Re: [ccp4bb] Refining against images instead of only reflections

[James Holton]

At the risk of creating another runaway thread, I have spent some time 
trying to reconcile what Ian was talking about and what I was talking 
about.  The discussion actually is still relevant to the original posted 
question about refining against images, so I am continuing it here.


Ian made a good criticism of one of my statements, which I should take 
back: diffuse scatter does contain information about the disorder in the 
structure, and this can be measured under favorable conditions.  The 
point I was trying to make, however, is that one is still at the mercy 
of the lattice transform when looking at diffuse scatter, and the total 
scattering is the product of the molecular transform and the lattice 
transform.  There is generally no a-priori way to deconvolute the two!  
And this will make refinement against images difficult.


However, Colin makes a good point that the differences are largely 
semantic.  Unlike crystallographers, crystals, atoms, electrons and 
photons don't really care what names we call them.  They just do 
whatever it is they do, and the photons make little pops when they hit 
the detector.  That's all we really know.


So, in an effort to clear things up (both in my head and on this 
thread), I have assembled some simulated diffraction patterns from my 
nearBragg program here:

http://bl831.als.lbl.gov/~jamesh/diffuse_scatter/

I have included some limited discussion about how the images were made, 
but the point here is that all these images are generated by simply 
computing the general scattering equation for a constellation of atoms.  
I found in an instructive exercise and perhaps other interested parties 
will as well.


-James Holton
MAD Scientist


Colin Nave wrote:

 Nice overview from Ian - though I think James did make some good points
too.

I thought it might be helpful to categorise the various contributions to
an imperfect diffraction pattern. Categorising things seems to be one of
the English (as distinct from Scottish, Irish or Welsh!) diseases. 


1. Those that contribute to the structure of a Bragg reflection
i) Mosaic structure - limited size and mosaic spread
ii) Dislocations, shift and stacking disorders
iii) More macroscopic defects giving "split" spots
iv) Unit cell variations (e.g. due to strain on cooling)
v) Twinning (?)

2. Diffuse scatter
i) Uncorrelated disorder - broad diffuse scatter distributed over image
ii) Disorder correlated between cells - sharper diffuse scatter centred
on Bragg peaks 
iii) Related to above inelastic scattering - Brillouin scattering,

acoustic scattering, scattering from phonons
iv) Compton scattering (essentially elastic but incoherent)
v) Fluorescence
vi) Disordered material between crystalline "blocks" but within whole
crystal
vii) Scatter from mother liquor
viii) Scatter from sample mount

3. Instrument effects
i) Air scatter
ii)Scatter from apertures, poorly mounted beamstop
iii) Smearing of spot shapes due to badly matched incident beams, poor
detector resolution, too large a rotation range, 
iv) Detector noise



The trouble with categorisation is that one can (Oh no) 
i) Have multiple categories for the same thing

ii) Miss out something important
iii) Give impression that categories are distinct when they might merge
in to each other. Categorising seagulls (or any species) is an example,
perhaps categorising protein folds is too. Not sure about categorising
in to English, Scottish etc.

All of these flaws will be in the categories above. Despite this, I
believe it would help structure determination to have an accurate as
possible model of the crystal. This should be coupled with the ability
to determine the parameters of the model from the best possible
recording instrument. Such a set up would enable better estimates of the
intensity of weak Bragg spots in the presence of a high "background".
There may be an additional gain by exploiting information from the
diffuse scatter of the protein.

At present, the normal procedure is to treat the background components
as the same, have some parameter called "mosaicity" and use learned
profiles derived from nearby stronger spots (ignoring the fact that the
intrinsic profiles of a hkl and a 6h 6k 6l reflection will be closely
related). The normal procedure is obviously very good but we don't know
what we are missing!

Any corrections additions to the categories plus other comments welcome

Regards
   Colin


  

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On 
Behalf Of Ian Tickle

Sent: 22 January 2010 10:54
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refining against images instead of only 
reflections



 > -Original Message-


From: owner-ccp...@jiscmail.ac.uk
[mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton
Sent: 21 January 2010 08:39
To: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Refining against images instead of only 
reflections


It is interesting and relevant here I think that if you measure

[ccp4bb] Announcing a new web forum for structural biology: BioKlatch.com

[Matt Harrington]

Dear all,


Brief Summary:

BioKlatch (http://www.BioKlatch.com) is a new web forum meant to
supplement mailing lists.  It uses software that's popular with
mathematicians and software developers on http://mathoverflow.com and
http://stackoverflow.com.  A post can be given multiple tags such as
"crystallography", "protein-purification", and "immunology".  It's
easy to see which questions have not been answered, and then users
can step up to answer them.  It's easy to search, and the system
automatically looks for similar questions before a new one is posted.

The word "klatch" comes from German, and in English means "an informal
gathering".  Typically it's used in the phrase "coffee klatch".  It's
the closest synonym to "forum" I could find which wasn't taken.  It's
nearly impossible finding a domain name in 2010.


Details:

BioKlatch isn't about replacing mailing lists.  Among other things,
it's meant to give a home to questions which don't fit within the
scope of existing lists.  For example, a lot of protein purification
questions are posted to ccp4bb.  Nobody seems to mind (I like seeing
them), but my hunch is that a lot of people don't ask questions
because they don't want to be off-topic.

BioKlatch also attempts to increase participation by the community.
 There certainly are a lot more crystallographers in the world than
those who participate on ccp4bb.  On BioKlatch, you can post questions
and give answers without even signing up for the site.  There are no
hoops to jump through to make a simple post.

It uses software popular in the mathematics, astronomy, and software
development communities.  It's been quite a success in those fields,
and I wish I had written the software myself.  I merely set it up.  It's
different from other forum software out there and is generally very
well liked.

Here are questions tagged "crystallography" that I pulled from a list
of unanswered questions on ccp4bb, with permission granted by the original
authors:

http://www.bioklatch.com/questions/tagged/crystallography

Key points:

** When you post a new question, it automatically searches for
previously asked questions.  This avoids duplicates.
** It's easy to see which questions haven't already been answered.
People may then step up to provide an answer.
** Questions can be given relevant tags.  You only have to pay
attention to tags which interest you, and tags can be followed by RSS
readers like Google Reader.
** Questions can be edited by power users for clarity.
** Good answers and good posts are awarded points by other users,
which seems to encourage quality.  At least where this software is
used elsewhere, certain users enjoy trying to accumulate as many
points as possible.  See http://mathoverflow.net/users.
** Greek letters are supported for equations.  Other non-English
letters are supported for that matter. See http://bit.ly/6bc4YF.
** Program output can be formatted and offset from the text
of your post.  See http://bit.ly/6RhRct.
** Email addresses are never made public.  Spammers cannot get your
email address from BioKlatch.

The Great Leap Forward is that BioKlatch uses OpenID to sign on.
You can post to the site without signing up, but an account gives you
capabilities such as creating new tags.  If you don't want to use an
existing OpenID account (Google, Yahoo, etc.), then you can easily
create one on http://www.myopenid.com.  Then use that account to sign
onto BioKlatch.  If you're not familiar with it, OpenID lets you use
one account to sign onto thousands of participating sites without
sharing your password with them.  The NIH uses OpenID in a pilot
program, so if you're a researcher in the US you may need one in the
future anyhow.  It takes a few brain cycles to see the light about
OpenID, but the benefits soon become apparent.

The software is not open source, so I can't make any changes to it.
It's also not free, so at some point when the beta period ends I'll
have to come up with a way to defray the cost, perhaps through a
sponsorship or ads.  I'm told that's what the other scientific
communities plan on doing.

Feel free to take a look and let me know of any comments.  Also
feel free to post something you've had on your mind, but for whatever
reason haven't sent to a mailing list.  Again, you don't even need
an account for that.  Nearly all of the posts up there were unanswered
on ccp4bb.  Some authors received responses via private email, but
said they wouldn't mind getting a few more answers.  So, any answers
given would likely be much appreciated.  If you see
a useful question or answer, give it an up vote.  Most of all, have
fun with it.


Regards,

Matt


P.S. The first few posts were made to just test the system out and
have been already discussed at length on ccp4bb (e.g. http://bit.ly/7yw2cy).

[ccp4bb] Only two weeks remain to apply for RapiData 2010. Seats are still open.

[Robert Sweet]

We are offering RapiData 2010, the twelfth 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 11-16 April 2010.  Students could be at any level from 
advanced undergraduate to full professor.  The course should accommodate 48 
students total. All students are encouraged to bring their own specimens for 
data collection, and to bring old data for the data-reduction and 
structure-solving tutorials.  Please read the Course Announcement at 
http://www.bnl.gov/RapiData/.  You'll see that many experts in the field will 
be available for lectures and tutorials. You'll find the application materials 
on the Course Application tab at this site.


For the eighth time we will hold a short lecture course on the fundamentals of 
crystallography for roughly five hours on Sunday 11 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,

Bob Sweet, Sal Sclafani, and Alex Soares

Course Announcement at http://www.bnl.gov/RapiData/

=
Robert M. Sweet E-Dress: sw...@bnl.gov
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)
=

Re: [ccp4bb] Purchase of Protein Samples

[Ho Leung Ng]

Hello Stephen,

 Of course it depends on what proteins you want. You can buy some
easily crystallizable proteins from Hampton Research. Some purified
proteins (proteases, lysozyme, calmodulin, etc) can be purchased from
Sigma. Or are you looking for custom expression and purification?


ho
ConfometRx


Date:Mon, 25 Jan 2010 18:49:14 +0800
From:"Dr. STEPHEN SIN-YIN, CHUI" 
Subject: Purchase of Protein Samples

Dear all CCP4 experts,

Hello, I'm not molecular biologist and quite new in this field. I would like to
know what companies (i.e. Sigma/Aldrich) are possibe for me to purchase
purified protein samples. Any suggestion is welcomed.

Many thanks in advance.

stephen

--
Dr. Stephen Sin-Yin Chui
Research Assistant Professor,
Department of Chemistry,
The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China.
Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)

[ccp4bb] Re Anions in Protein Structures

[Clayton, Gina Martyn]

 
Hi CCP4ers

As requested I have compiled the list of responses I got regarding anions in 
protein structures. I did not receive a huge number (wrong time of day 
perhaps..) but I do think that the list below covers the various aspects 
(specific examples as well as various studies) and was very useful and 
interesting (thanks!). 

In no particular order

1. Anion binding sites in protein structures.Chakrabarti P.
J Mol Biol. 1993 Nov 20;234(2):463-82.

2. On the routine use of soft X-rays in macromolecular crystallography. Part 
IV. Efficient determination of anomalous substructures in biomacromolecules 
using longer X-ray wavelengths.
Mueller-Dieckmann C, Panjikar S, Schmidt A, Mueller S, Kuper J, Geerlof A, 
Wilmanns M, Singh RK, Tucker PA, Weiss MS.
Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):366-80. Epub 2007 Feb 21.

3. Structural effects of monovalent anions on polymorphic lysozyme crystals.
Vaney MC, Broutin I, Retailleau P, Douangamath A, Lafont S, Hamiaux C, Prangé 
T, Ducruix A, Riès-Kautt M.
Acta Crystallogr D Biol Crystallogr. 2001 Jul;57(Pt 7):929-40. Epub 2001 Jun 21.

4. Data mining of metal ion environments present in protein structures.
Zheng H, Chruszcz M, Lasota P, Lebioda L, Minor W.
J Inorg Biochem. 2008 Sep;102(9):1765-76. Epub 2008 May 28.

5. Use of complementary cation and anion heavy-atom salt derivatives to solve 
the structure of cytochrome P450 46A1.
White MA, Mast N, Bjorkhem I, Johnson EF, Stout CD, Pikuleva IA.
Acta Crystallogr D Biol Crystallogr. 2008 May;64(Pt 5):487-95. Epub 2008 Apr 19.

6. Direct interaction between a human digestive protease and the mucoadhesive 
poly(acrylic acid).
Pallarès I, Fernández D, Comellas-Bigler M, Fernández-Recio J, Ventura S, 
Avilés FX, Bode W, Vendrell J.
Acta Crystallogr D Biol Crystallogr. 2008 Jul;D64(Pt 7):784-91. Epub 2008 Jun 
18.

7. The Oligomeric states of Haloarcula marismortui malate dehydrogenase are 
modulated by solvent components as shown by crystallographic and biochemical 
studies.
Irimia A, Ebel C, Madern D, Richard SB, Cosenza LW, Zaccaï G, Vellieux FM.
J Mol Biol. 2003 Feb 21;326(3):859-73.

8. Is the bond-valence method able to identify metal atoms in protein 
structures?
Müller P, Köpke S, Sheldrick GM.
Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):32-7. Epub 2002 Dec 19.


Best
Gina
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Re: [ccp4bb] Help with MR in P21

[George M. Sheldrick]

Dear Michele,

Your 'pseudo-translation' is too close to an origin, it cannot be
real. The problem is probably your model, it wasn't derived from
an NMR structure by any chance? It would seem to me that your
structure would be very suitable for ACHIMBOLDO.

Best wishes, 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


On Mon, 25 Jan 2010, Michele Lunelli wrote:

> Dear all,
> 
> I am trying to solve a structure at 2.05 A resolution by molecular 
> replacement. The space group
> seems to be P21, with unit cell dimension 52.63, 29.43, 104.970 and beta = 
> 95.60.
> Only one copy of the protein should be present in the asymmetric unit, with 
> 58% of solvent content.
> The search model used for MR is a truncated construct of the same protein, 
> comprising more that 60%
> of the residues. However, no convincing MR solution is found (I used phaser, 
> molrep, epmr and also
> mr.bump). No solutions refine to R and Rfree lower than 51-52%.
> 
> The CCP4 documentation about twinning states that "Monoclinic with na + nc ~ 
> a or na + nc ~ c can be
> twinned". This is not clear to me, but I have c = 2a, and therefore n = 2/3.
> Nevertheless all the tests run by ctruncate (and sfcheck) exclude twinning. 
> The observed cumulative
> distribution for |L| almost overlap the expected untwinned, and the observed 
> cumulative intensity
> distribution is not sigmoidal at all (actually it is growing faster that the 
> theoretical). Also the
> acentric and centric moments exclude twinning, for example the acentric:
>  =  0.858 (Expected value = 0.886, Perfect Twin = 0.94)
>  =  1.442 (Expected value = 1.329, Perfect Twin = 1.175)
>  =  2.438 (Expected value = 2, Perfect Twin = 1.5)
> 
> Both ctruncate and sfcheck found a pseudo-translation vector:
> ctruncate (0.050,  0.000,  0.957), ratio 0.23
> sfcheck (0.954, 0.000, 0.040), ratio 0.218
> However a second copy cannot be present in the asymmetric unit (there would 
> be 16% of solvent
> content). Since the protein is expected to form a coiled-coil, I think that 
> the detected
> pseudo-translation arises from the helices.
> Alternatively, it is possible that the space group is wrong? And if so, how 
> can I figure out the
> correct one?
> 
> 
> Thank you in advance,
> Michele
> 

[ccp4bb] Help with MR in P21

[Michele Lunelli]

Dear all,

I am trying to solve a structure at 2.05 A resolution by molecular replacement. 
The space group
seems to be P21, with unit cell dimension 52.63, 29.43, 104.970 and beta = 
95.60.
Only one copy of the protein should be present in the asymmetric unit, with 58% 
of solvent content.
The search model used for MR is a truncated construct of the same protein, 
comprising more that 60%
of the residues. However, no convincing MR solution is found (I used phaser, 
molrep, epmr and also
mr.bump). No solutions refine to R and Rfree lower than 51-52%.

The CCP4 documentation about twinning states that "Monoclinic with na + nc ~ a 
or na + nc ~ c can be
twinned". This is not clear to me, but I have c = 2a, and therefore n = 2/3.
Nevertheless all the tests run by ctruncate (and sfcheck) exclude twinning. The 
observed cumulative
distribution for |L| almost overlap the expected untwinned, and the observed 
cumulative intensity
distribution is not sigmoidal at all (actually it is growing faster that the 
theoretical). Also the
acentric and centric moments exclude twinning, for example the acentric:
 =  0.858 (Expected value = 0.886, Perfect Twin = 0.94)
 =  1.442 (Expected value = 1.329, Perfect Twin = 1.175)
 =  2.438 (Expected value = 2, Perfect Twin = 1.5)

Both ctruncate and sfcheck found a pseudo-translation vector:
ctruncate (0.050,  0.000,  0.957), ratio 0.23
sfcheck (0.954, 0.000, 0.040), ratio 0.218
However a second copy cannot be present in the asymmetric unit (there would be 
16% of solvent
content). Since the protein is expected to form a coiled-coil, I think that the 
detected
pseudo-translation arises from the helices.
Alternatively, it is possible that the space group is wrong? And if so, how can 
I figure out the
correct one?


Thank you in advance,
Michele

Re: [ccp4bb] Measuring membrane proteins with Nanodrop photometer

[hari jayaram]

Hello Florian,
We routinely measure membrane protein samples in detergent with much problem
on the nanodrop. The concentration of detergent is often many times the CMC
. We have found the drop does form quite well as long as the surface is
clean.
Often this can be easily achieved by repeated "buffing" of the surface with
a "kimwipe".
Also at moderate protein concentrations used with crystallography i.e the
6-25 mg/ml range with 5 to 20 mM detergent ( CMC around 0.7 mM) , the A280
measurement is seemless ..you put the drop there ( 3 to 5  µl ) and read the
A280. Only about one out of ten times , the drop collapses and fails to give
a good reading.  Then you just buff the surface , and repeat the reading.
So in summary , there is no problem. I would also read a ccp4bb discussion
on this topic which occurred on Dec 4th
2004
.
Hope this helps
Hari

On Mon, Jan 25, 2010 at 6:14 AM, Florian BrŸueckner <
f.brueck...@imperial.ac.uk> wrote:

> Dear all,
>
> can anyone share experience with measuring membrane protein
> concentration in detergent containing buffer with a nanodrop photometer
> e.g. Thermo Scientific ND2000. Specifically, does the reduction in
> surface tension caused by the detergent pose any problems?
>
> Thanks!
>
> Cheers
>
> Florian
>
> --
> ---
>
> Dr Florian Brueckner
> MPL Group (Prof So Iwata), Imperial College
> Diamond Light Source Ltd
> Diamond House, Harwell Science and Innovation Campus
> Didcot, Oxfordshire
> OX11 0DE
> England
>
> Phone (Office): +44-1235-77-8465
> Phone (Lab):+44-1235-77-8794
> Email: f.brueck...@imperial.ac.uk
>

Re: [ccp4bb] pdb-care & co?

[Randy Read]

Hi,

I was in touch with Thomas Luetteke recently about this, and he is hoping to 
move the server to his current location in Giessen, probably around February.  
He says that it would be difficult, at least at the moment, to install locally.

Regards,

Randy Read

On 25 Jan 2010, at 12:06, Tim Keys wrote:

> Hi Judit,
> 
> Thomas Lütteke developed pdb-care and several of the other glycosciences.de 
> tools. Although he has since moved on, I understand he still devotes time to 
> maintaining these services.
> 
> Last known address t.tuetteke AT chem.uu.nl
> 
> All the best,
> Tim
> 
> 
> 
> 
> -Original Message-
> From: CCP4 bulletin board on behalf of Debreczeni, Judit
> Sent: Mon 25.01.2010 12:39
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] pdb-care & co?
> 
> Dear all,
> 
> 
> 
> I am looking for the sugar-validation tool pdb-care --  the
> glycosciences.de website seems to be down, sadly.
> 
> 
> 
> Are pdb-care and the other rather valuable glycosciences tools available
> somewhere else? I'd prefer to run them locally -- are they available as
> stand-alone applications? If so, where to get them?
> 
> 
> 
> many thanks
> 
> JED.
> 
> 
> 
> 
> 
> 
> 
> 
> --
> AstraZeneca UK Limited is a company incorporated in England and Wales with 
> registered number: 03674842 and a registered office at 15 Stanhope Gate, 
> London W1K 1LN.
> Confidentiality Notice: This message is private and may contain confidential, 
> proprietary and legally privileged information. If you have received this 
> message in error, please notify us and remove it from your system and note 
> that you must not copy, distribute or take any action in reliance on it. Any 
> unauthorised use or disclosure of the contents of this message is not 
> permitted and may be unlawful.
> Disclaimer: Email messages may be subject to delays, interception, 
> non-delivery and unauthorised alterations. Therefore, information expressed 
> in this message is not given or endorsed by AstraZeneca UK Limited unless 
> otherwise notified by an authorised representative independent of this 
> message. No contractual relationship is created by this message by any person 
> unless specifically indicated by agreement in writing other than email.
> Monitoring: AstraZeneca UK Limited may monitor email traffic data and content 
> for the purposes of the prevention and detection of crime, ensuring the 
> security of our computer systems and checking Compliance with our Code of 
> Conduct and Policies.
> 
> 

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

Re: [ccp4bb] pdb-care & co?

[Tim Keys]

Hi Judit,

Thomas Lütteke developed pdb-care and several of the other glycosciences.de 
tools. Although he has since moved on, I understand he still devotes time to 
maintaining these services. 

Last known address t.tuetteke AT chem.uu.nl

All the best,
Tim




-Original Message-
From: CCP4 bulletin board on behalf of Debreczeni, Judit
Sent: Mon 25.01.2010 12:39
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] pdb-care & co?
 
Dear all,

 

I am looking for the sugar-validation tool pdb-care --  the
glycosciences.de website seems to be down, sadly.

 

Are pdb-care and the other rather valuable glycosciences tools available
somewhere else? I'd prefer to run them locally -- are they available as
stand-alone applications? If so, where to get them?

 

many thanks

JED.

 

 

 


--
AstraZeneca UK Limited is a company incorporated in England and Wales with 
registered number: 03674842 and a registered office at 15 Stanhope Gate, London 
W1K 1LN.
Confidentiality Notice: This message is private and may contain confidential, 
proprietary and legally privileged information. If you have received this 
message in error, please notify us and remove it from your system and note that 
you must not copy, distribute or take any action in reliance on it. Any 
unauthorised use or disclosure of the contents of this message is not permitted 
and may be unlawful.
Disclaimer: Email messages may be subject to delays, interception, non-delivery 
and unauthorised alterations. Therefore, information expressed in this message 
is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by 
an authorised representative independent of this message. No contractual 
relationship is created by this message by any person unless specifically 
indicated by agreement in writing other than email.
Monitoring: AstraZeneca UK Limited may monitor email traffic data and content 
for the purposes of the prevention and detection of crime, ensuring the 
security of our computer systems and checking Compliance with our Code of 
Conduct and Policies.

[ccp4bb] pdb-care & co?

[Debreczeni, Judit]

Dear all,

 

I am looking for the sugar-validation tool pdb-care --  the
glycosciences.de website seems to be down, sadly.

 

Are pdb-care and the other rather valuable glycosciences tools available
somewhere else? I'd prefer to run them locally -- are they available as
stand-alone applications? If so, where to get them?

 

many thanks

JED.

 

 

 


--
AstraZeneca UK Limited is a company incorporated in England and Wales with 
registered number: 03674842 and a registered office at 15 Stanhope Gate, London 
W1K 1LN.
Confidentiality Notice: This message is private and may contain confidential, 
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[ccp4bb] Measuring membrane proteins with Nanodrop photometer

[Florian BrŸueckner]

Dear all,

can anyone share experience with measuring membrane protein
concentration in detergent containing buffer with a nanodrop photometer
e.g. Thermo Scientific ND2000. Specifically, does the reduction in
surface tension caused by the detergent pose any problems?

Thanks!

Cheers

Florian

--
---

Dr Florian Brueckner
MPL Group (Prof So Iwata), Imperial College
Diamond Light Source Ltd
Diamond House, Harwell Science and Innovation Campus
Didcot, Oxfordshire
OX11 0DE
England

Phone (Office): +44-1235-77-8465
Phone (Lab):+44-1235-77-8794
Email: f.brueck...@imperial.ac.uk

[ccp4bb] Purchase of Protein Samples

[Dr. STEPHEN SIN-YIN, CHUI]

Dear all CCP4 experts,

Hello, I'm not molecular biologist and quite new in this field. I would like to
know what companies (i.e. Sigma/Aldrich) are possibe for me to purchase
purified protein samples. Any suggestion is welcomed.

Many thanks in advance.

stephen

-- 
Dr. Stephen Sin-Yin Chui
Research Assistant Professor,
Department of Chemistry,
The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China.
Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)