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CCP4BB  April 2011

CCP4BB April 2011

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Subject:

Re: viewing and scoring diffraction using the PX Scanner

From:

Jens Kaiser <[log in to unmask]>

Reply-To:

Jens Kaiser <[log in to unmask]>

Date:

Tue, 19 Apr 2011 02:41:08 -0700

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (745 lines)

OK,
  I took the challenge. I got 7 out of 10. The three I missed were 2
questions about multi-well crystals which would be better (no problem)
and the capillary (no problem either, because you can mount it)...
  I wouldn't be that snipe and braging (pun intended) if I would not
agree with Klaus....

Jens

 On Tue, 2011-04-19 at 03:02 -0600, Marcus Winter wrote:
>  

>  
> 
>  
> 
> Dear Klaus, 
> 
>  
> 
>  
> 
> Thanks for your note.  Yes: we do understand the point that you make 
> 
> and, sincerely, we are sensitive to this possible criticism.  However,
> we trust 
> 
> that you would agree that this was not a blatant advertisement.  Also,
> my 
> 
> original posting was in direct response to a not unrelated one.
> 
>  
> 
> Thank you for recognising the contributions made by the manufacturers.
> 
> No doubt, we're – all of us, dependent upon public funding to some
> extent - directly 
> 
> or indirectly, and, similarly, we're taxpayers too... 
> 
>  
> 
>  
> 
> Anyway: why not entertain yourself by taking two minutes out for the
> 
> PX Scanner Crystal Challenge:
> 
>  
> 
>  
> 
> signature_crystalchall
> 
>  
> 
>  
> 
>  
> 
> Many Thanks and Very Best Regards,
> 
>  
> 
> Marcus (Agilent Technologies)
> 
>  
> 
>  
> 
>  
> 
> -----Original Message-----
> From: Klaus Fütterer [mailto:[log in to unmask]] 
> Sent: 19 April 2011 09:40
> To: WINTER,MARCUS (A-UnitedKingdom,ex1)
> Cc: [log in to unmask]
> Subject: Re: [ccp4bb] viewing and scoring diffraction using the PX
> Scanner
> 
>  
> 
> Dear Marcus,
> 
>  
> 
> I always feel a bit uneasy about the advertisement-like posts that  
> 
> Agilent (and others) place on this BB. Of course, there are  
> 
> interactions between users and suppliers on many fronts, not least
> the  
> 
> support you guys provide in the form of sponsorship to meetings and  
> 
> conferences.
> 
>  
> 
> Still, the original purpose of this bulletin board is the exchange
> of  
> 
> expertise and advice on a particular software package. No doubt,  
> 
> company-based crystallographers make valuable contributions to  
> 
> discussions on the BB. This is, however, different to placing an
> open  
> 
> sales pitch. I can remember that some in the community were miffed  
> 
> when discussions on non-CCP4 software packages became prominent.
> 
>  
> 
> I think it is only fair to ask suppliers to minimise marketing of  
> 
> their products here. After all, the infrastructure for the BB is
> paid  
> 
> for by public money.
> 
>  
> 
> With the obligatory '2 cents worth',
> 
>  
> 
> Klaus
> 
>  
> 
>  
> 
> =======================================================================
> 
>  
> 
>                      Klaus Fütterer, Ph.D.
> 
>                  Reader in Structural Biology
> 
>                    Undergraduate Admissions
> 
>  
> 
> School of Biosciences                          P: +44-(0)-121-414 5895
> 
> University of Birmingham         F: +44-(0)-121-414 5925
> 
> Edgbaston                         E: [log in to unmask]
> 
> Birmingham, B15 2TT, UK           W: http://tinyurl.com/futterer-lab
> 
> =======================================================================
> 
>  
> 
>  
> 
>  
> 
>  
> 
>  
> 
> On 19 Apr 2011, at 08:22, Marcus Winter wrote:
> 
>  
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > Dear Artem,
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > Thanks for your reply.  You raise a number of points.
> 
> > 
> 
> > 
> 
> > 
> 
> > Immediately, I should comment that the price of the PX Scanner is
> very
> 
> > 
> 
> > considerably less than the $400k that you mention.
> 
> > 
> 
> > 
> 
> > 
> 
> > Whilst - with the proteins and crystallisation conditions that you  
> 
> > may be working
> 
> > 
> 
> > with, visual inspection may be sufficient to differentiate salt
> from  
> 
> > protein
> 
> > 
> 
> > crystals (as you suggest), you will accept that generally this may  
> 
> > not be the
> 
> > 
> 
> > case.  Thus, ‘direct’ inspection, using X-rays, must surely be the  
> 
> > most appropriate way ?
> 
> > 
> 
> > As you will be aware, the best looking crystals are seldom the
> best  
> 
> > diffracting.
> 
> > 
> 
> > This is well demonstrated through the PX Scanner ‘Crystal  
> 
> > Challenge’, of course.
> 
> > 
> 
> > Clearly, that’s another prime purpose of the PX Scanner: to
> identify  
> 
> > the ‘best’ crystals
> 
> > 
> 
> > from amongst a multitude of candidates in a single droplet or
> across  
> 
> > a plate, etc.
> 
> > 
> 
> > Also, using the PX Scanner, we can check the effect of added cryo- 
> 
> > protect. prior to
> 
> > 
> 
> > freezing.
> 
> > 
> 
> > 
> 
> > 
> 
> > Therefore, with this range of uses, the PX Scanner is clearly not  
> 
> > intended for full
> 
> > 
> 
> > ‘data-collection’ – but rather to most effectively support  
> 
> > crystallisation optimisation and
> 
> > 
> 
> > as a complement to in-house and central facility data-collection  
> 
> > work.  From the feedback
> 
> > 
> 
> > that we receive, the PX Scanner is much valued by the number of  
> 
> > groups which are
> 
> > 
> 
> > now using these systems worldwide.
> 
> > 
> 
> > 
> 
> > 
> 
> > However, even the proof of Grandma’s apple pie is not until the  
> 
> > eating.  Accordingly,
> 
> > 
> 
> > we most cordially invite you to visit one of our application labs
> –  
> 
> > or perhaps one of our
> 
> > 
> 
> > customer sites (by arrangement), with you, hopefully, being able
> to  
> 
> > bring one or more
> 
> > 
> 
> > of your crystallisation plates for inspection using the PX Scanner  
> 
> > system.  Since you
> 
> > 
> 
> > are based in North America, I believe, one of my responsible  
> 
> > colleagues will take up
> 
> > 
> 
> > this invitation with you, off-BB.
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > We look forward to our continuing discussions – with yourself, and  
> 
> > all others who
> 
> > 
> 
> > may be interested.
> 
> > 
> 
> > 
> 
> > 
> 
> > Many Thanks and Best Regards,
> 
> > 
> 
> > 
> 
> > 
> 
> > Marcus Winter (Agilent Technologies)
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > <image002.gif>
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > From: Artem Evdokimov [mailto:[log in to unmask]]
> 
> > Sent: 19 April 2011 02:50
> 
> > To: WINTER,MARCUS (A-UnitedKingdom,ex1)
> 
> > Cc: [log in to unmask]
> 
> > Subject: Re: [ccp4bb] viewing and scoring diffraction using the PX  
> 
> > Scanner
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > Hi,
> 
> > 
> 
> > 
> 
> > 
> 
> > So what's your secret - how did you pack an entire synchrotron
> into  
> 
> > a little box?
> 
> > 
> 
> > 
> 
> > 
> 
> > OK, so I am being facetious a little. However, I cannot help
> asking  
> 
> > myself why would I want to spend so much money on a system that is  
> 
> > basically a (vertical) X-ray diffractometer in a box, with fixed  
> 
> > distance, and sans the ability to collect data? I can only guess  
> 
> > that the system costs in the range of $400K (am I right?) and for  
> 
> > that money one could get a pretty nice actual X-ray diffraction
> set- 
> 
> > up...
> 
> > 
> 
> > 
> 
> > 
> 
> > Now, if this thing cost say ... $80K I may be interested, although  
> 
> > most of our crystals are so small that this set-up will uniformly  
> 
> > score them as 'no idea' because they don't even diffract at home
> on  
> 
> > a 'real' X-ray source with a CCD.
> 
> > 
> 
> > 
> 
> > 
> 
> > Artem
> 
> > 
> 
> > P.S. the day I start routinely confusing protein and salt crystals  
> 
> > is the day I stop working in the lab :)
> 
> > 
> 
> > On Mon, Apr 18, 2011 at 3:00 AM, Marcus Winter
> <[log in to unmask] 
> 
> > > wrote:
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > Dear Chris,
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > I’m prompted by your posting just to mention the Agilent
> Technologies
> 
> > 
> 
> > PX Scanner ‘Crystal Challenge’ at:
> 
> > 
> 
> > 
> 
> > 
> 
> > www.agilent.com/chem/crystalchallenge
> 
> > 
> 
> > 
> 
> > 
> 
> > Thus, the only really useful assessment, or ‘score’,  of objects  
> 
> > (putative
> 
> > 
> 
> > crystals) – or crystallisation conditions, is by the actual
> observed  
> 
> > diffraction
> 
> > 
> 
> > characteristics... and these preferably directly in situ, in the  
> 
> > horizontal
> 
> > 
> 
> > crystallisation plate, as achieved in the PX Scanner.
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > Many Thanks and Best Regards,
> 
> > 
> 
> > 
> 
> > 
> 
> > Marcus Winter (Agilent Technologies)
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf  
> 
> > Of Chris Ulens
> 
> > Sent: 18 April 2011 08:24
> 
> > To: [log in to unmask]
> 
> > Subject: [ccp4bb] viewing and scoring crystallization drops on the  
> 
> > iPad
> 
> > 
> 
> > 
> 
> > 
> 
> > Our laboratory has been developing an application to view and
> score  
> 
> > crystallization drops on the iPad. We would like to know if  
> 
> > crystallographers see potential benefits from the functionality of  
> 
> > the iPad to swipe and pinch through drops. We are looking for  
> 
> > specific comments from Formulatrix users, but other users are also  
> 
> > welcome to comment.
> 
> > 
> 
> > 
> 
> > 
> 
> > http://www.youtube.com/watch?v=LezurNhm0pA
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > Specific ideas for future development are:
> 
> > 
> 
> > - composition of crystallization buffers on a back-flip of the
> image  
> 
> > drop
> 
> > 
> 
> > - back-sync of crystallization scores on the iPad with the image  
> 
> > database
> 
> > 
> 
> > - emailing a drop image to colleague
> 
> > 
> 
> > 
> 
> > 
> 
> > Thanks.
> 
> > 
> 
> > -Chris
> 
> > 
> 
> > 
> 
> > 
> 
> > ---------------------------------------------------
> 
> > 
> 
> > Chris Ulens, Ph.D.
> 
> > 
> 
> > Lab of Structural Neurobiology
> 
> > 
> 
> > Department of Molecular Cell Biology
> 
> > 
> 
> > Campus Gasthuisberg, ON1
> 
> > 
> 
> > Herestraat 49, PB 601
> 
> > 
> 
> > B-3000 Leuven
> 
> > 
> 
> > Belgium
> 
> > 
> 
> > http://www.xtal.be
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
>  
> 
> 

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