Re: [ccp4bb] How many microfocus beamlines are in the world?

[CHAVAS Leonard]

I tend to like considering below 10microns as a micro-focus, below the micron 
as a sub-micron beamline. I don't know if any nano-focus, sort to say. XFELs 
are dealing with 100 nm, without the wings, which is really sub-micron to me.

Regards, Leo

-
Leonard Chavas
-
Synchrotron SOLEIL
PROXIMA-1
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
-
Phone : +33 169 359 746
Mobile : +33 644 321 614
E-mail : leonard.cha...@synchrotron-soleil.fr
-

> On 27 Jun 2020, at 14:35, John R Helliwell  wrote:
> 
> Hi,
> At the ISDSB 2019 in Osaka last November I asked Stephen Burley about the 
> BioSync pages, commending how useful they are. Stephen said they had asked 
> for a budget line in their last renewal to help keep the pages up to date but 
> it had been cut. At the next renewal, or earlier, we should write our Letters 
> of Support for the BioSync pages.
> Best wishes,
> John
> Emeritus Professor John R Helliwell DSc
> 
> 
> 
> 
>> On 27 Jun 2020, at 10:41, Rasmus Fogh  wrote:
>> 
>> Dear All,
>> 
>> The link http://biosync.rcsb.org/index.jsp looked very interesting, but a 
>> cursory look found the following line in a beamline description:
>> 
>> "Next proposal submission period Mid 2013"
>> 
>> Not 100% up to date, then.
>> 
>> Yours,
>> Rasmus
>> 
>>> On 25/06/2020 09:36, Andrew Leslie wrote:
>>> Dear Morpholino,
>>> I think 10 microns or under is a reasonable way to define a micro focus 
>>> beam line. There is a list of all MX beamlines at the following web site:
>>> http://biosync.rcsb.org/index.jsp
>>> This gives details of each beam line, including beam size, but you would 
>>> have to go through them all to find the actual number. Also I’m not totally 
>>> sure how often this is updated.
>>> Best wishes,
>>> Andrew
> On 24 Jun 2020, at 23:23, Murpholino Peligro  > wrote:
 
 That's a good point...
 I was thinking that a decent crystal has a size in the hundreds of 
 micrometers (say 100 in a, b and c). So, with such a specimen we can use 
 any MX beamline.
 But if the crystal is smaller (say 10 micrometers in a, b and c) You must 
 use a microfocus beamline.
 *Please correct me if I am wrong.*
 So what are the number of MX beamlines that can get useful data from 
 smaller crystals (as defined above)?
 
 Thanks again
 
 El mié., 24 de jun. de 2020 a la(s) 13:02, James Holton (jmhol...@lbl.gov 
 ) escribió:
 
   Define "micro focus" ?
 
   -James Holton
   MAD Scientist
 
   On 6/24/2020 9:18 AM, Murpholino Peligro wrote:
>   I would like to know how many MX beamlines are micro focus?
> 
> 
>   Thanks.
> 
>   
> 
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>> 
>> 
>> -- 
>> Rasmus H. Fogh   Tel.: +44 (0)1223 353033
>> Global Phasing Ltd., Fax.: +44 (0)1223 366889
>> Sheraton House,
>> Castle Park,
>> Cambridge CB3 0AX
>> United Kingdom
>> 
>> 
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Re: [ccp4bb] dewar horror stories

[CHAVAS Leonard]

Users had issues, back at SOLEIL in France, with FedEx, DHL, UPS, French 
post... at many levels. I guess it just depends on luck, or bad luck in the 
present case. The worst case encountered so far though was Dewars lost in 
transit for a couple of weeks. Not to mention countries where import taxes are 
so expensive that it becomes cheaper to buy new Dewars...

Regards, Leo

-
Leonard Chavas
-
Synchrotron SOLEIL
PROXIMA-1
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
-
Phone : +33 169 359 746
Mobile : +33 644 321 614
E-mail : leonard.cha...@synchrotron-soleil.fr
-

> On 27 Jun 2020, at 01:57, Minmin 
> <3d6c0e364a92-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> A collaborated group met the similar situation with FedEx before and they 
> switched to World courier afterwards. 
> 
> When your shipping dewar is no longer leaking of course, maybe you would like 
> to check out the following link below. According to our users, crystals 
> stored in the CombiPuck seem to get less or no ice up after shipment, 
> possibly because the vials inside the puck helped keep the LN2 temp well.  
> The 16pins puck base format of the CombiPuck is the same format as the 
> UniPuck. It is easy to switch from crystals stored in canes or any other 
> formats of the pucks to the CombiPuck. It is also easy to retrieve the 
> crystals from the CombiPuck back to the canes or any other pucks when needed.
> 
> https://www.mitegen.com/product/combipuck-system/
> 
> 
> 
> On Thu, 25 Jun 2020 at 7:34, Jan Dohnalek
>  wrote:
> We have the suspicion (after several heavy FEDEX failures) they just toss 
> them around ... then the neck easily breaks off.
> That only explains everything we have seen with completely damaged samples, 
> lost, flying around the dewar etc ...
> When trying to communicate seriously with FEDEX about these issues - they 
> even did not reply ...
> 
> Jan
> 
> 
> 
> On Wed, Jun 24, 2020 at 9:27 PM Patrick Loll  wrote:
> Hello community,
> 
> We recently had a dry shipping dewar fail catastrophically (while en route to 
> the beam line, so, major trauma). I sent it to a company that specializes in 
> repair and refurbishing of cryogenic tanks, and they told me it has an 
> internal leak, and hence is not reparable. I was expecting that the valve had 
> failed, so the internal leak diagnosis came as a surprise.
> 
> Has anyone else had a similar experience? Any ideas about how an internal 
> leak might come about? The dewar is (was) a Taylor/Wharton CX100, and it was 
> traveling in its bespoke shipping case.
> 
> Thanks for any insights that might satisfy my curiosity and/or prevent future 
> mishaps of this sort.
> 
> Cheers,
> 
> Pat
> 
> __
> 
> Patrick J.  Loll, PhD
> Professor of Biochemistry & Molecular Biology
> Drexel University College of Medicine
> Room 10-102 New College Building
> 245 N. 15th St.
> Philadelphia, PA 19102-1192 USA
> 
> (215) 762-7706
> pj...@drexel.edu
> 
> 
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> 
> 
> 
> -- 
> Jan Dohnalek, Ph.D
> Institute of Biotechnology
> Academy of Sciences of the Czech Republic
> Biocev
> Prumyslova 595
> 252 50 Vestec near Prague
> Czech Republic
> 
> Tel. +420 325 873 758
> 
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Better Beamline suggestion!

[CHAVAS Leonard]

Dear Chandra

SLS and ourselves (SOLEIL) are dealing rather often with large unit cells and 
fancy crystal orientations. No great secret, and things have already been 
mentioned: combining three-axis goniometry, large area Pixel detector, low 
background, small wedges and/or helical scans, Staraniso...

This works pretty well at SOLEIL, and I do know it works probably better at 
SLS. We can discuss off-line about more details if you wish.

Best.

leo

-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-

> On 21 Aug 2019, at 21:47, Frank Von Delft  wrote:
> 
> We also described how to bend the loops in this article:  
> http://doi.org/gcb8j3  Figure 4 specifically.
> 
> 
> On 21/08/2019 18:21, Edwin Pozharski wrote:
>> 
>> In the absence of such you can resort to carefully bending the loop or 
>> bending the pin (Jim Holton made a nifty device for bending the pin) while 
>> keeping the xtal bathed in the cold stream.
>> 
>> 
>>  I would also mention these 
>> 
>> https://hamptonresearch.com/product-Adjustable-Mounted-CryoLoop-385.html
>> 
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[ccp4bb] Thoughtful remark...

[CHAVAS Leonard]

Dear all

I had one interesting comment today at the beamline, that I would like to share 
with you for your advice on how to answer this...

Is it better to have no diffraction from a crystal you shoot, or to have no 
crystal in the loop?

Hum, difficult one...

Cheers, leo

-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-



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[ccp4bb] Post-doctoral position at the Synchrotron SOLEIL (France)

[CHAVAS Leonard]

Dear all

please consider the following post-doctoral position available at the 
Synchrotron SOLEIL in France. Would you or colleagues be interested, I would 
greatly appreciate if you could forward this message to them.

Cheers, leo

Postdoctoral position in life sciences (24 months) 
Synchrotron SOLEIL 
Application deadline: 9AM on October 15, 2018.

microfluidic-based sample handling
Post-doctoral position at the Synchrotron SOLEIL

SOLEIL is the French national synchrotron facility, located on the Saclay 
Plateau in the Paris suburbs. It is a multi-disciplinary instrument and a 
research laboratory, whose mission is to run research programs using 
synchrotron radiation, to develop state-of-the-art instrumentation on the 
beamlines, and to make those available to the scientific community. SOLEIL, a 
unique tool for both academic research and industrial applications across a 
wide range of disciplines including physics, biology, chemistry etc., is used 
by over 5,000 researchers coming from France and abroad. It is based on a 
state-of-the-art synchrotron source, both in terms of brilliance and stability. 
The facility is a "public" company employing about 350 people, founded by the 
CNRS and the CEA, and partner of the Paris-Saclay University. 

Applications are invited for a Postdoctoral Researcher to work at the 
Synchrotron SOLEIL, within the Biology and Health scientific sections and the 
microfluidic laboratory for a fixed-term period of 24 months.

The Synchrotron SOLEIL regroups several instruments applied to fundamental 
research as well as industrial applications. Within SOLEIL, the Health and 
Biology (HelioBio) scientific section makes use of specific approaches applying 
a large spectrum of the synchrotron light to tackle problematics relevant to 
life sciences in an integrated approach. Moreover, annex instruments are in 
place to favour sample preparation and characterisation, for a better 
understanding of the systems being studied.

For further information, please contact: 
Dr. Léonard CHAVAS - HelioBio scientific section responsible: 
leonard.cha...@synchrotron-soleil.fr 
 
Missions
The postdoctoral duties will include coordinating most of the instruments, and 
more specifically the microfluidic laboratory and related equipments, provided 
by SOLEIL for studying the biology of oxygen sensitive samples in an integrated 
manner within the HelioBio team. The project involves developing specific tools 
for handling crystalline samples in oxygen-free environments. The overall 
project is in line with the scientific program of the HelioBio scientific 
section. In this context, the postdoctoral candidate will be involved in both 
the instrumental and scientific programs of different beamlines and 
laboratories within the section. 
 
Qualifications and expertises
The postdoctoral candidate should hold a PhD degree in Physics, Materials 
Sciences, Life Sciences, or a relevant discipline, or have submitted his/her 
thesis prior to taking up the appointment. The candidate should have practical 
skills and experience in synchrotron facilities and resulting methodologies for 
imaging, sample characterisation and/or structure determination. Previous 
experience with microfluidic devices will be greatly appreciated.

The following aspects will be considered with the greatest attention:

expertise in molecular and cellular biology
proven knowledge of macromolecular crystallography
capability in developing complex experimental equipment
demonstrated experience in organizing the activity at shared experimental 
facilities

The candidate must be fluent in English (written and spoken). Knowledge of 
French is also desirable but not mandatory. 

General conditions
The offer concerns a post-doctoral contract (2-year). The place of work will be 
the Synchrotron SOLEIL site at Saint-Aubin (Essonne-91, France).

This position is open to people with disabilities.

Applications should include a motivation letter and Curriculum Vitae with the 
contact information of two referees.

Contact
Leonard Chavas
Email: leonard.cha...@synchrotron-soleil.fr
Tel: +33(0)-644-321-614


-
Leonard Chavas
-
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
-
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-



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Re: [ccp4bb] Should we still keep copies of all raw data?

[CHAVAS Leonard]

Hi Frank

on the same lines: do we keep our crystals after frying them? Or do molecular 
biologists keep their agarose gels? Hummm... evolution and technologies do 
progress.

Yet, I would support keeping images, just as you may (but really will most 
likely never) want to re-process those with new software approaches etc. few 
years after the paper has been published ^^

Cheers, leo
 
-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-

> On 13 Jul 2018, at 16:36, Frank von Delft  wrote:
> 
> Are the LHC researchers that analyse the detector readout on the fly without 
> ever storing the data also guilty of malpractice?  Hardcore.
> 
> Just a few more years, a few more Eiger detectors, a few more serial 
> beamlines, a few more clusters and clouds, and a few more DIALS-style 
> programmers, before MX too throws in the towel and   starts trusting 
> real-time processing and stops bothering with storing "raw" images.  
> phx.
> 
> 
> On 13/07/2018 11:07, John R Helliwell wrote:
>> Dear Sergei,
>> Re “all”. As a researcher my perspective is that one’s funding agency 
>> requirement for a data management plan will be the core of what you would 
>> need to follow. Your employer may have additional policies and requirements 
>> placed on you as an employee. Eg the UK funding agency EPSRC requires data 
>> be retained for 10 years. My employer, University of Manchester, has a 
>> policy which regards data loss as research malpractice. 
>> Central facility data retention policies vary from facility to facility so 
>> you would need to check ie for the ones you use. 
>> For publication IUCr encourages raw data underpinning a publication be 
>> archived and its doi cited. That doi can also be entered into the relevant 
>> PDB deposition. 
>> Best wishes,
>> John
>> 
>> 
>> Emeritus Professor John R Helliwell DSc
>> 
>> On 13 Jul 2018, at 10:30, Sergei Strelkov  
>> wrote:
>> 
>>> Dear All,
>>> 
>>> 
>>> I believe this question may be of some interest.
>>> In the past, we always stored all raw data ever collected by the lab.
>>> 
>>> With the recent advances, such as
>>> (a) automated/on-the-fly processing offered by some (European) 
>>> synchrotrons, and
>>> 
>>> (b) an ongoing discussion on centralized raw data archiving,
>>> 
>>> I wonder if it is time to revise the strict policy of keeping all data 
>>> (before we invest in a new NAS system... )
>>> 
>>> 
>>> Best wishes,
>>> 
>>> Sergei
>>> 
>>> Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
>>> Pharmaceutical Sciences, KU Leuven 
>>> 
>>> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] new ContaMiner features

[CHAVAS Leonard]

Dear Gerard

I should certainly be the one to blame, as I was the one spotting this 
behaviour to Stefan. Telling this, it could indeed be a problem with the data 
set, yet submitting the original mtz to ContaMiner provided with the strangely 
hoped and expected ContaMiner negative result. I made few tests afterwards, 
quick ones, with other mtz files treated or not with Staraniso, and although 
the direct results were not exactly the same as the extreme 'all positive' 
results noted earlier, it behaved strange (all 'possible positive', while 
standard non-contaminant data give you all 'negative' results).

I then ran MorDa standalone and found the same behaviour: for the first trial, 
it did found a solution... while there were none. Interestingly, Rfac/Rfree in 
the resulting MorDa solved structure was something like 50/20... I strongly 
believe that MorDa, and hence ContaMiner, scores its results on the Rfree 
value. Errors could have been spotted by looking at the ratio, which clearly 
was showing that something wrong is happening, operation either on MorDa or on 
ContaMiner side (or even both). 

Additional investigations are obviously welcome, however and for now, I guess 
the message from Stefan was more in the idea to warn people that having too 
many positive hits for one single data probably means something is wrong with 
the ContaMiner/MorDa processing, more than something is wrong with the dataset 
itself. That goes without saying that something could go wrong if the dataset 
is wrong, obviously... 

To Gerard and good willing developers: would you need the badly behaving data, 
please do let me know and I shall send it to you offline.

Cheers, leo

-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-

> On 23 Nov 2017, at 23:53, Gerard Bricogne  wrote:
> 
> Dear Pierre,
> 
> Thank you for throwing some light on the circumstances under
> which the "suspicious" results cropped up :-) . Was the "Government
> Heatlh Warning" based on this one and only mtz file, then?
> 
> We would certainly be interested in examining this dataset for
> any anomalies in the anisotropy analysis and the mtz file it produced
> (perhaps you can simply give us the job ID on the server). However the
> "results" consist of the spurious recognition of molecules that are
> known not to be in the crystal, so they are the outcome of numerous
> unspecified steps downstream of the anisotropy analysis itself, that
> in the end produce a "score" that is misleading. It would be useful to
> have at least some idea of what those steps are in order to identify
> the possible causes of the erroneous detections. 
> 
> 
> With best wishes,
> 
>  Gerard.
> 
> --
> On Thu, Nov 23, 2017 at 10:05:09PM +, LEGRAND Pierre wrote:
>> Dear Gérard,
>> 
>> As being part of the group how has initially raised the issue to Stefan, I 
>> stand out to try clarifying a misinterpretation.
>> In brief, because we are happy users of StarAniso, it happened that we have 
>> submitted an mtz that it had produced to the ContaMiner server. We were very 
>> surprised to find that almost all contaminants evaluated gave high scores 
>> according to MoRDa. On the contrary, using an "isotropicaly" treated mtz, no 
>> hit could be detected in by ContaMiner.
>> 
>> Being collected on PROXIMA-1 beamline, it coun't be a "badly collected 
>> datasets" ;-)
>> 
>> So, most probably, as you suggested, the issue is linked to some bad 
>> assumptions made by MoRDa or inadequate criteria choices _in_the_cases_ of 
>> "corrected" anisotropic data. 
>> We can probably provide some examples of datasets to the developers willing 
>> to pursue investigations on this.
>> 
>> I completely agree with Tristan! I have to admit having lost several weeks 
>> in my career (if not months) with "contaminated" crystals. And working on an 
>> MX beamline, I can testify that this is unfortunately happening regularly. 
>> 
>> I will finish with a big thanks to all the (StarAniso/ContaMiner/MoRDA) 
>> developers how are helping us to untwist the unavoidable experimental 
>> mess/reality.
>> 
>> Kind regards,
>> Pierre 
>> 
>> De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Gerard 
>> Bricogne [g...@globalphasing.com]
>> Envoyé : jeudi 23 novembre 2017 19:34
>> À : CCP4BB@JISCMAIL.AC.UK
>> Objet : Re: [ccp4bb] new ContaMiner features
>> 
>> Dear Stefan,
>> 
>> Regarding your final paragraph: your server carries a warning
>> with the exact wording:
>> 
>> "Submitting StarAniso files can give you suspicious results. Use
>> with care!"
>> 
>> It seems rather regrettable that you are posting such a public
>> warning without ever having contacted the STARANISO developers about
>> your observations, nor giving any 

Re: [ccp4bb] new ContaMiner features

[CHAVAS Leonard]

Dear all, 

to join Pierre's comments on what 'strange' things happen at the beamlines... 
yet not too strange for (too) many people: huge screening of salt crystals, 
complete data collection of dramatically low resolution data, full power 
coupled with 360Deg data collection etc. etc. etc. We do unfortunately see too 
many 'blind shots, deal with it later, and move on' experiments that it becomes 
depressive. I personally do not see why we would close our eyes to servers 
and/or data analysis tools that could help you think less, or better say help 
you understanding what is eventually happening with your data.

Cheers, leo

-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-

> On 24 Nov 2017, at 00:23, Edward A. Berry  wrote:
> 
> My 2 cents worth:
> I think contaminer is an extremely useful service. I may be a sloppy 
> biochemist,
> but I am not the only one. There are multiple structures in the database of 
> say
> bacterioferritin or AcrB that were solved from crystals that were supposed to
> be something else. I remember in a discussion with the organizer of my session
> at a Gordon conference, she excitedly announced that there would be 
> preliminary
> crystallographic data on respiratory Complex I. But by the time of the 
> conference
> the authors discovered they had crystallized something else. And the 
> beautiful crystals
> of Paracoccus Complex II (from Doug Rees's lab?) that graced the catalog of
> Hampton Research (And I believe were part of the basis for the first membrane
> protein screen) never saw publication.  The authors of
>  http://www.sciencedirect.com/science/article/pii/S0304416506000894
> certainly feel there is a real problem.  Some proteins crystallize readily 
> even when
> present as minor contaminants. And some protein complexes become more 
> heterogeneous
> if over-purified due to partial loss of loosely-bound subunits.
> Most of my career I've worked with high-abundance natural-source proteins.
> During a recent foray into the realm of overexpressed proteins, my group has
> crystallized (and solved) at least a half dozen wrong proteins from E. coli.
> I spent months on one of these (ATCase in Rhomb sg with low-level 
> obverse/reverse
> twinning that caused it to sometimes index as P3) Then solved the rest rapidly
> by checking the closest several hits with nearest-cell.  All of these E.coli 
> proteins
> were already present in the PDB. I wonder how many were from accidental 
> crystals.
> And now bacterioferritin (this time from M. smegmatis) keeps coming back to 
> haunt us.
> 
> I would say any time with a new crystal when a molecular replacement 
> unexpectedly fails,
> and even before you start to collect heavy atom or selenomet data, it would 
> be worth
> to submit to nearest-cell and contaminer. I would be more likely to question 
> the
> utility of an anisotropy correction server, given that modern 
> maximum-likelihood
> refinement programs can deal with weak data satisfactorily (speaking from
> ignorance- I'm sure supporting evidence and examples exist, I just haven't
> bothered to look them up. And I know my colleagues here at Upstate have used
> anisotropy correction to good effect with a difficult problem- I hope they
> weren't using filled-in maps!)
> eab
> 
> On 11/23/2017 03:24 PM, Tristan Croll wrote:
>> Dear Radu,
>> 
>> I think this is a little harsh. Biology is a fabulously messy thing, and 
>> very prone to doing the unexpected. See the excellent paper by 
>> Niedzialkowska et al. at 
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815408/#!po=13.6905 for some 
>> examples. Sometimes unexpected things (which just happen to have a similar 
>> size to your target) carry through all the purification steps - I remember 
>> having terrible trouble isolating his-tagged IGF-I (not for crystallization) 
>> from Sf9 lysates due to a cathepsin-like protease that stuck doggedly to the 
>> Ni-NTA column even under 8M urea, yet co-eluted in imidazole. Even if 
>> contaminant proteins are barely visible on your SDS-PAGE gel, if they 
>> crystallise easily and your target doesn’t...  all these things and many 
>> others have happened, and have undoubtedly driven the occasional poor grad 
>> student to the brink of giving it all up.
>> 
>> I guess in these days of relatively cheap and ubiquitous mass spec it may 
>> make sense to sacrifice a crystal to trypsin digest and MS/MS sequencing 
>> just for peace of mind, but in the average case I think that’s likely to be 
>> overkill. Shooting crystals at a synchrotron is now very routine, so I think 
>> it makes perfect sense to provide a computational check for the (hopefully 
>> rare) surprise case.
>> 
>> Best regards,
>> 
>> Tristan
>> Tristan Croll
>> Research Fellow
>> Cambridge Institute for Medical Research
>> 

Re: [ccp4bb] Fine Phi Slicing

[CHAVAS Leonard]

Reading back my email, when I mentioned 'just introduced', it is not giving 
justice to the reality and those who came up with the concept. I should have 
mentioned 'just reminded us', as the concept has been introduced quite a long 
time ago and few tens of communications. It is therefore a reminder that when 
coming to the will to collect good, clean and complete data, things aren't as 
simple as they would seem. Automation at our favourite beamlines do help by 
providing much more time thinking properly of the necessary strategies when 
coming to these difficult crystals so important to our hearts.

Sorry again for the confusion. No hurt feelings I hope.
Cheers, leo

-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-

> On 14 Jul 2017, at 14:07, CHAVAS Leonard 
> <leonard.cha...@synchrotron-soleil.fr> wrote:
> 
> Just to comment on what Graeme just introduced. We (and I know we are not the 
> first ones and not the only ones) are pushing our user community towards this 
> procedure as a standard: lowering the transmission (less juicy, yet...) and 
> getting few data with various chi. It does help greatly in getting fully 
> complete data, with no loss in resolution. Just fantastic!
> 
> Cheers, leo
> 
> -
> Leonard Chavas
> - 
> Synchrotron SOLEIL
> Proxima-I
> L'Orme des Merisiers
> Saint-Aubin - BP 48
> 91192 Gif-sur-Yvette Cedex
> France
> - 
> Phone:  +33 169 359 746
> Mobile: +33 644 321 614
> E-mail: leonard.cha...@synchrotron-soleil.fr
> -
> 
>> On 14 Jul 2017, at 07:36, Graeme Winter <graeme.win...@diamond.ac.uk> wrote:
>> 
>> Jacob
>> 
>> If you have a complete 360 deg data set and your sample is still alive, and 
>> you have a multi-axis gonio, I would recommend rotating the crystal about 
>> the beam (ideally by ~ maximum scattering 2-theta angle) and collecting 
>> again. This would record your blind region as well as moving the reflections 
>> to different pixels, and (as a bonus) also will move reflections out from 
>> the tile join regions into somewhere they can be measured, which would not 
>> happen for small 2-theta shift.
>> 
>> See http://scripts.iucr.org/cgi-bin/paper?BA0020 Figure 16 as excellent 
>> illustration of this.
>> 
>> Biggest risk with this is getting *moving* shadows on the data on the second 
>> run, as an effective 45-50 degree chi shift (say) will usually be a pretty 
>> wide opening angle for a kappa gonio. XDS and DIALS both have mechanisms to 
>> deal with this, and automated processing packages are able to apply these 
>> given a reasonable understanding of the beamline.
>> 
>> Also saves building 2-theta axes which can handle 92 kg ;o)
>> 
>> Cheers Graeme
>> 
>> On 13 Jul 2017, at 21:00, Keller, Jacob 
>> <kell...@janelia.hhmi.org<mailto:kell...@janelia.hhmi.org>> wrote:
>> 
>> I thought there was a new paper from the Pilatus people saying fine slicing 
>> is worth it even beyond the original 1/2 mosaicity rule?
>> 
>> I would think, actually, more gains would made by doing light exposures at, 
>> say, 1/3 mosaicity, collecting 360 deg, then shifting the detector in 2theta 
>> by a degree or two to shift uniformly the spots to new pixels, maybe 
>> accompanied by a kappa change. One would have to remember about the 
>> two-theta when processing, however!
>> 
>> JPK
>> 
>> -Original Message-
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerd 
>> Rosenbaum
>> Sent: Thursday, July 13, 2017 3:40 PM
>> To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
>> Subject: Re: [ccp4bb] weird diffraction pattern
>> 
>> Dear Gerard,
>> 
>>  my "sound like a sales person" was meant as poking a little fun - nothing 
>> serious, of course.
>> 
>> I and our users like our not-so-new-anymore Pilatus3 6M. It's a great 
>> detector in many ways. But, there is a lot of hype that this detector solves 
>> all-problem, for instance fine slicing that is claimed to be only possible 
>> with a pixel array detector. People get carried away and use
>> 0.01 degree slices even as the mosaicity of their sample is, say, 0.3 
>> degree. Slicing beyond 1/3 of the mosaicity will gain you very little - only 
>> more frames, more processing time.
>> 
>> This discourse is already drifting away from the original topic of the 
>> thread so I will comment on the other arguments  you made like resolution in 

Re: [ccp4bb] Fine Phi Slicing

[CHAVAS Leonard]

Attenuation... cut the beam with primary slits! We do not use attenuators, only 
for getting very very low when performing energy scans. Else, cutting the flux 
at the source is somehow much more reliable. Not mentioning scattering coming 
from the attenuators as well...

Cheers, leo

-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-

> On 14 Jul 2017, at 13:02, Keller, Jacob  wrote:
> 
> Hi Graeme,
> 
> I see your point about the blind region and also the tile lines. But 2-theta 
> would have the advantage of also shifting the low-res spots to entirely new 
> pixels, which would be harder through rotation. Also, wouldn't rotating about 
> the beam axis shift the spots to variable degrees across rotation space, with 
> some angles (+/- 90 deg) negligibly shifted?
> 
> Further, does it give anyone pause: Graeme makes a subtle implication that 
> most samples die before collecting 360 degrees, which I think may be true. 
> What can be done about this tragic lack of attenuation? One possibility is to 
> model the radiation damage in refinement, but wouldn't it make a lot more 
> sense to have a lot of good attenuators installed by default (or use 
> sealed-tube sources!).
> 
> JPK
> 
> 
> 
> -Original Message-
> From: graeme.win...@diamond.ac.uk [mailto:graeme.win...@diamond.ac.uk] 
> Sent: Friday, July 14, 2017 1:37 AM
> To: Keller, Jacob 
> Cc: ccp4bb@jiscmail.ac.uk
> Subject: Re: [ccp4bb] Fine Phi Slicing
> 
> Jacob
> 
> If you have a complete 360 deg data set and your sample is still alive, and 
> you have a multi-axis gonio, I would recommend rotating the crystal about the 
> beam (ideally by ~ maximum scattering 2-theta angle) and collecting again. 
> This would record your blind region as well as moving the reflections to 
> different pixels, and (as a bonus) also will move reflections out from the 
> tile join regions into somewhere they can be measured, which would not happen 
> for small 2-theta shift.
> 
> See http://scripts.iucr.org/cgi-bin/paper?BA0020 Figure 16 as excellent 
> illustration of this.
> 
> Biggest risk with this is getting *moving* shadows on the data on the second 
> run, as an effective 45-50 degree chi shift (say) will usually be a pretty 
> wide opening angle for a kappa gonio. XDS and DIALS both have mechanisms to 
> deal with this, and automated processing packages are able to apply these 
> given a reasonable understanding of the beamline.
> 
> Also saves building 2-theta axes which can handle 92 kg ;o)
> 
> Cheers Graeme
> 
> On 13 Jul 2017, at 21:00, Keller, Jacob 
> > wrote:
> 
> I thought there was a new paper from the Pilatus people saying fine slicing 
> is worth it even beyond the original 1/2 mosaicity rule?
> 
> I would think, actually, more gains would made by doing light exposures at, 
> say, 1/3 mosaicity, collecting 360 deg, then shifting the detector in 2theta 
> by a degree or two to shift uniformly the spots to new pixels, maybe 
> accompanied by a kappa change. One would have to remember about the two-theta 
> when processing, however!
> 
> JPK
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerd 
> Rosenbaum
> Sent: Thursday, July 13, 2017 3:40 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] weird diffraction pattern
> 
> Dear Gerard,
> 
>   my "sound like a sales person" was meant as poking a little fun - nothing 
> serious, of course.
> 
> I and our users like our not-so-new-anymore Pilatus3 6M. It's a great 
> detector in many ways. But, there is a lot of hype that this detector solves 
> all-problem, for instance fine slicing that is claimed to be only possible 
> with a pixel array detector. People get carried away and use
> 0.01 degree slices even as the mosaicity of their sample is, say, 0.3 degree. 
> Slicing beyond 1/3 of the mosaicity will gain you very little - only more 
> frames, more processing time.
> 
> This discourse is already drifting away from the original topic of the thread 
> so I will comment on the other arguments  you made like resolution in a 
> private e-mail.
> 
> Best regards,
> 
> Gerd
> 
> On 13.07.2017 14:00, Gerard Bricogne wrote:
> Dear Gerd,
> 
> I can assure you that I have no shares in Dectris nor any commecial 
> connections with them. What I do have is a lot of still vivid memories of CCD 
> images, with their wooly point-spread function that was affected by 
> fine-grained spatial variability as well as by irredicible inaccuracies in 
> the geometric corrections required to try and undo the distortions introduced 
> by the fiber-optic taper. By comparison the pixel-array detectors have a very 
> regular structure, so that slight 

Re: [ccp4bb] Fine Phi Slicing

[CHAVAS Leonard]

Just to comment on what Graeme just introduced. We (and I know we are not the 
first ones and not the only ones) are pushing our user community towards this 
procedure as a standard: lowering the transmission (less juicy, yet...) and 
getting few data with various chi. It does help greatly in getting fully 
complete data, with no loss in resolution. Just fantastic!

Cheers, leo

-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-

> On 14 Jul 2017, at 07:36, Graeme Winter  wrote:
> 
> Jacob
> 
> If you have a complete 360 deg data set and your sample is still alive, and 
> you have a multi-axis gonio, I would recommend rotating the crystal about the 
> beam (ideally by ~ maximum scattering 2-theta angle) and collecting again. 
> This would record your blind region as well as moving the reflections to 
> different pixels, and (as a bonus) also will move reflections out from the 
> tile join regions into somewhere they can be measured, which would not happen 
> for small 2-theta shift.
> 
> See http://scripts.iucr.org/cgi-bin/paper?BA0020 Figure 16 as excellent 
> illustration of this.
> 
> Biggest risk with this is getting *moving* shadows on the data on the second 
> run, as an effective 45-50 degree chi shift (say) will usually be a pretty 
> wide opening angle for a kappa gonio. XDS and DIALS both have mechanisms to 
> deal with this, and automated processing packages are able to apply these 
> given a reasonable understanding of the beamline.
> 
> Also saves building 2-theta axes which can handle 92 kg ;o)
> 
> Cheers Graeme
> 
> On 13 Jul 2017, at 21:00, Keller, Jacob 
> > wrote:
> 
> I thought there was a new paper from the Pilatus people saying fine slicing 
> is worth it even beyond the original 1/2 mosaicity rule?
> 
> I would think, actually, more gains would made by doing light exposures at, 
> say, 1/3 mosaicity, collecting 360 deg, then shifting the detector in 2theta 
> by a degree or two to shift uniformly the spots to new pixels, maybe 
> accompanied by a kappa change. One would have to remember about the two-theta 
> when processing, however!
> 
> JPK
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerd 
> Rosenbaum
> Sent: Thursday, July 13, 2017 3:40 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] weird diffraction pattern
> 
> Dear Gerard,
> 
>   my "sound like a sales person" was meant as poking a little fun - nothing 
> serious, of course.
> 
> I and our users like our not-so-new-anymore Pilatus3 6M. It's a great 
> detector in many ways. But, there is a lot of hype that this detector solves 
> all-problem, for instance fine slicing that is claimed to be only possible 
> with a pixel array detector. People get carried away and use
> 0.01 degree slices even as the mosaicity of their sample is, say, 0.3 degree. 
> Slicing beyond 1/3 of the mosaicity will gain you very little - only more 
> frames, more processing time.
> 
> This discourse is already drifting away from the original topic of the thread 
> so I will comment on the other arguments  you made like resolution in a 
> private e-mail.
> 
> Best regards,
> 
> Gerd
> 
> On 13.07.2017 14:00, Gerard Bricogne wrote:
> Dear Gerd,
> 
> I can assure you that I have no shares in Dectris nor any
> commecial connections with them. What I do have is a lot of still
> vivid memories of CCD images, with their wooly point-spread function
> that was affected by fine-grained spatial variability as well as by
> irredicible inaccuracies in the geometric corrections required to try
> and undo the distortions introduced by the fiber-optic taper. By
> comparison the pixel-array detectors have a very regular structure, so
> that slight deviations from exact registering of the modules can be
> calibrated with high accuracy, making it possible to get very small
> residuals between calculated and observed spot positions. That, I
> certainly never saw with CCD images.
> 
> I do think that asking for the image width was a highly
> pertinent question in this case, that had not been asked. As a
> specialist you might know how to use a CCD to good effect in
> fine-slicing mode, but it is amazing how many people there are still
> out there who are told to use 0.5 or even 1.0 degree image widths.
> 
> Compensating the poor PSF of a CCD by fine slicing in the
> angular dimension is a tall order. With a Pilatus at 350mm from the
> crystal, the angular separation between 174-micron pixels is 0.5 milliradian.
> To achieve that separation in the angular (rotation) dimension, the
> equivalent image width would have to be 0.03 degree. For an EIGER the
> numbers become 75 microns, hence 0.21 milliradian i.e. 0.012 

Re: [ccp4bb] Protein or DNA crystals

[CHAVAS Leonard]

Dear Kumar

you said 'shot from other conditions': we do not know then if you shot these 
crystals or not.

Else: 
- DNA should give you an X pattern, most of the time.
- protein should give you at least low resolution pattern, or faint rings if it 
is powder pattern like
- salt should give you diffraction at very high angle, in which case you need 
sometime to have the detector very close to the sample

That is, if those are diffracting crystals.

Agarose and/or SDS/Silver staining gels on the diluted crystals would be good 
as well. There are worth nothing as it anyway.

Cheers, leo


-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-

> On 19 Jun 2017, at 18:25, Gyanendra Kumar  wrote:
> 
> Hi Joseph,
> 
> Are you having trouble getting bigger crystals. You said you shot them, and 
> they are not salt. Do they diffract at all? If they are diffracting to any 
> extent, you could optimize the crystallization condition to get better, 
> bigger crystals and shoot them. A simple way of growing fewer, bigger 
> crystals in the same condition is to set up bigger drops and dilute the well 
> solution by water to 95%, 90%, 85%... And if that doesn't work, you can try 
> additive screen on this current crystallization condition.
> 
> As a control for determining if these are complex crystals or just DNA 
> crystals, you can set up a crystallization in the same crystallization 
> condition with just DNA, no protein.
> 
> -Gyan 
> 
> On Mon, Jun 19, 2017 at 9:20 AM, Joseph Ho  wrote:
> Dear all:
> 
> I would like to seek your opinion on our crystal hits. We are working
> on protein/dsDNA complex. By changing different protein and DNA
> (14-22bp) constructs, we recently got some hits from commercial
> screens using sitting drop vapor diffusion (very small xtals). The
> precipitant is PEG and the picture of crystals are attached. In this
> particular condition, it is 30%PEG3350, sodium succinate pH5.5 and
> 100mM NaCl. The crystal seems floating and sit in the bottom. We do
> some test shot from other conditions and it is not salt crystals. The
> crystals can suck in izit dye.  I do some google and it seems izit dye
> also turns dsDNA crystal into blue. We also do UV/Vis microscope but
> no Trp fluorescence (6 Trp in 256 aa). It may due to low Trp.
> 
> This is our first time to work on protein/DNA complex crystals and we
> are not certain if this is just DNA or protein/DNA crystals. Can you
> provide your comments on our hits?
> 
> Thank you for your help
> 
> Joseph
> 
> 
> 
> -- 
> Gyanendra Kumar, PhD
> Associate Scientist,
> St. Jude Children's Research Hospital,
> Department of Structural Biology,
> 262, Danny Thomas Place, MS-311
> Memphis, TN 38105
> Cell: 631-875-9189
> https://www.linkedin.com/in/gyanendrakumar
> https://scholar.google.com/gyanendrakumar
> https://www.researchgate.net/profile/Gyanendra_Kumar3
> http://stjude.academia.edu/GyanendraKumar
> ---

Re: [ccp4bb] Contouring 2Fo-Fc map, large blobs in Fo-Fc

[CHAVAS Leonard]

Do you have continuous chains all the way through? Any possibility of domain 
swapping?

leo

-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-

> On 05 May 2017, at 17:12, Roger Shek  wrote:
> 
> Hello Randy,
> 
> I appreciate all your help. Phaser found 12 molecules after some long 
> computing time. However, it looks like some molecules are clashing. Though, 
> the electron density looks pretty good. However, where the molecules are not 
> clashing (the two gray and orange molecules), there is still the original 
> problem, but the ED looks good when contoured up to ~>4 sigma. The rest of 
> the molecules found do not have that problem and looks good at 1.5 sigma 
> although the clashes are still an issue. Any tips on how to proceed? I ran 
> phaser from scratch with the search model as a monomer and not using the 
> three molecules found as the search model.
> 
> <1dotfivesigma.PNG>
> 
> On Wed, Apr 26, 2017 at 4:52 PM, Randy Read  wrote:
> Dear Roger,
> 
> You left a lot of very relevant detail out of your presentation of the 
> problem!  It seems that your data have been merged as P6222, but then you’re 
> using Phaser to expand that back out to P1 and search for multiple copies.  
> Assuming the data merged well in point group 622, then either that’s the 
> right symmetry or the crystal is twinned.  I’m guessing from the 2nd moments 
> in the Phaser log file that it probably is twinned, but the presence of tNCS 
> will mask the twinning in those moment statistics.
> 
> I’m guessing you haven’t really looked at the log file in any detail and 
> tried to understand the warnings it is giving you.  You’re searching for 4 
> copies, but the suggestion of 12 is more likely.  If you had 622 point group 
> symmetry, there would be 12 symmetry related copies, but then that wouldn’t 
> explain the presence of tNCS, which requires more than one unique copy per 
> asymmetric unit.  However, it does fit with the idea that the true symmetry 
> is somewhat lower.  So trying P1 instead of all the many other subgroups 
> (which Phaser would have listed for you before you set the symmetry to P1) is 
> a good first choice, but you have to look for the right number of copies.
> 
> The next warning is that the default NMOL of 2 (where NMOL is the number of 
> tNCS-related copies in the same orientation) doesn’t fit with the analysis.  
> It makes more sense to have 3 copies related by a sort of lattice tripling, 
> i.e. the original copy, one translated by about 1/3,2/3,0 and a third 
> translated by 2/3,1/3,0 (remember that 2*2/3=4/3 is equivalent to 1/3, after 
> taking account of the unit cell translation).  So you need to run a job 
> specifying NMOL 3.  I’m not surprised it didn’t work with the wrong NMOL.  On 
> the other hand, when you turn off the tNCS correction, any potential solution 
> that places copies related by the Patterson vector will look good, because it 
> explains the biggest feature in the data, the systematic modulation caused by 
> the tNCS.
> 
> Finally, you didn’t mention that you have hundreds of solutions.  When you 
> don’t get a unique solution, you have to start worrying about what went 
> wrong.  There’s no reason to believe that the first one is correct.
> 
> By the way, why did you set the estimated RMS error to 2A?  Did you try a run 
> first in which you specified the sequence identity?  That usually works 
> better, and any model that is so bad that 2A is a suitable RMS error is very 
> unlikely to work.  If you give too large a number, you’re effectively 
> throwing away a large amount of information, because Phaser doesn’t expect to 
> be able to fit data beyond 3.6A resolution and therefore omits those data 
> from the calculation.
> 
> If you’re lucky, if you run a job setting NMOL to 3, specifying that there 
> are 12 copies in the a.u. and looking for 12 copies with an appropriate 
> setting for the model quality, you might get something promising!
> 
> Randy
> 
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical ResearchTel: +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
> 
> > On 26 Apr 2017, at 22:27, Roger Shek  wrote:
> >
> > actually I turned off corrections for tNCS because it failed to find a MR 
> > solution. The logfile is attached.
> >
> > On Wed, Apr 26, 2017 at 4:19 PM, Randy Read  wrote:
> > Could you send me the logfile from the job that found 3 copies?  Normally 
> > when there is tNCS and Phaser uses it, you get the 

Re: [ccp4bb] Another puzzle: 5gnn: SOLVED

[CHAVAS Leonard]

Could we write to them as a community? As the 'CCP4 Peer Reviewing Organisation 
for Structural Biology'?

Great job indeed!

Cheers, leo

-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-

> On 09 Sep 2016, at 13:39, Manfred S. Weiss 
>  wrote:
> 
> 
> Good job Randy!
> 
> Now, in order to finish this off properly somebody should
> refine the structure, alert the editor of the journal as well
> as the corresponding author of the paper.
> 
> If we leave it at that, the only thing we have is the satisfaction
> that we managed to "peer review" this structure, but nothing else is
> going to happen.
> 
> Cheers, Manfred
> 
> 
> On 09.09.2016 13:34, Gerard Bricogne wrote:
>> Dear Randy,
>> 
>> Congratulations for this terrific piece of work!
>> 
>> As James Fraser was writing two days ago, this case establishes a
>> new paradigm for the "peer review" of structural papers :-) .
>> 
>> 
>> With best wishes,
>> 
>>  Gerard.
>> 
>> --
>> On Fri, Sep 09, 2016 at 12:20:53PM +0100, Randy Read wrote:
>>> Dear all,
>>> 
>>> Following on from Paul’s suggestion that the space group is wrong, I 
>>> thought it might be interesting to try to solve this structure from 
>>> scratch, using what I’m currently teaching students at a CCP4 workshop.  
>>> What worked was to find some distant homologues with HHpred (top 3 hits 
>>> after ignoring 5gnn), make a trimmed ensemble, and search with that.  This 
>>> gave a very clear solution for one molecule in P65.  Model completion from 
>>> that point works really well, given the resolution, using either 
>>> phenix.autobuild or ARP/wARP.
>>> 
>>> For the edification of the members of the BB, the ARP/wARP model is 
>>> attached!  (Hopefully no flames for an attachment of 135kB…) This model 
>>> hasn’t had some really obvious rotamer fixes or extensions of the termini 
>>> applied, but it has good stereochemistry, and R/Rfree are 0.241/0.285.
>>> 
>>> Given the vastly improved statistics for a different space group and the 
>>> huge differences in the model, it is to be hoped that the authors retract 
>>> the original publication and PDB entry.  Thanks to Gerard for pointing out 
>>> the issues with this!
>>> 
>>> Best wishes,
>>> 
>>> Randy Read
>>> 
>> 
>> 
>>> 
>>> 
>>> -
>>> Randy J. Read
>>> Department of Haematology, University of Cambridge
>>> Cambridge Institute for Medical ResearchTel: +44 1223 336500
>>> Wellcome Trust/MRC Building Fax: +44 1223 336827
>>> Hills Road
>>> E-mail: rj...@cam.ac.uk
>>> Cambridge CB2 0XY, U.K.   
>>> www-structmed.cimr.cam.ac.uk
>>> 
 On 7 Sep 2016, at 16:51, Paul Adams  wrote:
 
 Dear Gerard,
 
 thanks for pointing this structure out. This is indeed very startling. The 
 paper indicates that the structure was refined with Phenix. However, if I 
 download the model/data and refine (with Phenix) the starting R-factors 
 are 0.36/0.38 and these get worse during refinement. Clearly the deposited 
 model is not consistent with the R-factors reported in the paper, or in 
 the wwPDB. In addition, analysis of the data suggests strongly that the 
 true symmetry is P6 (possibly with a screw axis) - I suspect that this is 
 the genesis of statements about twinning, but it isn’t clear if that was 
 used in the refinement. Being charitable I can imagine that the wrong 
 model was deposited in the wwPDB. However, this doesn’t explain the 
 R-factors reported by the wwPDB, or the less than convincing images of the 
 structure shown in the paper. I very much agree with you that there must 
 have been ample alarms sounded along the way. It is cautionary that this 
 wasn’t caught at some point. For me this highlights that the issues go 
 beyond the naivety or impatience of a single student.
 
 Cheers,
Paul
 
> On Sep 7, 2016, at 7:20 AM, Gerard Bricogne  
> wrote:
> 
> Dear all,
> 
>   While the thread on "Another MR pi(t)fall" is still lukewarm, and
> the discussion it triggered hopefully still present in readers' minds,
> I would like to bring another puzzling entry to the BB's attention.
> 
>   When reviewing on Monday the weekend's BUSTER runs on the last
> batch of PDB depositions, Andrew Sharff (here) noticed that entry 5gnn
> had been flagged as giving much larger R-values when re-refined with
> BUSTER (0.3590/0.3880) than the deposited ones (0.2210/0.2500). This
> led us to carry out some investigation of that entry.
> 
>   The deposited coordinates were flagged by BUSTER as having 4602
> bond-length violations, 

Re: [ccp4bb] Implementation of the ESRF Data Policy

[CHAVAS Leonard]

Dear all

something I am not completely aware of: can the ESRF users decide on having 
their data destroyed from the ESRF servers? One way to go I would think could 
be proper would be to announce getting open access for all the data on the 
servers or wherever after 3 years (or few months for what it is), or ask the 
users to get their data back home and destroy whatever has been transferred. 
The *fault* goes then to the users, who are legally bound to publish within x 
years, with the synchrotron facility that would not be in a legally bad 
situation.

I am certainly missing important points here, and probably oversimplify the 
whole problem.

Cheers, leo

> On 08 Apr 2016, at 12:25, Mark J van Raaij  wrote:
> 
> Hola Xavi,
> 
> I agree three years is short for many projects. However, from the news item, 
> the three-year embargo period appears to be renewable on request: "The 
> experimental team will have sole access to the data during a three-year 
> embargo period, renewable if necessary.” 
> Imo, what they should do is include this renewal clause explicitly in the 
> statement you sign/agree with.
> If this renewal is indeed possible, and renewal requests are dealt with 
> properly, I don’t see a problem with the new policy.
> 
> The journal issue is more complicated I think, as was discussed on ccp4bb not 
> long ago (topic “questionable structures"), with people in favour and against 
> policies like that of NSMB - I, for one, am in favour of it, I see no reason 
> to treat crystallographic data differently than other data, all data can be 
> faked, and all data can be scooped…
> Your alternative policy also sounds ok, although authors could then 
> reasonable also ask for a similar policy on other kind of data.
> 
> Saludos,
> 
> Mark
> 
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> c/Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij
> 
> 
> 
> 
> 
> 
>> On 8 Apr 2016, at 11:47, F.Xavier Gomis-Rüth  wrote:
>> 
>> Dear CCP4ers,
>> I received the message below from the ESRf User Office some weeks ago and 
>> was wondering if others within the community had, too, and would 
>> put this up for discussion within the BB. But as this is apparently not the 
>> case, I will come to the fore ;-) .
>> I must say this is a unilateral decision by ESRF, I was completely unaware 
>> that this was under discussion. While I am truly not against
>> transparency, in particular in the case of publicly funded research, in this 
>> case I consider that things have simply gone too far. A really challenging
>> project in MX currently ALWAYS takes more than 3 years to be published after 
>> the very first dataset was collected, so this regulation poses an
>> additional, completely artificial and gratuitous pressure on researchers to 
>> finish everything within a determined and clearly too short time span.
>> Another font of unnecessary pressure is provided by some journals, such as 
>> NSMB, which now impose that not only the coordinates be send for review of a 
>> manuscript but rather the cif files with the reflections, while, obviously, 
>> reviewers keep their anonymity. Given the particular characteristics of our 
>> field, where
>> who publishes first irreversibly relegates competitors to the absolute 
>> irrelevance, such policies rather favor fraud but on the other side, on that 
>> of
>> potentially desperate competitors, whose very existence depends on relevant 
>> publications and who easily could take advantage of this information. 
>> While sound cases of fraud, historical and recent, clearly impose the 
>> necessity of stringent control, this must happen in a rational way and 
>> following
>> consensus within the community, which has not happened in the aforementioned 
>> cases. In the case of ESRF, this could be easily accomplished as in the PDB, 
>> where data are released upon publication. In the case of journals, by 
>> performing an exhaustive verification of structures AFTER the manuscript has 
>> been
>> pre-accepted, as a final condition for definitive acceptance.
>> I would be very interested in the opinion of the BB.
>> Best,
>> Xavier
>> 
>> 
>> 
>>  Forwarded Message 
>> Subject: Implementation of the ESRF Data Policy
>> Date:Mon, 29 Feb 2016 17:04:43 +0100 (CET)
>> From:user...@esrf.fr
>> To:  xgr...@ibmb.csic.es
>> 
>> Dear ESRF User,
>> 
>> The new ESRF data policy stipulates that all raw data and the associated 
>> metadata from peer reviewed access experiments at the ESRF will be open 
>> access after an initial embargo period of 3 years, during which access is 
>> restricted to the experimental team, represented by the Main Proposers. 
>> Proprietary research experiments are excluded.
>> 
>> Acceptance of this policy is a condition for the request of ESRF beamtime.
>> 
>> For more details and information, 

Re: [ccp4bb] extra density between inter-chain cysteine

[CHAVAS Leonard]

When running non-denaturing gel (SDS-gel without reducing agent should work), 
do you see a dimer? Same question during your sample preparation, if you are 
performing anything like SEC. If you do have DTT in lysis buffer, that could 
do. If nothing as such anywhere, honestly no idea...

Cheers, leo


> On 21 Mar 2016, at 15:09, Manjula Ramu <manjula@gmail.com> wrote:
> 
> I had no reducing agent in my protein buffer as wel as in crystal condition. 
> I have only sodium citrate in the condition.
> 
> On Mar 21, 2016 6:54 PM, "CHAVAS Leonard" 
> <leonard.cha...@synchrotron-soleil.fr> wrote:
> DTT perhaps?
> 
> Cheers, leo
> 
> > On 21 Mar 2016, at 14:04, Pedro Matias <mat...@itqb.unl.pt> wrote:
> >
> > Does it make sense to consider 2 extra S-atoms bridging the 2 cysteines? 
> > What would be the bond distances? What is the meaning of the red e.d. in 
> > the 2nd figure?
> >
> > Às 12:44 de 21/03/2016, Eleanor Dodson escreveu:
> >> No idea, but it is a lovely map.
> >>
> >> Are you sure the residue is CYS? You could check the anom map to see if 
> >> the S give a signal.
> >> Eleanor
> >>
> >> On 20 March 2016 at 04:36, Manjula Ramu <manjula@gmail.com> wrote:
> >> Dear community,
> >>
> >> I have got a crystal structure of 16Kda protein, which was solved at 1.9 
> >> A. Protein crystallised in dimer form and I could observe a continuous 
> >> extra density between cysteine of  two chains. Distance between two 
> >> intermolecular cysteine is 7.8 A.  Please help me to interpret this extra 
> >> density. Thanks in advance.
> >>  I have attached the screen shots of the map.
> >>
> >>
> >> Thanks and Regards,
> >> Manjula R
> >> Research Scholar
> >> Department of Biophysics
> >> National Institute of Mental Health and Neurosciences
> >> Bengaluru-29, Karnataka
> >> INDIA
> >> E-mail: manjula@gmail.com
> >> Mobile no:+91-9538553356
> >> http://www.nimhans.kar.nic.in/
> >>
> >>
> >>
> >>
> >
> >
> > --
> >
> > Industry and Medicine Applied Crystallography
> > Macromolecular Crystallography Unit
> > ___
> > Phones : (351-21) 446-9100 Ext. 1669
> >  (351-21) 446-9669 (direct)
> >  Fax   : (351-21) 441-1277 or 443-3644
> >
> > email :
> > mat...@itqb.unl.pt
> >
> >
> >
> > http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
> > http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
> >
> >
> > Mailing address :
> > Instituto de Tecnologia Quimica e Biologica
> > Universidade Nova de Lisboa
> > Av. da República - EAN
> > 2780-157 Oeiras
> > PORTUGAL
> >
> > ITQB, a great choice for your PhD
> >
> > https://youtu.be/de6j-aaTWNQ
> >
> >
> > Master Programme in Biochemistry for Health
> >
> > https://youtu.be/UKstDCFjYI8
> 
> -
> Leonard Chavas
> -
> Synchrotron SOLEIL
> Proxima-I
> L'Orme des Merisiers
> Saint-Aubin - BP 48
> 91192 Gif-sur-Yvette Cedex
> France
> -
> Phone:  +33 169 359 746
> Mobile: +33 644 321 614
> E-mail: leonard.cha...@synchrotron-soleil.fr
> -
> 

-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-

Re: [ccp4bb] extra density between inter-chain cysteine

[CHAVAS Leonard]

DTT perhaps?

Cheers, leo

> On 21 Mar 2016, at 14:04, Pedro Matias  wrote:
> 
> Does it make sense to consider 2 extra S-atoms bridging the 2 cysteines? What 
> would be the bond distances? What is the meaning of the red e.d. in the 2nd 
> figure?
> 
> Às 12:44 de 21/03/2016, Eleanor Dodson escreveu:
>> No idea, but it is a lovely map.
>> 
>> Are you sure the residue is CYS? You could check the anom map to see if the 
>> S give a signal.
>> Eleanor
>> 
>> On 20 March 2016 at 04:36, Manjula Ramu  wrote:
>> Dear community,
>> 
>> I have got a crystal structure of 16Kda protein, which was solved at 1.9 A. 
>> Protein crystallised in dimer form and I could observe a continuous extra 
>> density between cysteine of  two chains. Distance between two intermolecular 
>> cysteine is 7.8 A.  Please help me to interpret this extra density. Thanks 
>> in advance.
>>  I have attached the screen shots of the map.
>> 
>> 
>> Thanks and Regards,
>> Manjula R 
>> Research Scholar
>> Department of Biophysics 
>> National Institute of Mental Health and Neurosciences
>> Bengaluru-29, Karnataka
>> INDIA
>> E-mail: manjula@gmail.com
>> Mobile no:+91-9538553356
>> http://www.nimhans.kar.nic.in/
>> 
>> 
>> 
>> 
> 
> 
> -- 
> 
> Industry and Medicine Applied Crystallography
> Macromolecular Crystallography Unit
> ___
> Phones : (351-21) 446-9100 Ext. 1669
>  (351-21) 446-9669 (direct)
>  Fax   : (351-21) 441-1277 or 443-3644
> 
> email : 
> mat...@itqb.unl.pt
> 
> 
> 
> http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
> http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
> 
> 
> Mailing address :
> Instituto de Tecnologia Quimica e Biologica
> Universidade Nova de Lisboa
> Av. da República - EAN
> 2780-157 Oeiras
> PORTUGAL
> 
> ITQB, a great choice for your PhD
> 
> https://youtu.be/de6j-aaTWNQ
> 
> 
> Master Programme in Biochemistry for Health
> 
> https://youtu.be/UKstDCFjYI8

-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-

Re: [ccp4bb] Spacegroups, screw axes and ordering

[CHAVAS Leonard]

I guess again it depends on people and the procedure that scientists do adopt 
during their analysis. Yes, you could have more information in these specific 
cases in P1. Yet, those are specific cases and what would be the frequency of 
such happening? Biologically speaking, do we have so many homo-oligomers? I am 
not molecular biologist so cannot really comment on those, however I doubt it 
would justify putting everything in P1. You can take it the other way around 
then: for monomeric proteins, you would need to go down individual molecules 
and ignore these interactions. Pushing things a bit: you could even have 
referees asking for proving these interactions they see in the unit cell 
between molecules are not biologically meaningful etc. I am certainly pushing 
things a bit, but we do have a good working system and I don't feel strong 
enough science cases to force changing it. Saying that, I am a drop in the 
ocean of crystallographers, with what people might classify as zero knowledge 
in biology, just liking to argue things ^^

Leo

> On 29 Jan 2016, at 22:46, Quyen Hoang <qqho...@gmail.com> wrote:
> 
> Let get back to science for a moment, assuming that there is enough data (as 
> stated in my original post about this) would you not agree that the models 
> build into a P1 space group would represent the content of the unit cell more 
> accurately than a higher space group (albeit could be insignificant)?
> After your refinement has converged, don’t you always expand to look at the 
> packing and potential oligomeric states of your molecule? Let's say that you 
> have a true tetramer, what would be lost if you report your structural model 
> in P1 instead of P212121?
> I mean, is there a theoretical or scientific reason against reporting P1 for 
> a crystal system consisting of higher symmetry?
> 
> Cheers,
> Quyen
> 
>> On Jan 29, 2016, at 4:27 PM, CHAVAS Leonard 
>> <leonard.cha...@synchrotron-soleil.fr> wrote:
>> 
>> Sorry if I don't buy it. Just personal feeling. I don't see how someone 
>> capable of navigating through the coordinates, see meaningful interactions, 
>> highlight those and understand them, would not be able to press these 
>> buttons. While some programs indeed do not have these options (which makes 
>> me wonder about the usefulness of these programs by the way), most of those 
>> would. Let me join also Jacob's comment on the non usefulness of P1 in here, 
>> and send these non-experts either to PISA or to other experts more 
>> knowledgeable, say the people who solved these structures for instance.
>> 
>> Your point on the mtz file is interesting. We are now moving things toward 
>> some non-crystallographers in need to install quite a few programs, if not 
>> at least libraries, and put in these mtz files enough information to 
>> reproduce all the non-standard refinement procedures experts do apply for 
>> their structure refinement. Not to mention 5A structures for which auto 
>> build might be trickier to run than building in 1A maps.
>> 
>> Leo
>> 
>>> On 29 Jan 2016, at 22:02, Quyen Hoang <qqho...@gmail.com> wrote:
>>> 
>>> No, I wasn’t talking about crystal packing, I was thinking about potential 
>>> homo oligomeric interactions that might be important for function. 
>>> If we are talking about the simplicity of pushing couple buttons and saving 
>>> disk space and bandwidth, then I guess the same argument could be made that 
>>> a simple MTZ file containing phases should suffice?
>>> The non-crystallographer would simply press a few buttons to generate a 
>>> model with auto build?
>>> But I have a feeling those couple of buttons might not be so obvious to 
>>> people in other fields.
>>> 
>>> Quyen
>>> 
>>>> On Jan 29, 2016, at 3:16 PM, CHAVAS Leonard 
>>>> <leonard.cha...@synchrotron-soleil.fr> wrote:
>>>> 
>>>> Not sure I fully understand. Are we really talking about 
>>>> non-crystallographer scientists, often willing to understand how a 
>>>> biologically meaningful molecule / entity looks like? Are these 
>>>> non-crystallographers really interested in crystal packing issues? Is it 
>>>> so much difficult to press on a couple of buttons in the program with 
>>>> which you do open your coordinates to generate the symmetry related 
>>>> molecules? I am feeling we are a bit off here...
>>>> 
>>>> Leo
>>>> 
>>>>> On 29 Jan 2016, at 20:52, Quyen Hoang <qqho...@gmail.com> wrote:
>>>>> 
>>>>> Sure, but you would need to expand spa

Re: [ccp4bb] Spacegroups, screw axes and ordering

[CHAVAS Leonard]

Sorry if I don't buy it. Just personal feeling. I don't see how someone capable 
of navigating through the coordinates, see meaningful interactions, highlight 
those and understand them, would not be able to press these buttons. While some 
programs indeed do not have these options (which makes me wonder about the 
usefulness of these programs by the way), most of those would. Let me join also 
Jacob's comment on the non usefulness of P1 in here, and send these non-experts 
either to PISA or to other experts more knowledgeable, say the people who 
solved these structures for instance.

Your point on the mtz file is interesting. We are now moving things toward some 
non-crystallographers in need to install quite a few programs, if not at least 
libraries, and put in these mtz files enough information to reproduce all the 
non-standard refinement procedures experts do apply for their structure 
refinement. Not to mention 5A structures for which auto build might be trickier 
to run than building in 1A maps.

Leo

> On 29 Jan 2016, at 22:02, Quyen Hoang <qqho...@gmail.com> wrote:
> 
> No, I wasn’t talking about crystal packing, I was thinking about potential 
> homo oligomeric interactions that might be important for function. 
> If we are talking about the simplicity of pushing couple buttons and saving 
> disk space and bandwidth, then I guess the same argument could be made that a 
> simple MTZ file containing phases should suffice?
> The non-crystallographer would simply press a few buttons to generate a model 
> with auto build?
> But I have a feeling those couple of buttons might not be so obvious to 
> people in other fields.
> 
> Quyen
> 
>> On Jan 29, 2016, at 3:16 PM, CHAVAS Leonard 
>> <leonard.cha...@synchrotron-soleil.fr> wrote:
>> 
>> Not sure I fully understand. Are we really talking about 
>> non-crystallographer scientists, often willing to understand how a 
>> biologically meaningful molecule / entity looks like? Are these 
>> non-crystallographers really interested in crystal packing issues? Is it so 
>> much difficult to press on a couple of buttons in the program with which you 
>> do open your coordinates to generate the symmetry related molecules? I am 
>> feeling we are a bit off here...
>> 
>> Leo
>> 
>>> On 29 Jan 2016, at 20:52, Quyen Hoang <qqho...@gmail.com> wrote:
>>> 
>>> Sure, but you would need to expand space group X in order to see the 
>>> intermolecular interactions that would have been seen in P1. Also, it is 
>>> often discussed here about how non-crystallographers might use our 
>>> structural models deposited in the PDB‎, I doubt that many of them would 
>>> know how to expand. 
>>> 
>>> I am not advocating, just discussing. 
>>> 
>>> Cheers,
>>> Quyen 
>>> 
>>> Sent from my BlackBerry 10 smartphone.
>>> From: Keller, Jacob
>>> Sent: Friday, January 29, 2016 2:20 PM
>>> To: Quyen Hoang; CCP4BB@JISCMAIL.AC.UK
>>> Subject: RE: [ccp4bb] Spacegroups, screw axes and ordering
>>> 
>>>> I mean, would it not be more informative to have a P1 unit cell filled 
>>>> with molecules compared to a single molecule representing only a fraction 
>>>> of the unit cell?
>>> 
>>> No, it would not be more informative: a model in space group X can easily 
>>> be expanded to P1.
>>> 
>>> JPK
>>> 
>>> 
>>> Cheers,
>>> Quyen
>>> 
>>> On Jan 29, 2016, at 12:18 PM, Keller, Jacob <kell...@janelia.hhmi.org> 
>>> wrote:
>>> 
>>>> Sure, but wouldn’t the same could be achieved by NCS averaging?
>>> 
>>> Yes, with complete “NCS” constraints it would be the same. But why do P1 if 
>>> so—you’d have all the same issues when deciding which parts of the “NCS” to 
>>> constrain (it would be tantamount to SG determination.) Using unmerged 
>>> data, however, would have some advantages (one could model the variations 
>>> between reflections in a more direct way.)
>>> 
>>> I guess the final goal would be to reproduce as accurately as possible the 
>>> diffraction images. Thus, crystallographic refinement becomes data-faking 
>>> (I guess all science is this same data-faking, in a way.)
>>> 
>>> JPK
>>> 
>>> 
>>> 
>>> Ed, regarding the fractional problem with molecular replacement and data to 
>>> parameter ratio problem in refinement, I am sure that you know how to get 
>>> around these problems ;)
>>> 
>>> Quyen
>>> 
>>> On Jan 29, 2016, a

Re: [ccp4bb] Spacegroups, screw axes and ordering

[CHAVAS Leonard]

Not sure I fully understand. Are we really talking about non-crystallographer 
scientists, often willing to understand how a biologically meaningful molecule 
/ entity looks like? Are these non-crystallographers really interested in 
crystal packing issues? Is it so much difficult to press on a couple of buttons 
in the program with which you do open your coordinates to generate the symmetry 
related molecules? I am feeling we are a bit off here...

Leo

> On 29 Jan 2016, at 20:52, Quyen Hoang  wrote:
> 
> Sure, but you would need to expand space group X in order to see the 
> intermolecular interactions that would have been seen in P1. Also, it is 
> often discussed here about how non-crystallographers might use our structural 
> models deposited in the PDB‎, I doubt that many of them would know how to 
> expand. 
> 
> I am not advocating, just discussing. 
> 
> Cheers,
> Quyen 
> 
> Sent from my BlackBerry 10 smartphone.
> From: Keller, Jacob
> Sent: Friday, January 29, 2016 2:20 PM
> To: Quyen Hoang; CCP4BB@JISCMAIL.AC.UK
> Subject: RE: [ccp4bb] Spacegroups, screw axes and ordering
> 
> >I mean, would it not be more informative to have a P1 unit cell filled with 
> >molecules compared to a single molecule representing only a fraction of the 
> >unit cell?
>  
> No, it would not be more informative: a model in space group X can easily be 
> expanded to P1.
>  
> JPK
>  
>  
> Cheers,
> Quyen
> 
> On Jan 29, 2016, at 12:18 PM, Keller, Jacob  wrote:
>  
> >Sure, but wouldn’t the same could be achieved by NCS averaging?
>  
> Yes, with complete “NCS” constraints it would be the same. But why do P1 if 
> so—you’d have all the same issues when deciding which parts of the “NCS” to 
> constrain (it would be tantamount to SG determination.) Using unmerged data, 
> however, would have some advantages (one could model the variations between 
> reflections in a more direct way.)
>  
> I guess the final goal would be to reproduce as accurately as possible the 
> diffraction images. Thus, crystallographic refinement becomes data-faking (I 
> guess all science is this same data-faking, in a way.)
>  
> JPK
>  
>  
>  
> Ed, regarding the fractional problem with molecular replacement and data to 
> parameter ratio problem in refinement, I am sure that you know how to get 
> around these problems ;)
>  
> Quyen
>  
> On Jan 29, 2016, at 10:41 AM, Bernie  wrote:
>  
> Precision is always better when averaging is applied. Mirror planes and 
> rotations will be perfect rather than exact within experimental error. There 
> are also singularities in the refinement process that can force the structure 
> to be symmetrically imperfect. 
> 
> Sent from my iPhone
> 
> On Jan 29, 2016, at 8:10 AM, Quyen Hoang  wrote:
> 
> Given enough data and modern computing powers, why don’t we just use P1?
>  
> Quyen
> 
> On Jan 29, 2016, at 8:45 AM, George Sheldrick  
> wrote:
>  
> The collection and scaling requires the Laue group but not the space group. 
> For small molecule structure determination, many more space groups have to be 
> considered and the choice may be ambiguous (like I222 and I212121) or 
> difficult, so my current small molecule structure solution program SHELXT 
> only uses the input space group to deduce the Laue group. After solving the 
> structure with the data expanded to P1 it uses the phasesto determine the 
> space group and origin shift. In practice this is much more reliable than 
> using systematic absences. This was not my idea (see papers by Giacovazzo and 
> Palatinus), I just wrote a little program to implement it. How the user has 
> chosen a, b and c is irrelevant, the program outputs the solution in the 
> conventional setting for the space group in question (as the correct 
> enantiomorph based on the Friedel differences where appropriate). It also 
> finds the most compact arrangement of atoms and centers it is the unit-cell.
> 
> Whether this was worth the effort is debatable. SHELXT has been freely 
> available for the last couple of years, but the open access paper that 
> explains how it works (Acta A71 (2015) 3-8) is rarely cited.
> 
> George
> 
> 
> On 01/29/2016 01:06 PM, Ian Tickle wrote: 
> 
> Hi Kay
> 
> You are seriously misrepresenting how this works in practice.  Isomorphism 
> always takes precedence over convention: convention is not an absolute 
> requirement!  Convention is the _default_ in the absence of all other 
> criteria (that's why we have conventions!). Only the _first_ crystal in an 
> isomorphous series would be indexed by convention, the others would be 
> indexed using that as a reference (i.e. based on the intensity correlation, 
> _not_ the unit cell or the assumed space group which may not be reliable, 
> using REFINDEX, which is what we have always used, or POINTLESS) - very 
> simple!  At Astex we have be doing this for our large fragment screens for 15 
> 

Re: [ccp4bb] Protein precipitating at higher concentration!!

[CHAVAS Leonard]

Hi Ivan

this will not be an answer to your question, but did you consider not 
concentrating 'too much' your sample? It happened few times to me that the 
protein was precipitating when concentrating for SEC because of the presence of 
other impurities. Trying the good old AS precipitation helped a bit, but wasn't 
really the magical solution as I was losing a bit of the protein of interest as 
well. The solution was to concentrate only slightly the sample, and pass it 
though multiple (at the time it was quite a lot actually) runs of SEC. I ended 
up with again a lot of pure sample to concentrate, however, this sample was 
pure enough and did not precipitate.

Other than that, I guess playing with the salt concentration might help keeping 
things stable... or not. I know people also tried the addition of glycerol or 
EG, but I don't have personal experience in that and cannot really comment if 
it is working well or not.

Cheers, Leo

 On Jan 9, 2015, at 9:00 AM, xaravich ivan xaravich.i...@gmail.com wrote:
 
 Hi Xtallographers,
 I have been able to purify a protein that was initially going into inclusion 
 bodies from the excellent suggestions that I got here.
 
 So my lysis buffer has 0.5M Guanidium Hydrochoride, 2% TritonX-100, 500mM 
 NaCl, 5% Glycerol in 20 mM Tris-HCL pH 8.0
 
 The problem is that the protein is first purified as a SUMO-fusion protein 
 which is further proteolysed and passed through the Talon resin to get the 
 final SUMO-Free construct.
 
 However as I have around 250mM Imidazole (pH elution did not work) from the 
 elution of the first round, I have to dialyse the sample to get rid of the 
 imidazole so that I can use the proteolysed sample again on the column.
 
 All these I do in a buffer that does not have GuHCL or Triton. However I have 
 kept the NaCl concentration same (0.5 M).
 I start to see white insoluble precipitate right from the dialysis step. If I 
 spin the precipitate out, I still have a lot of protein to go to the next 
 step of proteolysis. The problem is that when I finally want to concentrate 
 the protein to run the SEC step, all my protein starts precipitating starting 
 from 5mg/ml to all the way to 25-30 mg/ml.
 
 Are there some smart ways to keep the protein soluble at higher 
 concentrations, assuming that I do not have to remove them before setting up 
 trays?
 
 Should I keep on using Guanidium Hcl and Triton for all the steps all the way 
 into the SEC column.
 
 Have people got any good results using  5% Acetronitrile, 50mM Arginine or 
 DTT? (used for NMR samples)
 Any help in this regard will be very helpful.
 
 The protein is an engineered bacterial transcription factor. (not a membrane 
 protein)
 
 Thanks in advance as always,
 ivan

Re: [ccp4bb] Question on Refmac5

[CHAVAS Leonard]

Dear Dialing

are you talking about the 'creating date' or the 'modified date'?

Leo

 On Jan 6, 2015, at 2:55 AM, Dialing Pretty 
 03f1d08ed29c-dmarc-requ...@jiscmail.ac.uk wrote:
 
 Dear All,
 
 When I run Refmac, it would produce a refined PDB file and mtz file. My 
 question is, if I started the refinement at 6:00 pm and completed at 8:00 pm, 
 I find the refined PDB file and mtz file were created in the target directory 
 at perhaps 6:30 pm. I think from 6:30 pm the created PDB file and mtz file in 
 the target directory would be automatically updated to 8: 00 pm when the 
 refinement finished, am I right?
 
 Dialing

Re: [ccp4bb] Restraints after refinement

[CHAVAS Leonard]

Dear Jeorge

just as a curiosity:
1- do you see a continuous electron density for the ligand, before and after 
performing the refinement?
2- do you have only one copy of the molecule(s), and if not, do you see the 
same behaviour for all the ligands?
3- what are the B-factor values for the ligand? Any hint that the phosphate 
could be very flexible and actually missing?
4- do you see any red (/ green) FoFc densities where the phosphate should (/ 
not) be? If so, do you see anything else by using 'less data', i.e. data that 
would be less prone to radiation damage?
5- what is the resolution of your data?
6- is it a known ligand? If you do have the same ligand, even only once, 
present in the PDB, why don't you take the coordinates and libraries from this 
already refined structure and try to fit it in your coordinates?
7- do you have chemical data showing that the ligand can stay for very long 
times in your protein without being shortened?
8- do you know how pure is your ligand solution? i.e. is your ligand stable at 
room temperature (or whatever temperature you did the soaking / complex 
formation).
9- similarly, if you did co-crystallisation instead of soaking, it could be 
that your protein somehow cleaved the molecule. It will all depend on how 
stable is the ligand in high concentrations of the protein, pH dependency and 
more.

Those are not real answers to your original question, just points of 
curiosity...

Cheers, Leo

 On Nov 22, 2014, at 4:26 AM, jeorgemarley thomas kirtswab...@gmail.com 
 wrote:
 
 Dear all, 
 
 I am working on my molecule, but after running
 Refmac5 restrained refinement the bonding distances and angles are broken. 
 I used Phenix to create the ligand and used Coot to place the ligand into the 
 correct location in the molecule, merged the ligand and molecule coordinates, 
 and saved the file. Then I went to run restrained refinement on
 the merged coordinates using the cif file provided from the phenix to the 
 refmac library,the rest of the settings were set at the defaults. During 
 fitting the model in the 2Fo-Fc map of the ligand there were no issue, but it 
 fitted well and after refinement of the same, the bond breaks and 
 distorted as observed in coot. The resolution is 1.6 Ang. 
 phosphate linkage bond is broken. What could be the best possible reason for 
 this and what can be solution for this ? Could you please suggest what should 
 I do for a complete model for the ligand ? I would like to run a round of 
 restrained refinement without breaking any geometric restraints that should 
 be imposed on my ligand.   
 
 Thank you for your help in advance,
 
 Jeorge
 

Re: [ccp4bb] Water molecules after refinement

[CHAVAS Leonard]

Dear Jeorge

are the water molecules without electron density properly coordinated? These 
could be ghosts... Additionally, did you solve the structure by molecular 
replacement? If so, in your search model, do you see these water molecules at 
the same / nearby location? Again, those could be model bias. Finally, 
depending on your resolution, you can expect a certain amount of water molecule 
(depends on other factors, obviously). If you find 'too many' (difficult to 
define 'too many'), it might be one indication that you are over-refining 
things.

I know I did not answer your question, but hope this could help. Others will 
have better comments I guess.

Cheers, Leo

 On 19 Nov 2014, at 07:33, jeorgemarley thomas kirtswab...@gmail.com wrote:
 
 Dear All, 
 
 I am sorry to ask this simple question, but I really need suggestions for 
 this. As the refinement has been done at 3.0 Angstrom after refinement the 
 water molecules were added by using find waters in coot. After adding water 
 refinement was done using Refmac 05. Now when I look on the added water 
 molecules some has density around it and some does not (even no red density 
 around it). Should I remove later water molecules. and again do the 
 refinement ? Please give some explanation also for this.  as the R free and R 
 meas has reduced to some extent, also the r m s d contour of map level was 
 kept at 1.09 after refinement. I welcome your suggestions, thanks in advance. 
 
 
 Regards
 
 Jeorge
 

Re: [ccp4bb] How to run CCP4 without source command

[CHAVAS Leonard]

read the documentation? Probably somewhere it should be mentioned to have the 
'source ' command in your bash file? I might have misunderstood your question 
though.

Leo

 On 16 Nov 2014, at 07:30, 陈昂 angsc...@outlook.com wrote:
 
 Dear all:
 
 I have installed CCP4 suit on my computer. The OS IS fedora 18. Every time I 
 open the software, I have to 
 
 use the command source. Does anyone else can run it in terminal without that 
 command?
 
 Thank u so much!
 
 best regards,
 
 Peter

[ccp4bb] Disturbing feature with access rights

[CHAVAS Leonard]

Dear all

I came along a disturbing feature and I would appreciate to get your lights on 
this.

After rebuilding our data server, plenty of access rights have been changed and 
various folders have been ‘secured’ by restricting access to few users and 
groups. The whole ccp4 suite has also been subjected to this new policy; no 
writing in the folders and in sensitive files can be done anymore by unknown 
users. Good to feel safe :D

Now, when running Refmac5, we came up with plenty of complains about library 
files not readable, or more specifically some library files that ‘failed to 
open’. After few juggling around, we understood what was wrong: all the 
involved library files needed to be ‘writable’ to be properly read.

Here is therefore my disturbing piece: why would you need to be able to write 
in a file if you just want to be able to read / execute it? I don’t think that 
this is a bug, but rather a feature, and would like to understand the logic 
behind it.

Please note that I did not check how other programs responded, nor other 
versions of the suite (I am on the latest CCP4 release). I haven’t deeply 
screened the bb either for a potential previous notice on this.

Cheers, Leo

-
Leonard Chavas
-
Mailing address:
Center for Free-Electron Laser Science (CFEL)
Deutsches Elektronen-SYnchrotron (DESY)
Notkestrasse 85. Bldg 99
22607 Hamburg, Germany
Room 03.051
Phone : +49 (0)40 8998 6384
Mobile: +49 (0)40 8998 96384
-
E-mail (DESY) : leonard.cha...@desy.de
E-mail (CFEL) : leonard.cha...@cfel.de
-

Re: [ccp4bb] small crystals

[CHAVAS Leonard]

Yes, Tim is right… for now… in few years, with the E-XFEL, we'll get to much 
less sample, and much more time available. But that's in few years.

Leo

On Dec 10, 2013, at 10:01 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:

 Dear Careina,
 
 you can also apply for beamtime at PETRA-III. You get away with the same
 size crystals but only require a nano liter drop rather than a few ml of
 your sample. And you probably get beamtime much quicker because all the
 equipment is installed and collecting a data set takes very short time.
 This was demonstrated at the ECM in Warwick this year, so no need for
 FEL (at least for structure determination).
 
 Best,
 Tim
 
 On 12/10/2013 04:36 AM, Jens Kaiser wrote:
 Careina,
  If your target is interesting enough, try to reproduce the small
 crystals in batch and apply for FELS time. Small crystals are actually
 an advantage there.
 
 Cheers,
 
 Jens
 
 
 On Wed, 2013-12-04 at 21:41 -0800, Careina Edgooms wrote:
 Hi all
 
 
 Any advice on how to get bigger crystals from conditions that give
 showers of tiny crystals? I am getting small pretty looking individual
 crystals but they are too small and they don't seem to grow. In fact,
 in some instances if left for a couple of days they actually dissolve.
 I have fiddled around with mother liquor volume, protein concentration
 as well as drop volume (I am using hanging drop method) but none seem
 to make any difference and I always get the same tiny crystals. I
 think I might try microseeding but I haven't tried that yet. 
 
 
 Any suggestions or tricks would be welcome 
 Careina.
 
 
 -- 
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 

Re: [ccp4bb] small crystals

[CHAVAS Leonard]

Indeed nothing is predictable. We can only assume things on what is *planed* 
and *promised*, and you can take my words on the fact that I will do my best to 
have it done properly and as close to the expectations as possible. But again, 
nobody can really predict the future.
Finger crossed.

Cheers, Leo

On Dec 10, 2013, at 10:13 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:

 'Will' is a fashionable word - but since even a Nobel prize was given
 based on promises never kept, who would be surprised...
 
 Best wishes from now,
 Tim
 
 On 12/10/2013 10:11 AM, CHAVAS Leonard wrote:
 Yes, Tim is right… for now… in few years, with the E-XFEL, we'll get to much 
 less sample, and much more time available. But that's in few years.
 
 Leo
 
 On Dec 10, 2013, at 10:01 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
 
 Dear Careina,
 
 you can also apply for beamtime at PETRA-III. You get away with the same
 size crystals but only require a nano liter drop rather than a few ml of
 your sample. And you probably get beamtime much quicker because all the
 equipment is installed and collecting a data set takes very short time.
 This was demonstrated at the ECM in Warwick this year, so no need for
 FEL (at least for structure determination).
 
 Best,
 Tim
 
 On 12/10/2013 04:36 AM, Jens Kaiser wrote:
 Careina,
 If your target is interesting enough, try to reproduce the small
 crystals in batch and apply for FELS time. Small crystals are actually
 an advantage there.
 
 Cheers,
 
 Jens
 
 
 On Wed, 2013-12-04 at 21:41 -0800, Careina Edgooms wrote:
 Hi all
 
 
 Any advice on how to get bigger crystals from conditions that give
 showers of tiny crystals? I am getting small pretty looking individual
 crystals but they are too small and they don't seem to grow. In fact,
 in some instances if left for a couple of days they actually dissolve.
 I have fiddled around with mother liquor volume, protein concentration
 as well as drop volume (I am using hanging drop method) but none seem
 to make any difference and I always get the same tiny crystals. I
 think I might try microseeding but I haven't tried that yet. 
 
 
 Any suggestions or tricks would be welcome 
 Careina.
 
 
 -- 
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 
 
 
 -- 
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 

Re: [ccp4bb] small crystals

[CHAVAS Leonard]

Dear Jens, Careina

this is not really an *advantage*, but rather a *convenience*. You can still 
use big crystals if you'd like to, but as they usually never survive more than 
one shot (few femtosec), you'd need a lot of these bigger crystals to collect a 
full data.

And yes, I would also highly recommend XFELs!

Cheers, Leo

On Dec 10, 2013, at 4:36 AM, Jens Kaiser kai...@caltech.edu wrote:

 Careina,
  If your target is interesting enough, try to reproduce the small
 crystals in batch and apply for FELS time. Small crystals are actually
 an advantage there.
 
 Cheers,
 
 Jens
 
 
 On Wed, 2013-12-04 at 21:41 -0800, Careina Edgooms wrote:
 Hi all
 
 
 Any advice on how to get bigger crystals from conditions that give
 showers of tiny crystals? I am getting small pretty looking individual
 crystals but they are too small and they don't seem to grow. In fact,
 in some instances if left for a couple of days they actually dissolve.
 I have fiddled around with mother liquor volume, protein concentration
 as well as drop volume (I am using hanging drop method) but none seem
 to make any difference and I always get the same tiny crystals. I
 think I might try microseeding but I haven't tried that yet. 
 
 
 Any suggestions or tricks would be welcome 
 Careina.

[ccp4bb] Positions available - Photon Factory, Japan

[CHAVAS Leonard]

Dear all

The Structural Biology Research Center at the Photon Factory (Japan) is 
advertising for several PostDoc positions in structural biology. Notably, one 
position will link methodology in structural biology applied to XFEL by 
comparison with 'classical' x-ray sources at synchrotrons.

Further details available below. You can also contact me directly, and have a 
look at the Structural Biology Research Center webpage for detailed information 
on our diverse activities:
http://pfweis.kek.jp/eng/index.html

Kind regards.

Leo CHAVAS

###DETAILS BELOW###

Title : Postdoctoral Fellow
Number of Job Opening : 1
Inst/Lab : Structural Biology Research Center
Term : The contract is for 1 year, but may be renewed at the end of the term 
until March 2017 at the longest
Start of the term : Successful candidate is expected to take the position as   
soon as possible
 
Job Description : 
In 2012, the Ministry of Education, Culture, Sports, Science  Technology in 
Japan (MEXT) launched a five-year program Key Strategic Research Projects 
Using X-ray Free Electron Laser, SACLA (XFEL). As a co-leader of one of its 
projects, for the Development of Rapid Structural Analysis Methodologies for 
Protein Drug Targets directed by Prof. So Iwata, KEK will pursue structural 
biology research on human proteins of medical interest. The KEK team will be 
responsible for developing new methodologies applicable to in vivo crystal 
growth and nano-crystallography using the XFEL. The successful candidate is 
expected to play a central role in the development of these methodologies, as 
well as directly applying them to the structural analysis of human protein 
crystals grown in vivo at the Japanese XFEL SACLA. The candidate is expected to 
have experiences in protein crystallography research including protein 
production, X-ray crystallography and relevant software developments.

Method of Selection : 
We will first make a selection by submitted documents and interview. Interview 
will take place on a first-come first-served policy. (We will inform of the 
interview date the candidates who passed our documentary screening.)
 
Documents to submit :
A4 size paper - 29.5 cm x 21 cm or similar including
1) Curriculum vitae: please write the possible date you would be able to start 
the job at the Synchrotron Radiation Science Division II. Please also write 
your birth date in the application form.
2) Research and job experience related to this application.
3) Publication list
4) Research and development plan at the SBRC if employed (should cover areas 
corresponding to the whole job description)
5) Reprints of major publications (fewer than 6)
6) Other reference materials (list of invited talks, awards etc.)
7) Recommendation of reference letter(s): recommendation of reference letter(s) 
must be addressed to Dr. Kazuyoshi Yamada, Director, IMSS, attention to 
Personnel Affairs Unit 1 of KEK.
 
For more information : 
Please contact
Assist. Prof. Leo Chavas, Synchrotron Radiation Science Division ll, Institute 
of Materials Structure Science.
Tel: +81 29-864-5200 (ext: 4901)
Fax: +81 29-864-2801
E-mail: leonard.cha...@kek.jp
 
Application to be mailed to:
Personnel Affairs Unit 1
KEK
1-1 Oho, Tsukuba, Ibaraki 305-0801 Japan
 
(We accept recommendation or reference letter(s) by email)
 
Others :
 - KEK is an equal-opportunity employer and encourages applications from women.
 - This program will be evaluated in the third year.

---
Chavas Leonard M.G., Ph.D.
Assistant Professor
Structural Biology Research Center
Photon Factory
High Energy Accelerator Research Organization (KEK)
305-0801 Tsukuba Oho 1-1
Japan
---
Phone : +81(0)29-864-5642 (4901)
Fax : +81(0)29-864-2801
E-mail : leonard.cha...@kek.jp
---