2.5   5042   3.4 8308238349  -0.033   2364
  8 0.1980  2.25  0.509   - 0.118   - 0 6611   5348
1.2   5286   2.2 6637192221  -0.016   1873
  9 0.2228  2.12  0.773   - 0.131   - 0 9030  33528
0.3   7036   1.6 66831941 6  -0.169   1906
 10 0.2475  2.01  1.043   - 0.142   - 0 4970  10229
0.5   6723   1.4 7108208110  -0.201   2084

 $$
">For inline graphs use a Java browser

 Overall: 0.142   - 0.142   - 045355  19774
2.3  13412   4.165367   18510   501  -0.062  19012
   Rmrg  Rfull   Rcum  Ranom  NanomAv_I  SIGMA I/ 
sigma   sd Mn(I/sd)  Nmeas   Nref  Ncent FRCBIAS  Nbias





On 4 Aug 2009, at 09:47, Eleanor Dodson wrote:

Cant you read the shell limits off the loggraphs? The numbers in the  
tables are given as 4sin**2/Lamba**2 I think but that is converted  
to As in the loggraph.

Is that what you mean though?
Eleanor

Francis E Reyes wrote:

Hello ccp4'ers


Where is / how can I obtain the resolution shell for each  
resolution bin in scala? My eyes can't seem to find it.



Thanks


FR

-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

[ccp4bb] detergent crystals

[Parveen Goyal]

Hi All,

I got some hexagonal crystals in one of my crystal condition. The protein is
a membrane protein and contains 0.05% DDM. Has anybody seen DDM crysals and
if yes, how do they look like?

thanks in advance

Parveen Goyal

[ccp4bb] Heavy atom derivatives for large structures

[George M. Sheldrick]

Why is the tantalum bromide cluster the cluster derivative of
choice for phasing large structures? As a inorganic chemist
(in a previous incarnation) I can think of a lot of other
possible clusters that might be suitable. I even have money
from a bioinorganic grant that could finance a PhD student 
from October 1st to work on a project with me in Goettingen
to investigate other clusters. In view of the recent 
success of Tobias Beck's 'magic triangle' phasing reagent I 
think that clusters containing several heavy atoms might well
be worth another look with modern phasing methods (potential
applicants should contact me by email).

George  

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

Re: [ccp4bb] detergent crystals

[Leigh Rees]

Hi Parveen,

Not a direct answer to your question but we could possibly help by
X-raying the crystals in-situ whilst protected and undisturbed in the
multi-well plate. This should definitively show whether they are protein
or detergent crystals.  

Depending on where you are located, we may have a friendly user or a
demo PX Scanner near you that can assist.

If we can help, please let me know.

All the best

Leigh
 

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Parveen Goyal
Sent: 04 August 2009 16:10
To: CCP4BB@jiscmail.ac.uk
Subject: [ccp4bb] detergent crystals

Hi All,

I got some hexagonal crystals in one of my crystal condition. The
protein is a membrane protein and contains 0.05% DDM. Has anybody seen
DDM crysals and if yes, how do they look like?

thanks in advance

Parveen Goyal

Re: [ccp4bb] detergent crystals

[Jose Antonio Cuesta Seijo]

Hi Parveen.

DDM crystals can look a bit like that. Like a pencil that has been
sharpened from both ends until there is very little pencil left, but often
the ends are flatter than that. You can get tons of these (also with DM) in
conditions with medium weight PEGs. Of course many proteins will also
crystallize as hexagonal rods with PEGs :-)
I'll take this chance to shre a thought with the community. When we say
"contains x% of detergent y", are we sure of what there is in the protein
stock? Most membrane protein stocks for crystallization will undergo a
concentration step in a filter, and the membrane proteins themselves can be
excellent detergent concentrators. For example, 0.05% DDM is about 1 mM
DDM, hardly enough to make a belt around proteins that are 100 uM or
higher.
Do people measure how much detergent there really is in the final
crystallization stock? It doesn't seem to get published, instead the
concentration in the last purification step is often mentioned.

Jose.

"Parveen Goyal" wrote:
> Hi All,
> 
> I got some hexagonal crystals in one of my crystal condition. The protein
is
> a membrane protein and contains 0.05% DDM. Has anybody seen DDM crysals
and
> if yes, how do they look like?
> 
> thanks in advance
> 
> Parveen Goyal
> 


--
***
Jose Antonio Cuesta-Seijo

Biophysical
Chemistry Group
Department of Chemistry
University of Copenhagen 
Tlf:
+45-35320261
Universitetsparken 5 
DK-2100 Copenhagen,
Denmark
***

[ccp4bb] Beamline Scientist PROXIMA 2

[SHEPARD William]

Hello CCP4BBers, 

 

A permanent scientist position is open on the PROXIMA 2 beamline at
SOLEIL. Please see below for more information.

 

Cheers, 

Bill

 

 

Beamline Scientist PROXIMA 2 (m/f)

(Ref: EXP-102)

SOLEIL is a state-of-the-art, third generation synchrotron radiation
centre dedicated to scientific research at an international level. The
PROXIMA 2 beamline will feature two undulators in canted geometry
providing for two independent experimental stations dedicated to
biological macromolecular crystallography (MX). The first branch,
PROXIMA 2A, will specialize in the collection of diffraction data from
micro-crystals and will start commissioning in 2010. The second branch,
PROXIMA 2B, is reserved for the future, and its objectives and design
are currently under study. 

 

We are seeking a motivated scientist with a strong background in MX.
Candidates must have hands-on experience working with instrumentation on
synchrotron MX beamlines. The duties will include the installation &
commissioning of the beamline, as well as the development of
methodologies related to micro-crystallography. Computing & programming
skills are desired. Experience in sample preparation and laboratory
techniques will be appreciated. This is a permanent scientific position
in the PROXIMA 2A team with ample opportunities to conduct in-house
research. A Ph.D. degree (or equivalent), plus post-doctoral experience,
in MX and instrumentation is a prerequisite for this position.

 

You will be part of a team of scientists who ensure the construction,
commissioning and smooth functioning of the PROXIMA beamlines. You will
also be expected to conduct research at a high level in a field
pertaining to structural biology employing synchrotron radiation. The
research may be pursued either independently or in collaboration.

 

Applications including the addresses of three referees should be
registered directly on the SOLEIL internet site 
http://candidature.synchrotron-soleil.fr/YourApplication
 .

 

More information is available at

http://www.synchrotron-soleil.fr/portal/page/portal/Soleil/OffresEmplois
/EXP-102

 

Or contact

 

William SHEPARD

tel. +33-1-6935-9636

william.shep...@synchrotron-soleil.fr
 

 

Jean-Pierre SAMAMA

tel. +33-1-6935-9775

jean-pierre.sam...@synchrotron-soleil.fr
 

 

Expiry date for applications: 30 September 2009

 

 

 

 

 

 



Dr. William SHEPARD

Principal Beamline Scientist PROXIMA II

Synchrotron SOLEIL

L'Orme des Merisiers

Saint Aubin, BP 48 

F-91192 GIF-SUR-YVETTE

France 

tel: +33 1 69 35 96 36

fax: +33 1 69 35 94 56

william.shep...@synchrotron-soleil.fr
 

 

 

 

<>

Re: [ccp4bb] detergent crystals

[Van Den Berg, Bert]

Hi Jose,

how do you know that those crystals were detergent and not protein? My 
impression is that it is really hard to crystallize DDM, and even harder for DM 
(solubilities > 20% in water). The easiest (?) way to check this may be to take 
some crystals, wash them well and run them out on a PAGE gel. If you don't see 
anything and you've taken enough crystals, then you're probably dealing with 
pure detergent crystals. As for your second point, you're right. For most 
low-cmc detergents the total detergent concentration will be substantially 
higher than reported, since a substantial amount is always bound to your 
protein. For 1 mM DDM, you would have only ~ 20 uM micelles, assuming an 
aggregation # of 50 (its higher). I don't think people measure the total 
detergent concentration in the end; for maltosides one could in principle do a 
Fehling's based assay to get the concentration.

Cheers, Bert

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: bert.vandenb...@umassmed.edu
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm



-Original Message-
From: CCP4 bulletin board on behalf of Jose Antonio Cuesta Seijo
Sent: Tue 8/4/2009 12:24 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] detergent crystals
 
Hi Parveen.

DDM crystals can look a bit like that. Like a pencil that has been
sharpened from both ends until there is very little pencil left, but often
the ends are flatter than that. You can get tons of these (also with DM) in
conditions with medium weight PEGs. Of course many proteins will also
crystallize as hexagonal rods with PEGs :-)
I'll take this chance to shre a thought with the community. When we say
"contains x% of detergent y", are we sure of what there is in the protein
stock? Most membrane protein stocks for crystallization will undergo a
concentration step in a filter, and the membrane proteins themselves can be
excellent detergent concentrators. For example, 0.05% DDM is about 1 mM
DDM, hardly enough to make a belt around proteins that are 100 uM or
higher.
Do people measure how much detergent there really is in the final
crystallization stock? It doesn't seem to get published, instead the
concentration in the last purification step is often mentioned.

Jose.

"Parveen Goyal" wrote:
> Hi All,
> 
> I got some hexagonal crystals in one of my crystal condition. The protein
is
> a membrane protein and contains 0.05% DDM. Has anybody seen DDM crysals
and
> if yes, how do they look like?
> 
> thanks in advance
> 
> Parveen Goyal
> 


--
***
Jose Antonio Cuesta-Seijo

Biophysical
Chemistry Group
Department of Chemistry
University of Copenhagen 
Tlf:
+45-35320261
Universitetsparken 5 
DK-2100 Copenhagen,
Denmark
***

Re: [ccp4bb] detergent crystals

[Pascal Egea]

Hi Jose,
It is quite difficult to crystallize DDM. The main problem is to estimate
detergent concentration in the final sample.
One method requires the use of chromatographic workstation coupled to a
light scattering detector and refraction index measurement unit. In this
case you can know if there is an excess detergent (particularly likely to be
the case if you are using a low CMC detergent like DDM and if you have been
concentrating your sample on a membrane with a cutoff smaller than the empty
micelles). This is more involved and requires a specialized equipment. But
you can detect both your protein and your excess detergent (if there is).
Also to test you crystals, you may want to see if you can access a
fluorescence microscope. If your protein contains tryptophan (and you have
the correct wavelength) then you protein crystals should glow. Your
detergent crystals should not. Those microscopes are getting more and more
popular so maybe you have one next by. It is very convenient.

Hope this helps

Pascal Egea, PhD
University of California Los Angeles
Department of Biological Chemistry

Re: [ccp4bb] detergent crystals

[R.M. Garavito]

Parveen,

Bert and Pascal are correct in that most alkyl glycoside detergent are  
notoriously difficult to crystallize in aqueous solution when you have  
the beta-anomer (what we normally buy).  However, the alpha-anomers  
can be quite easy to crystallize and can contaminate batches of beta- 
alkyl glycoside detergents.  While the quality control procedures are  
usually good enough to ensure that the alpha-anomer contamination of  
DDM, DM, and OG are low, it may not be low enough for all  
crystallization experiments.  Twenty or so years ago, I was even shown  
a batch of "pure" beta-OG from a company I shall not name which was  
insoluble in water.


Some people have complained about this, but the impact of alpha-anomer  
contamination on crystal growth and spurious detergent crystallization  
is unknown.  If this persists and you are sure that those are  
detergent crystals, you might ask to see information about alpha- 
anomer contamination for your batch of detergent.  Companies like  
Anatrace will be quite forthcoming with information, but larger  
companies (Sigma or Rohm & Haas) may give you the run around.


Good luck,

Michael


R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
513 Biochemistry Bldg.
Michigan State University
East Lansing, MI 48824-1319
Office:  (517) 355-9724 Lab:  (517) 353-9125
FAX:  (517) 353-9334Email:  garav...@msu.edu



On Aug 4, 2009, at 12:51 PM, Van Den Berg, Bert wrote:


Hi Jose,

how do you know that those crystals were detergent and not protein?  
My impression is that it is really hard to crystallize DDM, and even  
harder for DM (solubilities > 20% in water). The easiest (?) way to  
check this may be to take some crystals, wash them well and run them  
out on a PAGE gel. If you don't see anything and you've taken enough  
crystals, then you're probably dealing with pure detergent crystals.  
As for your second point, you're right. For most low-cmc detergents  
the total detergent concentration will be substantially higher than  
reported, since a substantial amount is always bound to your  
protein. For 1 mM DDM, you would have only ~ 20 uM micelles,  
assuming an aggregation # of 50 (its higher). I don't think people  
measure the total detergent concentration in the end; for maltosides  
one could in principle do a Fehling's based assay to get the  
concentration.


Cheers, Bert

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: bert.vandenb...@umassmed.edu
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm


"Parveen Goyal" wrote:
> Hi All,
>
> I got some hexagonal crystals in one of my crystal condition. The  
protein is
> a membrane protein and contains 0.05% DDM. Has anybody seen DDM  
crysals

> and > if yes, how do they look like?
>
> thanks in advance
>
> Parveen Goyal
>

Re: [ccp4bb] detergent crystals

[Jacob Keller]

A recommendation: try looking at the crystals while rotating the polarizers. 
Often you can get detergent or detergent-protein complex "crystals" which have 
sharp edges, but are actually liquid crystals. This will be manifest as a 
compact-disc (or vinyl LP, depending on your vintage) appearance which rotates 
in sync with the rotation of the polarizers. Several colleagues and I have been 
plagued with these false positives, which are in our experience extremely hard 
to optimize into real crystals.

Another possibility: crystallization with a fluorescent or otherwise detectable 
substrate analogue could also be helpful, at least for determining whether 
there is protein in the sharp-edged objects.

The best test, of course, is to mount the objects and put them in the x-ray 
beam.

Regards,

Jacob Keller


***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

  - Original Message - 
  From: R.M. Garavito 
  To: CCP4BB@JISCMAIL.AC.UK 
  Sent: Tuesday, August 04, 2009 12:37 PM
  Subject: Re: [ccp4bb] detergent crystals


  Parveen,


  Bert and Pascal are correct in that most alkyl glycoside detergent are 
notoriously difficult to crystallize in aqueous solution when you have the 
beta-anomer (what we normally buy).  However, the alpha-anomers can be quite 
easy to crystallize and can contaminate batches of beta-alkyl glycoside 
detergents.  While the quality control procedures are usually good enough to 
ensure that the alpha-anomer contamination of DDM, DM, and OG are low, it may 
not be low enough for all crystallization experiments.  Twenty or so years ago, 
I was even shown a batch of "pure" beta-OG from a company I shall not name 
which was insoluble in water.


  Some people have complained about this, but the impact of alpha-anomer 
contamination on crystal growth and spurious detergent crystallization is 
unknown.  If this persists and you are sure that those are detergent crystals, 
you might ask to see information about alpha-anomer contamination for your 
batch of detergent.  Companies like Anatrace will be quite forthcoming with 
information, but larger companies (Sigma or Rohm & Haas) may give you the run 
around.


  Good luck,


  Michael


  

  R. Michael Garavito, Ph.D.

  Professor of Biochemistry & Molecular Biology

  513 Biochemistry Bldg.   

  Michigan State University  

  East Lansing, MI 48824-1319

  Office:  (517) 355-9724 Lab:  (517) 353-9125

  FAX:  (517) 353-9334Email:  garav...@msu.edu

  





  On Aug 4, 2009, at 12:51 PM, Van Den Berg, Bert wrote:


Hi Jose,

how do you know that those crystals were detergent and not protein? My 
impression is that it is really hard to crystallize DDM, and even harder for DM 
(solubilities > 20% in water). The easiest (?) way to check this may be to take 
some crystals, wash them well and run them out on a PAGE gel. If you don't see 
anything and you've taken enough crystals, then you're probably dealing with 
pure detergent crystals. As for your second point, you're right. For most 
low-cmc detergents the total detergent concentration will be substantially 
higher than reported, since a substantial amount is always bound to your 
protein. For 1 mM DDM, you would have only ~ 20 uM micelles, assuming an 
aggregation # of 50 (its higher). I don't think people measure the total 
detergent concentration in the end; for maltosides one could in principle do a 
Fehling's based assay to get the concentration.

Cheers, Bert

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: bert.vandenb...@umassmed.edu
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm


"Parveen Goyal" wrote:
> Hi All,
>
> I got some hexagonal crystals in one of my crystal condition. The protein 
is
> a membrane protein and contains 0.05% DDM. Has anybody seen DDM crysals
> and > if yes, how do they look like?
>
> thanks in advance
>
> Parveen Goyal
>

Re: [ccp4bb] resolution shells for each bin in scala?

[Francis E Reyes]

I was hoping for a break down for each bin similar to that of d*trek..


for example:

Rmerge vs Resolution

 Resolution   AverageNum Num   I/sig  I/sig  Rducd  Model  
Rmerge Rmerge
range  counts   rejs   mults   unavgavg  ChiSq  Eadd*   
shell  cumul


 45.96 - 5.45 810211159710.5   19.9   0.85   0.06   
0.043  0.043
  5.45 - 4.33 565 401640 6.9   12.6   0.84   0.10   
0.074  0.056
  4.33 - 3.78 387 341633 4.68.5   0.91   0.15   
0.114  0.069
  3.78 - 3.43 245 371679 3.36.1   0.93   0.22   
0.172  0.081
  3.43 - 3.19 166 381676 2.74.8   1.04   0.28   
0.239  0.093
  3.19 - 3.00 126 311675 2.34.1   1.05   0.34   
0.288  0.104
  3.00 - 2.85 110 131664 2.13.6   1.11   0.39   
0.325  0.114
  2.85 - 2.73 101  31259 2.03.0   1.03   0.42   
0.313  0.119
  2.73 - 2.62  99  2 870 2.02.7   1.02   0.41   
0.308  0.121
  2.62 - 2.53  97  0 512 1.92.4   0.84   0.42   
0.287  0.122


 45.96 - 2.53 304409   14205 4.27.6   0.96   0.16   
0.122  0.122



The last resolution bin has a slice of 2.62 and 2.53 data. I would  
like those for every resolution listed.


FR

On Aug 4, 2009, at 3:25 AM, Phil Evans wrote:

The table has 1/d^2 and Dmin for the outer edge of each bin (columns  
2 & 3)


Phil

By  4SINTH/LASQ bins (all statistics relative to Mn(I))
__

codebase="/usr/local/CCP4versions/Clapham/ccp4-6.1.1/bin">name="table" value="

$TABLE: Analysis against resolution , New :
$GRAPHS: I/sigma, Mean Mn(I)/sd(Mn(I)):N:2,11,13:
: Rmerge v Resolution:N:2,4,5,7:
: Average I,sd and Sigma :A:2,9,10,12: : Fractional bias :A:2,17: $$
N 1/resol^2 Dmin(A) Rmrg  Rfull   Rcum  Ranom  NanomAv_I  SIGMA  
I/sigma   sd Mn(I/sd)  Nmeas  Nref  Ncent FRCBIAS  Nbias $$



  N 1/d^2 Dmin(A) Rmrg  Rfull   Rcum  Ranom  NanomAv_I  SIGMA I/ 
sigma   sd Mn(I/sd)  Nmeas   Nref  Ncent FRCBIAS  Nbias

$$
 1 0.0248  6.36  0.049   - 0.049   - 0   171815  17806
9.6  42009   7.3 3085 84481  -0.059899
 2 0.0495  4.49  0.068   - 0.058   - 092604  11948
7.8  22958   7.1 5715150884  -0.044   1765
 3 0.0743  3.67  0.113   - 0.080   - 0   136756  35595
3.8  33538   6.9 5188144655  -0.062   1499
 4 0.0990  3.18  0.161   - 0.099   - 080572  34834
2.3  21356   5.9 6512183257  -0.103   1898
 5 0.1238  2.84  0.129   - 0.102   - 035017   7334
4.8   9786   5.5 8897248481  -0.038   2663
 6 0.1485  2.59  0.192   - 0.107   - 017780   5282
3.4   6082   4.2 7234206957   0.002   2061
 7 0.1733  2.40  0.268   - 0.112   - 011018   4436
2.5   5042   3.4 8308238349  -0.033   2364
 8 0.1980  2.25  0.509   - 0.118   - 0 6611   5348
1.2   5286   2.2 6637192221  -0.016   1873
 9 0.2228  2.12  0.773   - 0.131   - 0 9030  33528
0.3   7036   1.6 66831941 6  -0.169   1906
10 0.2475  2.01  1.043   - 0.142   - 0 4970  10229
0.5   6723   1.4 7108208110  -0.201   2084

$$
">For inline graphs use a Java browser

Overall: 0.142   - 0.142   - 045355  19774
2.3  13412   4.165367   18510   501  -0.062  19012
  Rmrg  Rfull   Rcum  Ranom  NanomAv_I  SIGMA I/ 
sigma   sd Mn(I/sd)  Nmeas   Nref  Ncent FRCBIAS  Nbias





On 4 Aug 2009, at 09:47, Eleanor Dodson wrote:

Cant you read the shell limits off the loggraphs? The numbers in  
the tables are given as 4sin**2/Lamba**2 I think but that is  
converted to As in the loggraph.

Is that what you mean though?
Eleanor

Francis E Reyes wrote:

Hello ccp4'ers


Where is / how can I obtain the resolution shell for each  
resolution bin in scala? My eyes can't seem to find it.



Thanks


FR

-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D




-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

Re: [ccp4bb] detergent crystals

[Van Den Berg, Bert]

This has been elaborated before, but you can safely assume they are NOT 
detergent crystals. DDM may be harder to crystallize than your average membrane 
proteinI hope those crystals diffract!

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: bert.vandenb...@umassmed.edu
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm



-Original Message-
From: CCP4 bulletin board on behalf of Parveen Goyal
Sent: Tue 8/4/2009 11:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] detergent crystals
 
Hi All,

I got some hexagonal crystals in one of my crystal condition. The protein is
a membrane protein and contains 0.05% DDM. Has anybody seen DDM crysals and
if yes, how do they look like?

thanks in advance

Parveen Goyal

Re: [ccp4bb] CCP4 / Ubuntu 9.04 64-bit

[Sankar narayanan]

Thank you very much for the advice Dr. Weeks,

I could run CCP4 GUI now with out any problem.

As you have rightly said, I downloaded the COOT along with CCP4 as a package 
(generic linux x86 version). 

I will try downloading the CENT OS version and follow the method from the 
previous posts to run COOT.

sincerely
sankar

On Tue, 04 Aug 2009 Stephen Weeks wrote :
> Sankar,
> All the executables you downloaded (including 
> bltwish) from the CCP4
> site are compiled on a 32bit machine. You just need to 
> install the 32bit
> shared library package via synaptic. The following 
> terminal  command should
> do.
> 
> sudo apt-get ia32-libs
> 
> 
> As for coot for what platform is your version compiled 
> for ? We've had
> pretty good success with the Centos 64 bit version 
> running on Ubuntu 9.04
> (although you can't retrieve PDB files or maps from the 
> EDS server from
> within the program). You can also always build you own, 
> this was brought up
> on a another post on the BB. The coot version that 
> comes with CCP4, if you
> took that option, will not run on 64  bit ubuntu.
> 
> Stephen
> 
> 
> 2009/8/3 Sankar narayanan 
> 
> > hi
> >
> > I installed CCP4 with Coot downloaded as a binary 
> from the CCP4 website on
> > a 64bit Ubuntu 9.04.
> >
> > The installation was flawless and the setup scripts 
> ran like a charm.
> >
> > however, when i type ccp4i to get the GUI.
> >
> > i get the following error message:
> >
> > exec: 4: /usr/local/xtal/tcltk++/bin/bltwish: not 
> found
> >
> > bltwish is there in the specified directory, which i 
> manually checked.
> >
> > for coot,
> >
> > i get the following error messages:.
> >
> > COOT_PREFIX is /usr/local/xtal/Coot-0.5.2
> > /usr/local/xtal/Coot-0.5.2/bin/coot-real
> > /usr/local/xtal/Coot-0.5.2/bin/coot: 123:
> > /usr/local/xtal/Coot-0.5.2/bin/coot-real: not found
> > /usr/local/xtal/Coot-0.5.2/bin/coot: 130:
> > /usr/local/xtal/Coot-0.5.2/bin/guile: not found
> >
> > All these files are there in the specified 
> directories, which i checked
> > manually.
> >
> > But still i could not run.
> > Am i doing some thing terribly wrong ?
> >
> > sincerely
> > sankar
> >
> >
> >
> > On Sat, 04 Jul 2009 Thomas J Magliery PhD wrote :
> > > Hi, I just installed the 64-bit version of Ubuntu 
> 9.04
> > > Desktop, and then
> > > I installed CCP4 6.1.1 using the standard package 
> and
> > > installation
> > > script.  I can run ccp4i successfully.  However, 
> when I
> > > try to run Coot,
> > > I get a bunch of errors.  I think the problem is 
> that
> > > Coot was compiled
> > > with 32-bit libraries, which I don't have.
> > >
> > > Is there some way to fix this without compiling 
> Coot or
> > > re-installing
> > > with 32-bit Ubuntu?  Who knows how, but I have CCP4
> > > (6.0.2) and Coot
> > > (0.5-pre-1) working on my 64-bit FC8 laptop.
> > >
> > > Thanks,
> > > Tom
> > >
> > > ===
> > > COOT_PREFIX is /usr/local/CCP4/Coot-0.5.2
> > > /usr/local/CCP4/Coot-0.5.2/bin/coot-real
> > > Acquiring application resources from
> > > /usr/local/CCP4/Coot-0.5.2/share/coot/cootrc
> > > Gtk-Message: Failed to load module
> > > "canberra-gtk-module":
> > > /usr/lib/gtk-2.0/modules/libcanberra-gtk-module.so:
> > > wrong ELF class:
> > > ELFCLASS64
> > > INFO:: splash_screen_pixmap_dir
> > > /usr/local/CCP4/Coot-0.5.2/share/coot/pixmaps
> > > INFO:: Colours file: /usr/local/CCP4/Coot-0.5.2/shar-
> e/co-
> > > ot/colours.def
> > > loaded
> > > INFO:: Using Standard CCP4 Refmac dictionary from
> > > CLIBD_MON:
> > > /usr/local/CCP4/ccp4-6.1.1/lib/data/monomers/
> > > There are 118 data in
> > > /usr/local/CCP4/ccp4-6.1.1/lib/data/monomers//list/m-
> on_l-
> > > ib_list.cif
> > > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/d-
> ata/-
> > > monomers//a/ALA.cif
> > > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/d-
> ata/-
> > > monomers//a/ASP.cif
> > > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/d-
> ata/-
> > > monomers//a/ASN.cif
> > > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/d-
> ata/-
> > > monomers//c/CYS.cif
> > > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/d-
> ata/-
> > > monomers//g/GLN.cif
> > > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/d-
> ata/-
> > > monomers//g/GLY.cif
> > > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/d-
> ata/-
> > > monomers//g/GLU.cif
> > > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/d-
> ata/-
> > > monomers//p/PHE.cif
> > > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/d-
> ata/-
> > > monomers//h/HIS.cif
> > > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/d-
> ata/-
> > > monomers//i/ILE.cif
> > > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/d-
> ata/-
> > > monomers//l/LYS.cif
> > > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/d-
> ata/-
> > > monomers//l/LEU.cif
> > > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/d-
> ata/-
> > > monomers//m/MET.cif
> > > There are 2 data in /usr/local/CCP4/ccp4-6.1.1/lib/d-
> ata/-
> > > monomers//m/MSE.cif
> > > Ther

[ccp4bb] REMINDER: AsCA'09 - October 22-25, 2009, Beijing, China

[Mark Bartlam]

AsCA'09 Beijing
Joint Conference of the Asian Crystallographic Association and Chinese
Crystallographic Society
October 22-25, 2009, Beijing, China

Website: http://www.ciccst.org.cn/asca09/ 

PLEASE NOTE: The deadline for submission of abstracts has been extended to
August 5, 2009.

SPONSORS:
The Asian Crystallographic Association
Chinese Academy of Sciences
National Natural Science Foundation of China

LOCAL ORGANIZERS:
Chinese Crystallographic Society (CCrS)
Biophysical Society of China (BSC)
Institute of Biophysics, CAS (IBP)
Nankai University
Tsinghua University
Peking University

 
Dear Colleagues,

You are cordially invited to Beijing for the Joint Conference of the Asian
Crystallographic Association and Chinese Crystallographic Society, AsCA'09,
from October 22-25 2009. 

This conference is devoted to crystallography in Asia. The meeting aims to
cover all aspects of crystallography, ranging from inorganic and organic
small molecules to macromolecular proteins, viruses, and membrane proteins;
from crystal growth to protein engineering; from structural chemistry and
material science to nanoscience and nanotechnology; from crystal structure,
proteomics, and genomics, to drug design; from diffraction physics and ray
optics to the applications of electron, neutron, and synchrotron X-ray
photons for structural investigations, and so on.

Beijing, the host city of the 2008 Olympic Games, is the political,
educational and cultural capital of China. It offers an exciting and
stimulating blend of rich cultural heritage and thoroughly modern
facilities. The city is home to many beautiful historic sites, including the
Great Wall, the Forbidden City, the Temple of Heaven, and the Summer Palace.

The AsCA'09 meeting will be held in Jingyi Hotel, an elegant conference
facility opened prior to the 2008 Olympic Games. Boasting excellent meeting,
recreation and health facilities, Jingyi Hotel is located 6 km from downtown
Beijing and 40 km from Beijing International Airport. It is within easy
reach of many cultural sights, either via taxi or by subway from two nearby
subway stations.

We look forward to welcoming you to Beijing in 2009. With your
participation, we have every confidence that AsCA'09 will be a successful
meeting, both scientifically and socially.

Yours sincerely,
 
Zihe Rao
Chairman, AsCA'09
President of Nankai University
President of the Biophysical Society of China

Jianhua Lin
Chairman, AsCA'09
Vice President of Peking University
President of the Chinese Crystallographic Society



Invited speakers (secured so far):

PLENARY LECTURES:

Ted Baker: "Why crystallography?"
Hongkun Park: "Capturing Light and Poking Cells with Nanowires"
Yoshinori Fujiyoshi: "Structural physiology based on electron
crystallography"

KEYNOTE LECTURES:

Joel Sussman: "Proteopedia - a Scientific 'Wiki' Bridging the Rift Between
3D Structure and Function of Biomacromolecules"
David Owen: "Cargo recognition during clathrin-coated vesicle formation"
Matthew Rosseinsky: "Reactivity and flexibility in metal-organic frameworks:
amino-acid based and post-synthetically functionalised materials"
Thomas Mak: "Crystalline silver(I) complexes containing all-carbon and
carbon-rich anionic ligands"


Session Topics:

1. STRUCTURAL BIOLOGY
Membrane proteins
Protein-nucleic acid complexes
Structural genomics
Structural biology in disease/structure-based drug design
Macromolecular assemblies
New tools for macromolecular crystallography
Hot structures

2. CHEMICAL CRYSTALLOGRAPHY - STRUCTURE AND PROPERTIES
Inorganic and nano-materials
Charge density studies
Organic crystal engineering and structure
Metal-organic crystal engineering
Superconductivity and crystal properties

3. SPECIALISED TECHNIQUES
Neutron and synchrotron sources and applications
Advanced imaging techniques
Small angle scattering and soft materials crystallography
Powder diffraction
Electron microscopy and diffraction


A new feature of this AsCA meeting will be a Plenary Symposium Session for
young scientists, 'AsCA Rising Stars'.  Six speakers will be selected from
the submitted abstract to participate in this symposium.  Those eligible for
selection will either be current PhD students or a young post-docs (thesis
submitted after October 2006).

When the abstract is submitted, a letter must be provided by the young
scientist's supervisor requesting that he/she be considered for this session
and confirming their eligibility. The supervisor must then ensure that any
young scientist they are recommending comes prepared to give a 15 minute
plenary presentation.

Young scientists selected to participate will be notified the evening before
the 'Rising Stars' symposium.  Two speakers will be selected from each of
the meeting's main themes, Structural Biology, Chemical Crystallography, and
Specialized Techniques.

For further information and registration details, please visit the
conference website: http://www.ciccst.org.cn/asca09/