[ccp4bb] Neutron Protein Crystallography Call for Proposals

[Paul Langan]

PROTEIN CRYSTALLOGRAPHY STATION AT LANSCE -- CALL FOR PROPOSALS

for Run Cycle Beginning the June 2009

You are invited to apply for beam time on the neutron Protein 
Crystallography Station (PCS) at the Los Alamos Neutron Science Center. The 
deadline for submitting proposals is 6:00 p.m. (1800) Mountain Standard 
Time on Sunday, March 2, 2009.  Any proposals submitted after the due date 
will not be reviewed by the Program Advisory Committees and must be 
resubmitted for the following run cycle.  Rapid access proposals may be 
submitted at any time, but require compelling evidence of sufficient 
scientific urgency to justify special scheduling.


The PCS is a high performance neutron protein crystallography beam line 
funded by the Office of Biological and Environmental Research of the U.S. 
Department of Energy. Users of the PCS have access to free neutron 
beam-time, free perdeuration services and also support for data reduction 
and structure analysis.


For more technical information about the PCS and experimental requirements, 
contact Paul Langan (505) 665 8125, langan_p...@lanl.gov


Proposal Guidance and Submission
==
Proposals must be submitted using the process on the LANSCE website.  Only 
proposals submitted in this manner will be accepted.
-To access the proposal submission site, go to the LANSCE home page, 
http://lansce.lanl.gov/.
-From there, click on the Lujan tab then select "Submit a proposal for beam 
time".

-Step-by-step instructions can be found on the Proposal Home web page.

Should you have any questions or require assistance, please contact the 
LANSCE User Office by e-mail at 
lansce_us...@lanl.gov or by telephone at 
(505) 665-1010.

Re: [ccp4bb] Refmac5 and dual conformation of a dual conformation

[Dale Tronrud]

   I have battled a similar piece of structure in a recent project.  There
is no software in crystallography that can handle hierarchical alternative
conformations w/o tricks.  I was refining in Shelxl but the same trick
will work elsewhere.  I had to define a new residue type, with two heads.
The A conformation had atoms for both heads.  The B conformation didn't
have atoms that couldn't be seen.  I was missing the entire side chain
in that conformation so the SC had no atoms.

   Besides creating the new geometry restraint library, you will have to
ensure that no bad contacts are flagged between the two heads.

   In Shelxl you can tie all the occupancies together properly, with
a couple annoyances.  In other programs you are on your own.

   Another possibility is to create four conformations for the entire
stretch but then you'll have to have the program keep many pairs of
atoms superimposed.  I don't know if Refmac has that feature.

   You will, of course, have difficulties when you deposit this thing
with the PDB.  There is no way to correctly represent your model in
a PDB file, nor I believe in mmCIF.  It may be reasonable to switch
to the four conformation model for deposition, since you will not
have to worry about enforcing the superposition of atoms any longer.
That may be clearer to people who use the model at a later date.

Dale Tronrud

Andy Millston wrote:
> I am currently trying to refine a structure where a 5 residue stretch of
> a chain is in 2 conformations. Oddly enough, 1 of these 5 residues is in
> dual conformations in both the conformations! Is there a conventional
> nomenclature for defining such dual-dual conformations?
> 
> Refmac5 does not accept the intuitive way of naming such an atom.
> 
> For example: A normal dual conformer GLY would be named as AGLY and BGLY
> in PDB file and this is acceptable to Refmac5
> 
> When I name a "dual-dual" GLY as AAGLY and BAGLY, Refmac5 fails! Any
> idea, WHY??
> 
> Thank you!
> 
> Here is the error log:
> 
> Logical name: ATOMSF, Filename: /programs/ccp4-6.0.2/lib/data/atomsf.lib
> 
> ***
> * Information from CCP4Interface script
> ***
> The program run with command: refmac5 XYZIN "/home/../myfile.pdb" XYZOUT
> "...tmp" HKLIN "mtz" HKLOUT "tmp" LIBOUT "..._56_lib.cif"
> has failed with error message
> fmt: read unexpected character
> apparent state: internal I/O
> last format: (I4)
> lately reading sequential formatted internal IO
> ***
> 
> 
> #CCP4I TERMINATION STATUS 0 fmt: read unexpected character apparent
> state: internal I/O last format: (I4) lately reading sequential
> formatted internal IO
> 
> 

[ccp4bb] Refmac5 and dual conformation of a dual conformation

[Andy Millston]

I am currently trying to refine a structure where a 5 residue stretch of a 
chain is in 2 conformations. Oddly enough, 1 of these 5 residues is in dual 
conformations in both the conformations! Is there a conventional nomenclature 
for defining such dual-dual conformations?

Refmac5 does not accept the intuitive way of naming such an atom.

For example: A normal dual conformer GLY would be named as AGLY and BGLY in PDB 
file and this is acceptable to Refmac5

When I name a "dual-dual" GLY as AAGLY and BAGLY, Refmac5 fails! Any idea, WHY??

Thank you!

Here is the error log:

Logical name: ATOMSF, Filename: /programs/ccp4-6.0.2/lib/data/atomsf.lib

***
* Information from CCP4Interface script
***
The program run with command: refmac5 XYZIN "/home/../myfile.pdb" XYZOUT 
"...tmp" HKLIN "mtz" HKLOUT "tmp" LIBOUT "..._56_lib.cif" 
has failed with error message
fmt: read unexpected character
apparent state: internal I/O
last format: (I4)
lately reading sequential formatted internal IO
***


#CCP4I TERMINATION STATUS 0 fmt: read unexpected character apparent state: 
internal I/O last format: (I4) lately reading sequential formatted internal IO



  

[ccp4bb] Postdoctoral position on calcium channels in Vancouver, Canada

[Filip Van Petegem]

A postdoctoral position is available in the lab of Filip Van Petegem at the
University of British Columbia.

Our lab focusses on calcium channels in both the plasma membrane and
intracellular compartments.  Calcium is an important 2nd messenger and
channels allowing influx of calcium into the cytoplasm play major roles in
the contraction of cardiac and skeletal muscle, pacemaking in the heart,
release of neurotransmitters and hormones, and activation of the immune
system.  Mutations in these channels lead to severe genetic diseases and
they are major drug targets for treating cardiac diseases, epilepsy, and
chronic pain.

We use an integrated approach to understand how calcium channels function,
including electrophysiology, X-ray crystallography, calorimetry, and various
additional biophysical techniques. An overview of our research can be found
at http://crg.ubc.ca/VanPetegem.   Our lab is part of the cardiovascular
research group (http://crg.ubc.ca), and is housed in the new life sciences
centre at UBC.

We are looking for a highly motivated individual with a sincere interest in
the field of ion channels or neuroscience, and with experience in
crystallizing and solving structures of proteins. Alternatively, individuals
with strong electrophysiological skills and wishing to learn crystallography
are also encouraged to apply.

Both formal applications and informal enquiries can be addressed via email
to: pete...@interchange.ubc.ca


Sincerely,

Filip Van Petegem



-- 
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3

phone: +1 604 827 4267
email: filip.vanpete...@gmail.com
http://crg.ubc.ca/VanPetegem/

Re: [ccp4bb] error message on installation of ccp4i on linux red hat enterprise 5.0

[Eric Liu]

The problem was fixed. I changed the original RgbPath in /etc/X11/xorg.conf
from "/usr/X11R6/lib/X11/rgb" to "/usr/share/X11/rgb". I can now run ccp4i.

Thanks everyone for pointing it out.

Eric



On Mon, Feb 2, 2009 at 4:43 PM, Tru Huynh  wrote:

> On Mon, Feb 02, 2009 at 04:23:18PM -0500, Eric Liu wrote:
> > Hi Tru,
>
> Please keep the discussion on the mailing list and trim your quotes!
>
> >
> > I checked the file you mentioned. The RgbPath is
> "/usr/X11R6/lib/X11/rgb".
> > Should I add the "/usr/share/X11/rgb" below the line of
> > "/usr/X11R6/lib/X11/rgb"?
> >
> > Thanks,
> >
> > Eric
> < --- snip --->
>
> Tru (will answer to the mailing list, no direct email)
> --
> Dr Tru Huynh  | http://www.pasteur.fr/recherche/unites/Binfs/
> mailto:t...@pasteur.fr | tel/fax +33 1 45 68 87 37/19
> Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France
>

Re: [ccp4bb] error message on installation of ccp4i on linux red hat enterprise 5.0

[Tru Huynh]

On Mon, Feb 02, 2009 at 02:16:38PM -0500, Eric Liu wrote:
> Hi All,
> 
> I just downloaded and installed ccp4 in my home directory. The installation
...
> Error in startup script: unknown color name "black"

check your /etc/X11/xorg.conf for a missing/extra line
-> RgbPath "/usr/share/X11/rgb"

Tru
-- 
Dr Tru Huynh  | http://www.pasteur.fr/recherche/unites/Binfs/
mailto:t...@pasteur.fr | tel/fax +33 1 45 68 87 37/19
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  

Re: [ccp4bb] small lines in diffraction pattern

[Gloria Borgstahl]

Gees, I go to Washington DC for a couple of days and then a superbowl 
party, come back to my stack of emails
and find out I missed out on all the fun... again!

At first glance I thought it looked like a problem with the CCD detector 
overloads, but that apparently has been ruled out.
Looks like you have already analyzed this, and from what I briefly read it 
sounds like a superstructure
that is commensurate and can be solved by molecular replacement or twinned 
plates (if the crystals look like plates).

Would love to see more of the images though at different distances and 
delta phi. 

**
Gloria Borgstahl 
Eppley Institute for Cancer Research and Allied Diseases
987696 Nebraska Medical Center 
10732A Lied Transplant Center 
Omaha, NE 68198-7696

http://sbl.unmc.edu
Office (402) 559-8578
FAX (402) 559-3739

Professor 
Hobbies:  Protein Crystallography, Cancer, Biochemistry, DNA Metabolism, 
Modulated Crystals,  Crystal Perfection, X-ray Topography,
Interests:  "City of Ember", skateboarding, RAGBRAI, basketball, and 
rollerskating
***



James Holton  
Sent by: CCP4 bulletin board 
01/28/2009 09:59 PM
Please respond to
James Holton 


To
CCP4BB@JISCMAIL.AC.UK
cc

Subject
Re: [ccp4bb] small lines in diffraction pattern






I'm sure Gloria would be delighted if that were the case, but I don't 
think this is an incommensurate lattice.  These actually don't so much 
give you diffuse scattering as little satellite spots near the main 
spots at spacings that don't make any sense given the lattice repeat. 
My understanding is that these arise from something that is slowly 
varying from unit cell to unit cell (could be as simple as a side chain 
waving back and forth) in a repetitive pattern that just doesn't line up 
in any way with the repeat of the unit cells. 

Still, I'll ask her.

However, I think that the difference is that modulated lattices are 
gradual changes of structure across many unit cells and what I was 
talking about is a more simplistic case of two different kinds of unit 
cells with varying degrees of randomness in their arrangement.  That is, 
using the formalism I described below, a modulated lattice would have 
unit cells that go: ABCDEFGHGFEDCBABCDEFG... etc. where A is not that 
different from B, B similar to C, etc., but A and H are very different.

-James Holton
MAD Scientist

Jürgen Bosch wrote:
> Hi James,
>
> what your descriptions aims at is I think shown in this publication
> Borgstahl, G. E. O. "Incommensurate Crystallography by Sander van 
> Smaalen" Crystallography reviews 14 , 259-260 (2008).
>
> Or am I misunderstanding something here ?
>
> Jürgen
>
>
> On 28 Jan 2009, at 12:39, James Holton wrote:
>
>> I recommend you have a look at a book from OUP called "Diffuse X-Ray
>> Scattering and Models of Disorder" by T. R. Welberry.  The first 
chapter
>> explains quite well (I think) where all these streaky things come from.
>> It will also make you feel better about having it when you see all the
>> small molecule structures that have horrible diffuse scattering! (such
>> as urea).
>>
>> This looks to me like a fairly classic case of correlated static
>> disorder.  Best way to think about it is this:
>>
>> Imagine you have two different kinds of unit cells: A an B.  Doesn't
>> really matter what the difference between A and B is, could be a
>> two-headed side chain in conformer A vs conformer B, or it could be as
>> complicated as a domain motion.  But, for simplicity, lets assume it is
>> two rotamers of a side chain and also assume that each unit cell in 
your
>> crystal can only be one or the other (no "in betweens").
>>
>> Now, if the arrangement of these unit cells is perfectly correlated and
>> an "A" always occurs right next door to a "B" along the c-axis (say),
>> then what you really have is a bigger unit cell than you think.  That
>> is, you can draw a unit cell around each A-B pair and call it a
>> "supercell" with the contents of B as a simple NCS mate of A (with one
>> side chain in a different rotamer).  Some people might call this a
>> "pseudotranslation".  The effect on the diffraction pattern in this 
case
>> would be the appearance of a very weak spot in between each "old" spot
>> along your "c" axis.  That is, your "supercell" is twice as big along
>> "c" so the reciprocal-space lattice has twice as many spots in it.  The
>> new spots are weak because they only correspond to the differences
>> between A and B, which in this case is only a few atoms.
>>
>> Now lets say A and B are not perfectly correlated, but only slightly.
>> That is, in some parts of the crystal A and B are side-by-side, but in
>> other parts you get AAB, ABBA, BABBA, etc.  In each of these cases the
>> "supercell" you must draw is 3, 4 and 5x your original unit cell.  Each
>> of these will produce new weak spots with progressively 

[ccp4bb] Beam time available @ the NIGMS beam line at the NSLS

[Stojanoff, Vivian]

Beam time available @ X6A 

http://protein.nsls.bnl.gov


The NIGMS beam line X6A at the National Synchrotron Light Source provides FAST 
access to beam time through out the year. To apply submit a short proposal to 
http://protein.nsls.bnl.gov   at any time. Proposals are continuously reviewed 
and beam time can be scheduled within a week.

For comments or further questions please contact the scientific staff at:
x6an...@bnl.gov
or call:
+1 (631) 344 8375


-

Vivian Stojanoff
National Synchrotron light Source
Brookhaven National Laboratory
Bldg 725D
Upton, NY 11973 USA
Email: stoja...@bnl.gov; stoja...@yahoo.com
phone: +1 631 344 8375
fax:  +1 631 344 3238

[ccp4bb] error message on installation of ccp4i on linux red hat enterprise 5.0

[Eric Liu]

Hi All,

I just downloaded and installed ccp4 in my home directory. The installation
went quite smoothly. For individual ccp4 programs, it seems working ok.
however, when I type ccp4i, it gave a bunch error message. here are the
error message:
Top level CCP4 directory is /home/X/programs/ccp4-6.1.0
Using CCP4 programs from /home/X/programs/ccp4-6.1.0/bin
Error in startup script: unknown color name "black"
(processing "-background" option)
invoked from within
"toplevel .bubblehelp  -borderwidth 1  -background black"
(procedure "InitialiseBubbleHelp" line 8)
invoked from within
"InitialiseBubbleHelp"
(file "/home/X/programs/ccp4-6.1.0/ccp4i/src/taskbrowser.tcl" line
104)
invoked from within
"source [file join $env(CCP4I_TOP) src $system(RUN_MODE).tcl]"
("default" arm line 8)
invoked from within
"switch  $system(RUN_MODE) \
  script {
# Run a script ($CCP4I/scripts/project.script) with parameters from def file

source [file join $env(CCP4I_..."
(file "/home/Jiliu01/programs/ccp4-6.1.0/ccp4i/bin/ccp4i.tcl" line 163)
invoked from within
"source [file join $env(CCP4I_TOP) bin ccp4i.tcl]"
(file "/home/Jiliu01/programs/ccp4-6.1.0/ccp4i/bin/ccp4i" line 5)


I checked the version of my Tcl/Tk/BLT, they are 8.4/8.4/2.4. I sourced the
files required.

Can anybody give me hint why the ccp4i doesn't run?

Thanks,

Eric

Re: [ccp4bb] UV-transmissible plate seals 96-well format

[V. Nagarajan]

ClearSeal film from Hampton works with our UVEX UV microscope, despite some
attenuation of UV light.
For hanging drops, Greiner BioOne's films are the best.

V. Nagarajan
JAN Scientific, Inc.
http://janscientific.com

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Christoph Parthier
Sent: Monday, February 02, 2009 2:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] UV-transmissible plate seals 96-well format

Hi,

Can anyone recommend any UV-transmissible (280 nm), adhesive seals
(pre-cut) for 96-well crystallization plates (Greiner, MRC)?

We would like to use them on an crystal imaging system with UV option
(RIGAKU). I've checked seals from Zymark/Calliper Lifescience with a
regular photometer and they're not UV-transmissible. The Crystal Clear
tape from Hampton Research is actually UV-transmissible but it's less
convenient to apply from the roll onto the plates and it has to be cut
afterwards to make sure the plates fit in the plate hotel.

Anyone experience with this?

Thanks very much in advance,
Christoph

[ccp4bb] BEAMTIME AT SLS X06DA

[Meitian Wang]

=
SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY
AT THE SUPERBENDING MAGNET BEAMLINE  X06DA AT SLS
=
Deadline:  Sunday, February 15, 2009

Periods:
May 1, 2009 - August 31, 2009 ( Normal / Test proposals)
May 1, 2009 - April 30, 2011 ( Long-term proposals)
Beamline features:
- Fully tunable from 6.0 to 17.5 keV (2.07 - 0.71 Å)
- 4x10¹¹ photons/sec at sample position
- 90x70 microns focused beam
- MAR225 CCD detector
- Mini-hutch design for fast manual mounting
- Automatic sample changer (IRELEC CATS) with SPINE pucks, vials, and  
caps.

- http://sls.web.psi.ch/view.php/beamlines/px3/index.html
Proposal submission:
http://sls.web.psi.ch/view.php/users/experiments/proposals/opencalls/PX/index.html

Travel support:
http://sls.web.psi.ch/view.php/users/experiments/eusupport/index.html
Best regards,
meitian

__
Meitian Wang
Swiss Light Source at Paul Scherrer Institut
CH-5232 Villigen PSI - http://sls.web.psi.ch
Phone: +41 56 310 4175
Fax: +41 56 310 5292

Re: [ccp4bb] scaling a SAD data set

[Ethan A Merritt]

On Monday 02 February 2009, Vesna Serrano wrote:
> Dear all,
> I have a problem with a SAD data set. My crystal is very sensitive to
> radiation damage, so I have collected 2 110 frame data sets, 180 deg
> apart. I have processed the data with HKL2000 and it turns out that the 2
> sets have very different scales. My question is whether it would be
> possible to normalize the scales for these two data sets, so that I can
> use anomalous information in order to localize the anomalous scatterer in
> my structure.

You would do better to go back to the unscaled data, and feed the
unmerged intensities from both datasets into the SAD phasing program.
Let it do the scaling jointly.

Better yet would have been to collect the data in smaller wedges using
"inverse beam mode".

-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] dry shipper & FedEx

[Edward Snell]

If it is dry (charged with LN2 but empty of free liquid) you can ship it as 
non-Dangerous goods. The key words for FedEx (or any air shipping agent) are

"Non-Restricted"

Non-hazardous, non-toxic, and non-flammable are assumed as you are shipping it 
non-hazardous. It is useful to have on the shipper just in case. Charge it 
several times then before shipping empty the nitrogen out, i.e. follow the 
instructions from the manufacturer. 

A tip from our friendly FedEx office. Write "contains samples" on the lid of 
the Dewar (inside the outer shipping box). FedEx see crystals infrequently but 
ship many of these Dewars containing medical and agricultural specimens. They 
are less likely to open the Dewar and take a peak.

If it ships wet you do have to declare it as Dangerous Goods. If you do not, 
and liquid is found in it, there are steep fines and other unpleasant things. 
In the US it is possible to ship it wet by air but you need to be registered 
with FedEx which involves attending a training course and having a 24 hour 
telephone contact available.  You can also ship wet by ground. This also 
involves registration and an online training course. I'm not sure what the 
rules are for other countries.

Take these with a pinch of salt. I looked into this a couple of years ago and 
did the online course. If you talk to FedEx again, mention Dry Shipper and 
Non-Restricted. They should fairly quickly know what you are talking about. 
I've found them very helpful.

Cheers,

Eddie


Edward Snell Ph.D.
Assistant Prof. Department of Structural Biology, SUNY Buffalo,
Hauptman-Woodward Medical Research Institute
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Email: esn...@hwi.buffalo.edu  Telepathy: 42.2 GHz

Heisenberg was probably here!

From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of 
Aleksander Roszak
Sent: Monday, February 02, 2009 11:01 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fwd: [ccp4bb] dry shipper & FedEx



Hi Uli,

When we send our dry shipper from UK to ESRF, Grenoble, via FedEx we place a 
following note on the box:
DRY SHIPPER, Non-hazardous, non-toxic, non-flammable, non-restricted. Conforms 
with the IATA regulations Special Provision A800

We write the same in the Contents place of the International Air Waybill, we do 
not have to fill any special declaration for dangerous goods.
And this works fine for us.

I hope it will work for you too.
Cheers,
Aleks




On 2 Feb 2009, at 15:32, gohlke, ulrich wrote:
Dear colleagues,
 
 I am having the pleasure to organise a shipment of frozen crystals from 
Germany to the UK, and the only way to do this seems to send them by FedEx in a 
dry shipper (Taylor & Wharton CP100). My question is, has anybody (perhaps from 
Germany?) done this before and give me some advice? According to the people at 
FedEx, I need somebody who is trained and authorized to fill in and sign a 
"Shipper's Declaration for Dangerous Goods". This concerns mainly the transport 
of nitrogen (the crystals are harmless). Does anybody know, for instance, what 
the UN-No. for nitrogen in a dry shipper is? Is it the same for liquid N2 (UN 
1977) and the adsorbed  (vapour phase) form?
 
Thanks in advance and best regards,
 
 Uli
 
---
DR ULRICH GOHLKE
Staff Scientist - Macromolecular Structure and Interaction
Max-Delbrück-Centre for Molecular Medicine (MDC)

+49 30 9406 - 2725 (w)
+49 30 9406 - 2548 (fax)
ulrich.goh...@mdc-berlin.de
 
http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/
 


--
Aleksander W. Roszak, PhD   E-mail:     
al...@chem.gla.ac.uk
Protein Crystallography Web:
www.chem.gla.ac.uk/~aleks
University of Glasgow   Fax:    
+44-(0)141-330 3779
Level 2 Room B 219  Tel (X-ray 
lab):    +44-(0)141-330 3589
Glasgow Biomedical Research Centre  Mobile: 
+44-(0)780 9559996
120 University Place
Glasgow G12 8TA 
Scotland

[ccp4bb] Fwd: [ccp4bb] dry shipper & FedEx

[Aleksander Roszak]

Hi Uli,

When we send our dry shipper from UK to ESRF, Grenoble, via FedEx we  
place a following note on the box:
DRY SHIPPER, Non-hazardous, non-toxic, non-flammable, non- 
restricted. Conforms with the IATA regulations Special Provision A800


We write the same in the Contents place of the International Air  
Waybill, we do not have to fill any special declaration for  
dangerous goods.

And this works fine for us.

I hope it will work for you too.
Cheers,
Aleks




On 2 Feb 2009, at 15:32, gohlke, ulrich wrote:

Dear colleagues,

 I am having the pleasure to organise a shipment of frozen crystals  
from Germany to the UK, and the only way to do this seems to send  
them by FedEx in a dry shipper (Taylor & Wharton CP100). My  
question is, has anybody (perhaps from Germany?) done this before  
and give me some advice? According to the people at FedEx, I need  
somebody who is trained and authorized to fill in and sign a  
“Shipper’s Declaration for Dangerous Goods”. This concerns mainly  
the transport of nitrogen (the crystals are harmless). Does anybody  
know, for instance, what the UN-No. for nitrogen in a dry shipper  
is? Is it the same for liquid N2 (UN 1977) and the adsorbed   
(vapour phase) form?


Thanks in advance and best regards,

 Uli

---
DR ULRICH GOHLKE
Staff Scientist - Macromolecular Structure and Interaction
Max-Delbrück-Centre for Molecular Medicine (MDC)

+49 30 9406 - 2725 (w)
+49 30 9406 - 2548 (fax)
ulrich.goh...@mdc-berlin.de

http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/




--
Aleksander W. Roszak, PhD   E-mail: 
al...@chem.gla.ac.uk
Protein Crystallography Web:
www.chem.gla.ac.uk/~aleks
University of Glasgow   Fax:
+44-(0)141-330 3779
Level 2 Room B 219  Tel (X-ray 
lab):+44-(0)141-330 3589
Glasgow Biomedical Research Centre  Mobile: 
+44-(0)780 9559996
120 University Place
Glasgow G12 8TA 
Scotland

[ccp4bb] scaling a SAD data set

[Vesna Serrano]

Dear all,
I have a problem with a SAD data set. My crystal is very sensitive to
radiation damage, so I have collected 2 110 frame data sets, 180 deg
apart. I have processed the data with HKL2000 and it turns out that the 2
sets have very different scales. My question is whether it would be
possible to normalize the scales for these two data sets, so that I can
use anomalous information in order to localize the anomalous scatterer in
my structure.
Thanks for  the help,


Vesna

Vesna Serrano
Dept. of Chemistry
NC State University
Raleigh, NC 27695

[ccp4bb] dry shipper & FedEx

[gohlke, ulrich]

Dear colleagues,

 

 I am having the pleasure to organise a shipment of frozen crystals from 
Germany to the UK, and the only way to do this seems to send them by FedEx in a 
dry shipper (Taylor & Wharton CP100). My question is, has anybody (perhaps from 
Germany?) done this before and give me some advice? According to the people at 
FedEx, I need somebody who is trained and authorized to fill in and sign a 
"Shipper's Declaration for Dangerous Goods". This concerns mainly the transport 
of nitrogen (the crystals are harmless). Does anybody know, for instance, what 
the UN-No. for nitrogen in a dry shipper is? Is it the same for liquid N2 (UN 
1977) and the adsorbed  (vapour phase) form?

 

Thanks in advance and best regards,

 

 Uli 

 

---

DR ULRICH GOHLKE

Staff Scientist - Macromolecular Structure and Interaction

Max-Delbrück-Centre for Molecular Medicine (MDC)


+49 30 9406 - 2725 (w)

+49 30 9406 - 2548 (fax)

ulrich.goh...@mdc-berlin.de

 

http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/

 

[ccp4bb] Postdoctoral Position in Structural Biology

[Choel Kim]

We are seeking a talented and motivated individual to join  the  
Department of Pharmacology at Baylor School of Medicine (Vacancy  
number at BCM job site:175287AC). We study-function relationship of  
proteins in NO/cGMP signaling pathway. We use a highly  
interdisciplinary approach including x-ray crystallography, NMR, SAXS,  
yeast genetics and biochemistry. The laboratory is well equipped with  
state-of-the-art instruments for high-throughput crystallography.  
These include a Mosquito, liquid handling robot complete with an  
automated imaging system and Rigaku MicroMax 007 generator with have  
high flux mirrors and R-AXIS detector.  The successful candidates must  
have PhD degree in structural biology and experience in protein  
chemistry and macromolecular crystallography. Applicants should apply  
at BCM job site https://www.medschooljobs.org using Vacancy number,  
175287AC. Alternatively send curriculum vitae, a brief statement of  
research accomplishments and interests, and names of three references  
to: andr...@bcm.tmc.edu. The position is available immediately and  
review of applications begins in the middle of February, 2009 and will  
continue until the position is filled.
Located in the heart of the Texas Medical Center in Houston, Baylor  
School of Medicine is ranked 13th overall among the nations top  
medical schools for research and 7th for primary care by U.S.News &  
World Report. BCM also is listed No. 2 in the nation in federal  
funding for research and development in the biological sciences at  
universities and colleges by the National Science Foundation.


Choel Kim Ph.D.
Assistant Professor
Department of Pharmacology
Baylor College of Medicine
(713)798-8411
c...@bcm.tmc.edu
www.bcm.edu/pharmacology/?pmid=9685

Re: [ccp4bb] difficult MAD dataset

[Eleanor Dodson]

With a pseudo translation vector like that the SG could be any of the 8 
orthorhombic SGs; P222 P21 22 P21212 P212121 P2 21 2 P2 21 21 P 2 2 21


Test them all, and see if any give a dect solution..
Eleanor

Alison Li wrote:
We recently collected a complete 2.5A MAD dataset. However, finding a 
solution has not been as straightfoward for reasons unclear to us. We would 
be grateful for any helpful advice or suggestions.


The thin plate shaped crystal was grown from a relatively small protein (90 
residues).


The crystal diffracted well with visible and defined reflections up to ~2.8A 
range.


With both HKL2000 and mosflm, initial indexing indicated orthorhombic unit cell 
with dimension of 52 x 82 x 100.


Systematic absences along a and b axis were observed thus the dataset was 
scaled in P21212 space group.


The unit cell dimension and space group suggested 4 protein chains per ASU.

There is a pseudo-translation with 55 % peak at a fractional coordinate of 
0.5, 0.5, 0.48.


There are 7 methionines per chain. Thus we expect 28 Se per ASU. Mass 
spectroscopy and fluoresence scan both confirmed successful incorporation of 
Se-methionine in the crystal.


According to xtriage, anomalous signal extended to 3.0A at least in the peak 
dataset (The table of measurability as a function of resolution is shown 
below). 


unused: - 43.0868 [   0/5   ]
bin  1: 43.0868 -  5.3953 [2751/2902]  0.5838
bin  2:  5.3953 -  4.2836 [2893/2905]  0.4575
bin  3:  4.2836 -  3.7425 [2891/2899]  0.2820
bin  4:  3.7425 -  3.4005 [2888/2896]  0.1898
bin  5:  3.4005 -  3.1568 [2864/2898]  0.1222
bin  6:  3.1568 -  2.9708 [2835/2898]  0.0653
bin  7:  2.9708 -  2.8220 [2777/2906]  0.0458
bin  8:  2.8220 -  2.6992 [2714/2902]  0.0226
bin  9:  2.6992 -  2.5953 [2550/2865]  0.0168
bin 10:  2.5953 -  2.5057 [2307/2914]  0.0071
unused:  2.5057 - [   0/0   ]

However, HA search using hkl2map, Autosol, and Autosharp resulted in only 
3~4 HA sites. When hkl2map was used, most HA sites had poor CC and 
Patterson FOM and did not clearly stand out as they normally should.



Structural homologs suggest that the protein has a compact single core 
domain comprised of 4 a-helices. The positions of most HAs are unlikely to be 
located in the flexible region.
If any abnormalies are seen with the dataset, it's during scaling step in 
HKL2000.
Chi2 is unusually high at lower resolution (Chi2 is >3 from 3.5A as shown 
below) and there is a relatively high percentage of rejections (>1.5 %).


Shell Lower Upper Average  Average Norm. Linear Square
 limitAngstrom   I   error   stat. Chi**2  R-fac  R-fac
 50.00   5.38  4299.077.349.0  7.886  0.076  0.085
  5.38   4.27   2938.752.735.0  5.843  0.083  0.090
  4.27   3.73   2314.245.933.5  3.935  0.082  0.084
  3.73   3.39   1245.334.428.9  2.838  0.101  0.094
  3.39   3.15 658.628.125.9  1.957  0.132  0.127
  3.15   2.96 451.927.125.7  1.322  0.157  0.138
  2.96   2.82 307.227.126.3  1.001  0.201  0.169
  2.82   2.69 253.128.828.1  0.866  0.225  0.193
  2.69   2.59 199.331.531.0  0.801  0.262  0.233
  2.59   2.50 159.534.734.4  0.688  0.292  0.261
 All reflections  1312.939.031.9  2.748  0.100  0.089

Xtriage also complains that there are abnormal intensities at some resolution 
ranges.


Finally, the crystallization requires CdSO4, so we suspect that cadmium ions 
are incorporated in the crystal. If so, we suspect there may be weak 
anomalous signal contribution from Cd as well. 

In summary, we appear to have a complete dataset that shows strong 
anomalous signal. However it appears that we have overlooked something or 
there is an unusual crystallographic issue that we are not aware of.  Any 
suggestions will be very much appreciated.


Alison Li
Graudate student, Dr. Mark Paetzel's group
Simon Fraser University, BC, Canada



  

Re: [ccp4bb] Fobs - Fobs

[Eleanor Dodson]

Rana Refaey wrote:

Hi,

I was wondering if anyone knows what programme I need to use to subtract the 
Fobs of two different crystals from each other.

Regards,
Rana

_
Invite your mail contacts to join your friends list with Windows Live Spaces. 
It's easy!
http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us
  
Presumably the two data sets are in the same spacegroup with the same 
cell dimensons more or less?


You must cad the two data sets together with suitable olumn labels and 
add FC PHIC FOM from some suitable set of coordinates.



Scale them to the FC or to each other  - I use program SCALEIT to do this

Then use the FFT utility to do a differenc map Fobs1 -Fobs2 PHIC FOM

Eleanor

[ccp4bb] Barely one week remains to apply for RapiData, the BNL Course on Synchrotron Data Collection and Structure Solving.

[Robert Sweet]

The application deadline is 8AM EST Monday 9 February for RapiData 2009, 
the eleventh offering of our popular course:


Rapid Data Collection and Structure Solving at the NSLS: A Practical 
Course in Macromolecular X-Ray Diffraction Measurement


The course will be held 19-24 April 2009. Students could be at any level 
from advanced undergraduate to full professor. 48 students will be 
accepted; 24 will bring their own specimens for data collection. Please 
read the course description at http://www.px.nsls.bnl.gov/RapiData2009/. 
You'll see that many experts in the field will be available for lectures 
and tutorials, and you'll find the application materials at this site.


For the seventh time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 19 April. The body of the
RapiData course really requires that students have a healthy knowledge of
crystallography. For potential students who have some experience but are shaky
about fundamentals, this course will help. There will be a small additional fee
for the fundamentals course, to pay for Saturday night accomodations and food
on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and subsistence
costs for Latin-American students and junior faculty. Please apply for the
course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in
applying for a scholarship. In accordance with the standards of the
International Union of Crystallography, we observe the basic policy of
non-discrimination, affirming the right and freedom of scientists to associate
in international scientific activity without regard to such factors as
citizenship, religion, creed, political stance, ethnic origin, race, colour,
language, age, or gender, in accordance with the Statutes of the International
Council for Science. At this course no barriers will exist beyond the
application procedure that would prevent the participation of bona fide
scientists.

Please apply or send your students to our course,

Alex Soares, Sal Sclafani, and Bob Sweet

=
Robert M. Sweet E-Dress:  sw...@bnl.gov
Group Leader, PXRR: Macromolecular^ (that's L
Crystallography Research Resource at NSLS  not 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)
=

Re: [ccp4bb] brute force molecular replacement

[Anastassis Perrakis]

On Feb 2, 2009, at 11:39, Clemens Vonrhein wrote:


Hi Tassos,

On Mon, Feb 02, 2009 at 11:13:28AM +0100, Anastassis Perrakis wrote:

To be more detailed I would:

0. Put the mol rep solution in ARP/wARP and let it run (in the  
meantime

proceed to 1-3 if 0. fails ...)

^^^

You didn't tell us what point 1 is:

2. Do some  density modification using the model phases (if you are  
in ccp4

simplest is to use DM)
3. Use the DM phases and pretend this is an 'experimental' solution  
in

ARP/wARP


... are you hiding some secret, magic procedure from us?


Indeed. Point 1. was the NCS averaging for the dimeric coiled coil.
Then I realized it might not be a great idea for the coiled coil,  
deleted it, and did not renumber.


Oh well - its Monday morning. And I have still not recovered from my  
enthusiasm on the latest

magic of autoSHARP ;-)


A.






Cheers

Clemens

--

***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park
*  Cambridge CB3 0AX, UK
*--
* BUSTER Development Group  (http://www.globalphasing.com)
***


P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

Re: [ccp4bb] brute force molecular replacement

[Clemens Vonrhein]

Hi Tassos,

On Mon, Feb 02, 2009 at 11:13:28AM +0100, Anastassis Perrakis wrote:
> To be more detailed I would:
>
> 0. Put the mol rep solution in ARP/wARP and let it run (in the meantime 
> proceed to 1-3 if 0. fails ...)
 ^^^

You didn't tell us what point 1 is:

> 2. Do some  density modification using the model phases (if you are in ccp4 
> simplest is to use DM)
> 3. Use the DM phases and pretend this is an 'experimental' solution in 
> ARP/wARP

... are you hiding some secret, magic procedure from us?

Cheers

Clemens

-- 

***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--
* BUSTER Development Group  (http://www.globalphasing.com)
***

[ccp4bb] UV-transmissible plate seals 96-well format

[Christoph Parthier]

Hi,

Can anyone recommend any UV-transmissible (280 nm), adhesive seals
(pre-cut) for 96-well crystallization plates (Greiner, MRC)?

We would like to use them on an crystal imaging system with UV option
(RIGAKU). I've checked seals from Zymark/Calliper Lifescience with a
regular photometer and they're not UV-transmissible. The Crystal Clear
tape from Hampton Research is actually UV-transmissible but it's less
convenient to apply from the roll onto the plates and it has to be cut
afterwards to make sure the plates fit in the plate hotel.

Anyone experience with this?

Thanks very much in advance,
Christoph

Re: [ccp4bb] brute force molecular replacement

[Anastassis Perrakis]

Hi -

With good 2.0 A data (as you seem to have) and a correct solution,
I would be rather surprised if ARP/wARP - REFMAC5 would not refine and  
build a model without major trouble.

Did you try that at all ?

To be more detailed I would:

0. Put the mol rep solution in ARP/wARP and let it run (in the  
meantime proceed to 1-3 if 0. fails ...)
2. Do some  density modification using the model phases (if you are in  
ccp4 simplest is to use DM)
3. Use the DM phases and pretend this is an 'experimental' solution in  
ARP/wARP


More info and ideas are in:

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18094467

Note that both ARP/wARP runs above can be done in the web server  
without the need of local installation if you prefer.


http://cluster.embl-hamburg.de/ARPwARP/remote-http.html

Apologies for the shameless plug-ins but I really think its the  
easiest thing to do, even if it might now work.


Tassos

On Feb 2, 2009, at 10:10, Nicholas M Glykos wrote:



Hi Xie,


Many thanks to all who responded to my earlier query (Drs. Paul
Swepston, Randy Read and Nicholas Glykos). I am trying to determine  
the
structure of a very long coiled coil dimer (roughly 150 residues  
long)

by molecular replacement. I don't know if it forms a canonical coiled
coil from end to end (it probably doesn't).  I seem to get the right
solution using different lengths of polyala (and polygly and modeled
ones with side-chains) coiled coils as my search models (maps show  
some

density for unmodeled parts of the coiled coil structure).


If your current best phase-set gives you back correct information  
that was
not part of your model, you are doing fine. You are getting there  
(but it

may take a while).

Starting from your current best polyAla model, you can give it a try  
with
very many runs of torsion angle simulated annealing (starting from a  
high
temperature), or with rigid-body simulated annealing (both from  
within CNS
or XPLOR). Don't do positional refinement. With an almost perfect  
polyAla

model you should expect R-free and R in the low 40s (%) range for ~2A
data.



However, building a model accounting for the entire sequence, getting
the correct chain direction and placing residue side-chains have  
proved
difficult. And my R-facs have never improved beyond the low 50s  
during

different  refinement attempts. At the moment, I have 3 more or less
contiguous 30 residue stretches of coiled coil found by 3 independent
molecular replacement attempts using epmr (This was done to account  
for
possible bends, stutters in the dimer). I am trying to get the rest  
of

the model by new rounds of molecular replacement using epmr. I have
carried out exhaustive runs using epmr. But I haven't found the  
rest of

the model. What are the options available to me with molecular
replacement? I have tried molrep, phaser and amore from the ccp4  
suite.
My diffraction data is quite good (data between 25 and 2 A with an  
Rsym

of 8%).


I'm not sure whether what you really need is more molecular  
replacement.

Maybe you should invest more time with the maps (combined with 'safe'
simulated-annealing-based optimisation methods). What I've just said  
only

applies if these 90 residues you have can indeed produce correct
information that was not part of the initial model (as you said).



Can I run Qs when a partial structure is available?


No. Sorry.


Nicholas


--


Dr Nicholas M. Glykos, Department of Molecular
Biology and Genetics, Democritus University of Thrace,
  University Campus, 68100 Alexandroupolis, Greece, Fax +302551030613
 Tel ++302551030620 (77620),  http://www.mbg.duth.gr/~glykos/



P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

Re: [ccp4bb] brute force molecular replacement

[Nicholas M Glykos]

Hi Xie,

> Many thanks to all who responded to my earlier query (Drs. Paul 
> Swepston, Randy Read and Nicholas Glykos). I am trying to determine the 
> structure of a very long coiled coil dimer (roughly 150 residues long) 
> by molecular replacement. I don't know if it forms a canonical coiled 
> coil from end to end (it probably doesn't).  I seem to get the right 
> solution using different lengths of polyala (and polygly and modeled 
> ones with side-chains) coiled coils as my search models (maps show some 
> density for unmodeled parts of the coiled coil structure). 

If your current best phase-set gives you back correct information that was 
not part of your model, you are doing fine. You are getting there (but it 
may take a while).

Starting from your current best polyAla model, you can give it a try with 
very many runs of torsion angle simulated annealing (starting from a high 
temperature), or with rigid-body simulated annealing (both from within CNS 
or XPLOR). Don't do positional refinement. With an almost perfect polyAla 
model you should expect R-free and R in the low 40s (%) range for ~2A 
data.


> However, building a model accounting for the entire sequence, getting 
> the correct chain direction and placing residue side-chains have proved 
> difficult. And my R-facs have never improved beyond the low 50s during 
> different  refinement attempts. At the moment, I have 3 more or less 
> contiguous 30 residue stretches of coiled coil found by 3 independent 
> molecular replacement attempts using epmr (This was done to account for 
> possible bends, stutters in the dimer). I am trying to get the rest of 
> the model by new rounds of molecular replacement using epmr. I have 
> carried out exhaustive runs using epmr. But I haven't found the rest of 
> the model. What are the options available to me with molecular 
> replacement? I have tried molrep, phaser and amore from the ccp4 suite. 
> My diffraction data is quite good (data between 25 and 2 A with an Rsym 
> of 8%).

I'm not sure whether what you really need is more molecular replacement. 
Maybe you should invest more time with the maps (combined with 'safe' 
simulated-annealing-based optimisation methods). What I've just said only 
applies if these 90 residues you have can indeed produce correct 
information that was not part of the initial model (as you said).


> Can I run Qs when a partial structure is available?

No. Sorry.


Nicholas


-- 


 Dr Nicholas M. Glykos, Department of Molecular 
 Biology and Genetics, Democritus University of Thrace,
   University Campus, 68100 Alexandroupolis, Greece, Fax +302551030613
  Tel ++302551030620 (77620),  http://www.mbg.duth.gr/~glykos/