[ccp4bb] Job Opportunity: Beamline Scientist at Canadian Light Source

[Michel Fodje]

Hello everyone,

The Canadian Light Source, Inc. (CLSI) is seeking a qualified individual to 
join our MX team as a Scientist for the CMCF Beamlines. This role is pivotal in 
supporting and developing the beamlines' capabilities and collaborating with a 
diverse user community to enhance structural biology research.

Position Details:

  *   Job Title: Scientist, CMCF Beamlines
  *   Location: Canadian Light Source Inc., Saskatoon, SK
  *   Job Type: Full-time

The ideal candidate will have a strong background in X-ray crystallography or 
related fields, proven experience with beamline instrumentation, and excellent 
communication skills. For more information and to apply online, please visit 
the following link:

https://www.northstarats.com/Canadian-Light-Source

Please feel free to share this announcement with anyone who may be interested.

Regards

Michel Fodje
Senior Scientist, MX Group Leader | Canadian Light Source
44 Innovation Boulevard, Saskatoon, SK S7N 2V3
P: 306-657-3758

[cls_logo_signature]<http://www.lightsource.ca/>



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[ccp4bb] Scientist - CMCF Beamlines, Canadian Light Source

[Michel Fodje]

The Canadian Light Source Inc. (CLSI) is the national synchrotron research 
facility on the
University of Saskatchewan campus in Saskatoon. This facility serves national 
and international users from academia, industry, and government institutions. 
The CLS facilitates scientific research aimed at finding solutions for global 
challenges in agriculture, health, advanced materials, and the
environment.

The CLSI is now accepting applications for a Scientist at the Canadian 
Macromolecular Crystallography Facility (CMCF) within the Bio/Life Sciences 
department. The CMCF operates two beamlines, CMCF-ID and CMCF-BM which enable 
high-resolution structural studies of proteins, nucleic acids, and other
macromolecules, satisfying the requirements of challenging and diverse 
structural biology experiments. It is a unique national facility that supports 
Canadian macromolecular crystallography labs.

Responsibilities:

  *   Provides user support to general users, Beam Team members, 
fee-for-service clients and CLS staff. Provides the following functions:
 *   Beamline and endstation setup
 *   Assists with sample preparation
 *   User training and support including supervision
 *   Technical troubleshooting
  *   Solves difficult, complex or unusual problems relating to the beamline. 
Maintains, defines specifications, and software development for beamline 
software and technical troubleshooting.
  *   Prepares beamline documentation in the form of written reports, 
guidelines, and logbooks, ensuring CLS standards, and other relevant codes, 
standards and practices are met.
  *   Participates in the installation, maintenance, periodic upgrades and 
operation of specific components or endstations.
  *   Maintains beamline Quality Assurance and preventative maintenance 
procedures for the safe and efficient operation of the beamline.
  *   Undertakes and oversees medium to large projects of high complexity on 
the beamline, for example, the operation, maintenance and upgrade of a 
scientific endstation, providing scientific leadership within a project team.
  *   May provide expert technical review of beamtime proposals and input to 
the Peer Review Committee (PRC) concerning general user proposals.
  *   Develops recognized scientific expertise related to the beamline or 
equipment. Develops an approved research program (independently or 
collaboratively) that positions the CLS as a solutions provider in one of the 
four key sectors of health, agriculture, environment, and advanced materials, 
utilizing up to 20% of assigned CLS resources (time, equipment, materials, 
beamtime).

Required Qualifications:

  *   All applicants are expected to have completed a relevant Ph.D.
  *   Experience: A minimum of 1-2 years of directly related experience in a 
synchrotron or scientific laboratory.
  *   Experience in X-ray crystallography is a requirement for this position
  *   A background with hard X-ray synchrotron-based techniques is an asset
  *   Python programming experience would be considered an asset
  *   This position will be filled by an individual with a clear aptitude for 
science and instrumentation, and with a desire to participate in an active and 
exciting scientific program

Remuneration:
Remuneration will be commensurate with qualifications and experience. A 
comprehensive benefits package, including supplemental health & dental, life 
insurance, pension plan, and four weeks’ vacation is part of a competitive 
compensation package.

To Apply:
Submit a resume along with references, in confidence, online at  
https://www.lightsource.ca/careers. Applications will be considered as of 
November 5, 2021. While all applicants are thanked for their interest, only 
short-listed candidates will be contacted.

Canadian Light Source Inc. is an equal opportunity employer and encourages 
members of designated groups (women, Indigenous people, people with 
disabilities and visible minorities) to self-identify on their applications




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Re: [ccp4bb] External: Re: [ccp4bb] Unmodeled density

[Michel Fodje]

That looks like a magnessium hexahydrate.

From: CCP4 bulletin board  On Behalf Of Pearce, N.M. 
(Nick)
Sent: May 26, 2021 7:15 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: External: Re: [ccp4bb] Unmodeled density

Is it on a symmetry axis? If so it could be the superposition of two molecules 
(a molecule and a copy of itself).


On 26 May 2021, at 15:08, leo john 
mailto:ljohn16012...@gmail.com>> wrote:

Hi Group
Can you please suggest what this unmodeled blob can be (see appended picture)?
I have Malonate, Boric Acid and Peg in my condition, and crystals were soaked 
in GOL.

I have tried fitting PO4 and SO4 so far.

Thank You
John




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Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

[Michel Fodje]

I think the results from AlphaFold2, although exciting and a breakthrough are 
being exaggerated just a bit.  We know that all the information required for 
the 3D structure is in the sequence. The protein folding problem is simply how 
to go from a sequence to the 3D structure. This is not a complex problem in the 
sense that cells solve it deterministically.  Thus the problem is due to lack 
of understanding and not due to complexity.  AlphaFold and all the others 
trying to solve this problem are "cheating" in that they are not just using the 
sequence, they are using other sequences like it (multiple-sequence 
alignments), and they are using all the structural information contained in the 
PDB.  All of this information is not used by the cells.   In short, unless 
AlphaFold2 now allows us to understand how exactly a single protein sequence 
produces a particular 3D structure, the protein folding problem is hardly 
solved in a theoretical sense. The only reason we know how well AlphaFold2 did 
is because the structures were solved and we could compare with the 
predictions, which means verification is lacking.

The protein folding problem will be solved when we understand how to go from a 
sequence to a structure, and can verify a given structure to be correct without 
experimental data. Even if AlphaFold2 got 99% of structures right, your next 
interesting target protein might be the 1%. How would you know?   Until then, 
what AlphaFold2 is telling us right now is that all (most) of the information 
present in the sequence that determines the 3D structure can be gleaned in bits 
and pieces scattered between homologous sequences, multiple-sequence 
alignments, and other protein 3D structures in the PDB.  Deep Learning allows a 
huge amount of data to be thrown at a problem and the back-propagation of the 
networks then allows careful fine-tuning of weights which determine how 
relevant different pieces of information are to the prediction.  The networks 
used here are humongous and a detailed look at the weights (if at all feasible) 
may point us in the right direction.


From: CCP4 bulletin board  On Behalf Of Nave, Colin 
(DLSLtd,RAL,LSCI)
Sent: December 4, 2020 9:14 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

The subject line for Isabel's email is very good.

I do have a question (more a request) for the more computer scientist oriented 
people. I think it is relevant for where this technology will be going. It 
comes from trying to understand whether problems addressed by Alpha are NP, NP 
hard, NP complete etc. My understanding is that the previous successes of Alpha 
were for complete information games such as Chess and Go. Both the rules and 
the present position were available to both sides. The folding problem might be 
in a different category. It would be nice if someone could explain the 
difference (if any) between Go and the protein folding problem perhaps using 
the NP type categories.

Colin



From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Isabel Garcia-Saez
Sent: 03 December 2020 11:18
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

Dear all,

Just commenting that after the stunning performance of AlphaFold that uses AI 
from Google maybe some of us we could dedicate ourselves to the noble art of 
gardening, baking, doing Chinese Calligraphy, enjoying the clouds pass or 
everything together (just in case I have already prepared my subscription to 
Netflix).

https://www.nature.com/articles/d41586-020-03348-4

Well, I suppose that we still have the structures of complexes (at the moment). 
I am wondering how the labs will have access to this technology in the future 
(would it be for free coming from the company DeepMind - Google?). It seems 
that they have already published some code. Well, exciting times.

Cheers,

Isabel


Isabel Garcia-Saez  PhD
Institut de Biologie Structurale
Viral Infection and Cancer Group (VIC)-Cell Division Team
71, Avenue des Martyrs
CS 10090
38044 Grenoble Cedex 9
France
Tel.: 00 33 (0) 457 42 86 15
e-mail: isabel.gar...@ibs.fr
FAX: 00 33 (0) 476 50 18 90
http://www.ibs.fr/




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Re: [ccp4bb] External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

[Michel Fodje]

In Ascoidea asiatica where CUG is translated as both Leu and Ser.
Mühlhausen S., Schmitt H.D., Pan K.T., Plessmann U., Urlaub H., Hurst L.D., 
Kollmar M. Endogenous stochastic decoding of the CUG codon by competing Ser- 
and Leu-tRNAs in Ascoidea asiatica. Curr. Biol. 2018; 28:2046-2057.

Perhaps, this is not a mutation at all but points to the origin of this virus.

/Michel.

From: CCP4 bulletin board  On Behalf Of Carter, Charlie
Sent: March 21, 2020 7:48 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19




Begin forwarded message:

From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>>
Subject: Re: [ccp4bb] CCP4BB vs COVID19
Date: March 21, 2020 at 8:07:53 AM EDT
To: James Holton mailto:jmhol...@lbl.gov>>

Brilliant post, James. Thanks so much!

I also find what you describe interesting, because of work done by a colleague, 
Manuel Santos, who showed that in fungi,

The CUG codon is decoded in vivo as serine and not leucine in Candida albicans
MAS Santos, MF Tuite
Nucleic acids research 23 (9), 1481-1486

I may be hallucinating, but I recall something to the effect that this genetic 
ambiguity also related to the ability of Candida to adapt to life in high 
concentrations of SDS.

Charlie

On Mar 20, 2020, at 6:59 PM, James Holton 
mailto:jmhol...@lbl.gov>> wrote:

You might think that as a structural biologist you won't be able to do much 
about COVID-19 anytime soon, but that is not true.  Yes, real-world 
therapeutics and vaccines take time, but we have already seen just how fast we 
can get started.  There are 21 PDBs already and some even have bound ligands.  
Good job Frank et al. BTW!  And my personal thanks to all of you out there who 
are already hard at work on this.

I believe this forum is an ideal place to share information and ideas on the 
structural biology of SARS-CoV-2 as we move forward. It's a big virus, but 
there are not that many proteins in it.  If all of us independently do the same 
bioinformatics and literature searches and end up trying exactly the same thing 
in every lab all over the world, then that would be more than unfortunate.  To 
that end, I am personally interested on ORF8 for reasons I will go into below.  
Has anyone tried to solve it yet?  What happened?  Didn't express? Bad 
diffraction?  What?  Do tell.

Some of us, as you may have heard, are stuck at home, our beamlines and labs 
dark while we shelter-in-place.  That doesn't mean our hands are tied.  We are 
still allowed to think. The fraction of the human race that has a snowball's 
chance in Hades of figuring out this bug is very very small.  Structure may be 
your main skill set, but you are still a biologist.  Do you know how to run a 
PCR machine?  Do you know how to pipette?  You might think that anybody can do 
it, but that is really not the case. Ever trained a new student on sterile 
technique?  How many days did that take?  Now remember that your student was no 
dummy and already studying biology.  Everyone reading this will make an 
excellent volenteer at the very least.  I'm not saying this to belittle the 
average human, only to say that we scientists, moving in the circles we do, 
often forget that we have uncommon capabilities.

For example, I also believe we can be useful in assay development. The void 
left by the dearth and delay of test results has been filled with fear, and 
that is a big problem.  The tests, as defined, are straightforward, but also 
extremely regimented like any good laboratory protocol should be.  The US CDC's 
instructions for academic labs are here:
https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
My question is: how can this test be made faster, using more commonplace 
supplies, in high-throughput mode and still valid?  Not just for clinical but 
for academic use?  I think more than a few people on this list could be 
regarded as experts in making a complex biochemical task faster, more 
efficient, high-throughput and nonetheless valid.  Yes, there are other people 
who do virus testing for a living, but right now they are all rather busy.  
Maybe if we put our minds to it we can help?

As for why ORF8.  I am basing my interest on the bioinformatics done in this 
article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for "T8517C" and you 
will find what I'm talking about.  The authors found two "types" of SARS-CoV-2. 
 They call them "S" and "L" because the only conserved amino acid change 
involved is S84L in ORF8.  The "S" type is believed to be the ancestor of "L".  
What is interesting is how tightly linked this mutation is to a silent mutation 
on the other end of the genome: the "L" type has a faster codon for Ser in 
ORF1.  Such tight coupling (r^2=0.945) means there must be significant 
selective pressure preventing both of these mutations occurring in the same 
virus at the same time.  That, I believe, is interesting.  Espeically since 
they are so far apart I expect this selective pressure might work in 

Re: [ccp4bb] A polite reminder to xia2 users

[Michel Fodje]

Hardware: Say I do a lot of screening on Beamline A (many hours used), collect 
a low resolution anomalous dataset on Beamline B, which helps me to solve the 
structure, then I collect a high resolution native dataset on Beamline C (in 
just a few minutes) for refinement and model building. Many people deposit just 
the data from C and acknowledge beamline C and perhaps B. Beamline A is almost 
always ignored.  I think all three beamlines contributed directly to the paper 
should be cited. There is no other way for the beamline A to assess its impact 
if it isn't cited.

Software: How many of you have ever cited FFTW, CBFLib, etc when those 
libraries were used behind the scenes by the other programs?  Should you be 
expected to cite them? How far down the dependency chain should that citation 
list go? I don't think the license should be the determining factor on what 
gets cited or not. It is a nice suggestion for pipelines to generate a list of 
relevant citations for the given dataset which includes references to all the 
software used.  But if the pipeline itself was published, and cites all those 
packages, users should not need to cite the individual packages again.

We certainly do not want a situation in which the list of references is 10x 
longer than the rest of the paper. Just like we do not include all the 
citations from the papers we cite, we shouldn't be expecting authors to include 
all the software/libraries used vicariously. Are we perhaps abusing the 
citation system as a way of "tipping" the hardware/software people? We need a 
better way of measuring impact, and then using impact for funding applications 
rather than citations.

If I cite XIA2, there should be a mechanism for XDS or MOSFLM to see an 
increase in their impact due to the XIA2 citations -- because it's 2015. I do 
not think it is a good idea to *politely* force users of XIA2 to cite all the 
other programs as well.

http://article-level-metrics.plos.org/


/Michel


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Graeme 
Winter
Sent: November 6, 2015 3:42 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] A polite reminder to xia2 users

Dear All,

Slightly ignorant and certainly oblique question perhaps, but are there still 
journals out there which limit the number of references allowed? This used to 
be a “reason” people would use for not properly citing all of the resources 
they used in arriving at the results included in the manuscript. In real life, 
particularly with the move to electronic publication, there should be no 
excuses or reasons for incomplete citations or citations in supplementary 
materials (I feel).

I guess it should be possible for e.g. processing software to identify the 
beamline from the correctly populated image header (*) and make for the user’s 
convenience some kind of mmCIF file (perhaps) with the appropriate citations 
for beamline and software for *that* data set – though this would require some 
infrastructure to exist in a public place (PDB?) where this was stored so the 
software developers could access it to get the right info. This sounds like 
something we were all discussing in 2006 ☹

Also, I guess people should know where their data came from & be capable of 
correctly acknowledging this, but it sounds like this is not the case perhaps? 
*should* pipeline developers be doing more here?

Cheerio Graeme

=

(*) no a given I know…

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Marjolein 
Thunnissen
Sent: 06 November 2015 09:12
To: ccp4bb
Subject: Re: [ccp4bb] A polite reminder to xia2 users

Hi All,

This is slightly OT for the list as such but it is of interest of the current 
thread.

I would like to argue that just as important it is to reference to the software 
in an adequate way, it is also important to give due to the hardware, i.e. the 
beam lines on which most of the data is collected. Most beamlines have now 
publications that describe them, it is very important to us that these will be 
referenced to. This will make it easier for us in the long end to keep them in 
the best state possible so that you can obtain the best data possible.

best regards

Marjolein Thunnissen

[cid:image001.png@01D11875.0BBFE260]




Dr. Marjolein Thunnissen
Science Coordinator Structural Biology
Chair Special Interest Group 1 (MX) ECA

MAX IV Laboratory
Lund University
P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Ole Römers väg 1, 223 63 Lund
Telephone: +46 766 32 04 17
www.maxlab.lu.se


On 05 Nov 2015, at 20:32, Tim Gruene 
> wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Jacob,

I tend to follow the authors' suggestion. When you start refmac, even without 
any options, it says:
Main reference
  "REFMAC5 for the refinement of macromolecular crystal structures:"
  G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, 

Re: [ccp4bb] Puzzling Structure

[Michel Fodje]

Just to round up this topic, a bug report was submitted to PDBe concerning 
entry 2wlv and the PDB has how responded acknowledging the problem. An updated 
entry will be available in one week.

As pointed out by Savvas, it is very likely the CRYST1 record was manually 
edited prior to deposition resulting in the wrong spacegroup being parsed in by 
AutoDep and subsequent processing moving the waters around in the wrong space 
group. Since there is no logical reason for the authors to do this, it was 
probably inadvertent. I imagine somebody accidentally deleted a space between P 
21 21 2 and 18 and tried to fix it by adding it back, between 1 and 8.  

/Michel

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Edward A. Berry
Sent: April-14-13 9:59 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Puzzling Structure

Robbie Joosten wrote:
 Hi Martyn,

 I think the question is where the error was made - seeing the
 uploaded file would clear this up. But it seems unlikely to me that
 the depositor saw a huge R factor discrepancy at the end of refinement
and just blithely uploaded it.
 So scenario 3 :-
 PDB : we cannot reproduce your R factor with our programs Depositor :
 that's your problem mate - it was fine when it left me...up to you to sort
it...
 Which seems a sort of reasonable attitude to me.

 Not quite, the depositor has to give, i.e. type, the space group (example
depositions: https://www.ebi.ac.uk/pdbe-
xdep/autodep/AutoDep?param=QovCsvhNv06Mpnr%2BvIkqqfuqeeBd8leFN
AVymZgS%2Fe7mULyfrCaTMN8jsyaGZUTyUDQyN3gMF3o%3D). Don't ask me
why, because it is clearly a source of error.


In my experience with RCSB autodep2, assuming the information was in the
uploaded pdb file, this information is already pre-filled and the depositor 
just
glances over to see it is correct. A missing or extra (1) might not be 
noticed.
So perhaps it is a parsing error, perhaps related to the different ways the
space group is represented on the CRYST1 card, and the different stringency
of different programs in interpreting the CRYST1 card.

But the validation report is included with the approval request letter, and
major discrepancies are noted in the text of the validation letter in case the
depositor is too busy to actually read the validation report.
So if the depositor read more than the first line or two of the letter he 
should
have known there was a problem.

Then there is the 2-week default release policy:

  No major issues were raised during data processing. A summary of some of
the key annotations
  in your entry is shown below. Please verify that these are correct. If we do
not hear from
  you within two weeks, we will consider this entry to have been approved by
you. The entry
  will then be released according to the release/hold instructions you have
provided.

If this 2-week default release is the rule even when there are issues, the
depositor may have put it aside to find the problem when time was available,
and waited too long and let the default release kick in.

eab

[ccp4bb] Puzzling Structure

[Michel Fodje]

Has anyone else noticed a problem with the structure  of the N-terminal capsid 
domain of HIV-2  PDB 2wlv.
Load it up to in coot and navigate to residue B118.

/Michel.

Re: [ccp4bb] Puzzling Structure

[Michel Fodje]

By the way, you will need to show symmetry atoms to see the problem.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Michel Fodje
Sent: April-12-13 1:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Puzzling Structure

Has anyone else noticed a problem with the structure  of the N-terminal
capsid domain of HIV-2  PDB 2wlv.

Load it up to in coot and navigate to residue B118.



/Michel.

Re: [ccp4bb] very informative - Trends in Data Fabrication

[Michel Fodje]

Very interesting 

Response to Detection and analysis of unusual features in the structural model 
and structure-factor data of a birch pollen allergen
doi:10.1107/S1744309112008433

a quote from the response:

Author Schwarzenbacher admits to the allegations of data fabrication and 
deeply apologizes to the co-authors and the scientific community for all the 
problems this has caused 

.

Note added in proof: subsequent to the acceptance of this article for 
publication, author Schwarzenbacher withdrew his admission of the allegations.






From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp 
(Hofkristallrat a.D.) [hofkristall...@gmail.com]
Sent: Saturday, March 31, 2012 12:42 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication

This is an unresolved problem, and no real satisfactory solution exists, 
because the underlying reasons for zero occupancy can be different.
For people who understand this and look at electron density, it is not a 
problem. For users who rely on some graphics program
displaying only atom coordinates, it can be. The same holds for manipulation of 
B-factors, ‘trading’ high B-factors against reduced occupancy,
and other (almost always purely cosmetic but still confusing or inconsistent) 
practices.

Best, BR
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nian Huang
Sent: Saturday, March 31, 2012 11:29 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication

I don't model zero occupancy in my model. But can't the refinement programs 
just treat those atoms with zero occupancy as missing atoms?

Nian Huang
On Sat, Mar 31, 2012 at 10:26 AM, Bosch, Juergen 
jubo...@jhsph.edumailto:jubo...@jhsph.edu wrote:
really fascinating, bringing back the discussion for a repository for your 
collected frames.

Jürgen


Acta Cryst. (2012). F68, 366-376
doi:10.1107/S1744309112008421http://dx.doi.org/10.1107/S1744309112008421

Detection and analysis of unusual features in the structural model and 
structure-factor data of a birch pollen allergen
B. 
Rupphttp://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Rupp,%20B.

Abstract: Physically improbable features in the model of the birch pollen 
structure Bet v 1d (PDB entry 
3k78http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78) are faithfully reproduced 
in electron density generated with the deposited structure factors, but these 
structure factors themselves exhibit properties that are characteristic of data 
calculated from a simple model and are inconsistent with the data and error 
model obtained through experimental measurements. The refinement of the 
3k78http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78model against these 
structure factors leads to an isomorphous structure different from the 
deposited model with an implausibly small R value (0.019). The abnormal 
refinement is compared with normal refinement of an isomorphous variant 
structure of Bet v 1l (PDB entry 
1fm4http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?1fm4). A variety of analytical 
tools, including the application of Diederichs plots, R plots and bulk-solvent 
analysis are discussed as promising aids in validation. The examination of the 
Bet v 1d structure also cautions against the practice of indicating poorly 
defined protein chain residues through zero occupancies. The recommendation to 
preserve diffraction images is amplified.
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742tel:%2B1-410-614-4742
Lab:  +1-410-614-4894tel:%2B1-410-614-4894
Fax:  +1-410-955-2926tel:%2B1-410-955-2926
http://web.mac.com/bosch_lab/

Re: [ccp4bb] tcl tk RHEL 6.2

[Michel Fodje]

Your 64bit system does not have the 32bit LSB libraries installed.  Install the 
packages redhat-lsb.i686 and redhat-lsb-graphics.i686 using yum as follows:

yum install redhat-lsb.i686 redhat-lsb-graphics.i686

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Kenneth A. Satyshur
Sent: February-06-12 10:17 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] tcl tk RHEL 6.2

I just installed ccp4 6.2.0 on a new RHEL6.2 system and I get this error.
Anyone know how to fix this? I installed tcl and tk into the system but ccp4
seems to want to use its own version.

[xray@paprika ~/Desktop]$ /home/xray/ccp4/ccp4-6.2.0/ccp4-
6.2.0/bin/ccp4i: /home/xray/ccp4/ccp4-6.2.0/tcltkplusplus/bin/wish: /lib/ld-
linux.so.2: bad ELF interpreter: No such file or directory
/home/xray/ccp4/ccp4-6.2.0/ccp4-6.2.0/bin/ccp4i: line 4:
/home/xray/ccp4/ccp4-6.2.0/tcltkplusplus/bin/wish: Success

thanks
kas


--
Kenneth A. Satyshur, M.S.,Ph.D.
Associate Scientist
University of Wisconsin
Madison, Wisconsin 53706
608-215-5207

Re: [ccp4bb] raw data deposition

[Michel Fodje]

Every dataset costs money to produce. Is it more cost effective to expect that 
those wishing to use the data repeat the expenditures by repeating the 
experiments?  To exaggerate the point, imagine a world without published 
research articles, would it be more expensive to do science or less? We should 
not simply dismiss an idea just because we think today that 640K is more 
memory than anyone will ever need


 On Oct 27, 2011, at 3:47 PM, Adrian Goldman wrote:
 2) I agree with Susan.  In a time of limited funding, is this the most 
 important use of money?

Re: [ccp4bb] linux flavors

[Michel Fodje]

The preferred method to get NVIDIA drivers for Fedora is to use the RPM Fusion 
repositories (http://rpmfusion.org/Howto/nVidia). 
Drivers installed this way will be automatically updated with the kernel as 
required.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David 
Schuller
Sent: February-22-11 9:30 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] linux flavors

Installation of the proprietary nVidia driver is easier with Fedora 14; 
the hassles with removing the Nouveau driver have been greatly simplified.

We use Fedora, although I certainly cannot claim that it has been 
problem free. It does seem better suited for centrally-managed systems, 
as compared with the most frequently mentioned alternative, Ubuntu, 
which is perhaps more suitable for a single owner-operator environment.


On 02/22/11 10:16, David Roberts wrote:
 Hello all,

 Quick question on linux varieties.  For years (and years) I have used
 fedora (after Ultrix of course).  In fact, most of my computers are
 running FC7 (that long ago), it's very stable and works fine.  However,
 since it is no longer supported, I'm toying with upgrading.

 I upgraded one machine to FC13.  However, this nouveau driver thing is
 killing me, and getting my nvidia drivers installed is hopeless (I have
 followed every thread on this and I simply give up - it's not worth
 it).  With a Zalman monitor it doesn't matter - nouveau works fine and
 my stereo is good - so I don't really care (or do I).

 The question is this - what flavors of linux out there are simplest to
 install - work instantly with various hardwares, and run stereo
 seamlessly (either Zalman stereo or hardware stereo with an emitter).
 For zalman anything works - which is why I'm going that way - but I
 still need hardware stereo on a few machines.  So, for hardware, I need
 my nvidia drivers to install easily.

 I'm downloading ubuntu - is that a good choice?  Can I run different
 flavors of linux with nfs and share drives in a local network (so one
 has fc7, one has fc13, and another has ubuntu)?

 Thanks

 Dave


-- 
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu

Re: [ccp4bb] JAC (2010), 43,1242-1249

[Michel Fodje]

It is available online at

http://www.stat.ucla.edu/history/essay.pdf



Michel Fodje
Staff Scientist
Canadian Macromolecular Crystallography Facility
Canadian Light Source
Tel: 306 657 3758



From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jürgen 
Bosch
Sent: October-18-10 8:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] JAC (2010), 43,1242-1249

Lesenswert !
Worth reading !
http://journals.iucr.org/j/issues/2010/05/02/issconts.html

Could somebody send me the pdf from Bayes 1763 ?

Jürgen
-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.mac.com/bosch_lab/http://web.me.com/bosch_lab/

Re: [ccp4bb] Help with Bayes's theorem

[Michel Fodje]

The opinionator piece is misleading about the meaning of probability, 
especially as it implies that you could reformulate every problem into one 
about frequencies.  As was pointed out a long time ago by Harold Jeffreys and 
repeated by Ed Jaynes,

The essence of the present theory is that no probability, direct, prior, or 
posterior, is simply a frequency -- H. Jeffreys (1939)  

... a probability is a theoretical construct, on the epistemological level, 
which we
assign in order to represent a state of knowledge, or that we calculate from 
other probabilities according to the rules of probability theory. A frequency 
is a property of the real world, on the ontological level, that we measure or 
estimate. So for us, probability theory is not an Oracle telling how the world 
must be; it is a mathematical tool for organizing, and ensuring the consistency 
of, our own reasoning. -- E.T. Jaynes[1]

There are lots of simple problems you will not be able to reason correctly if 
you assume a probability is a frequency (e.g. Bernoulli's Urn). Not every event 
can be repeated a large number of times such that a frequency is obtained. This 
difficulty has often pushed frequentists, to be confused between the result 
of measuring one thing many times and the result of measuring many things one 
time.  For example, one could ask, by what basis do you draw a conclusion from 
the few that were surveyed to the millions that were not?  

Monitoring 1000 women and finding that 0.8% of them get breast cancer, tells 
you nothing about the health of the patient standing in front of you! Unless 
you have some other prior information linking the one to the one-thousand. What 
is really relevant would be to measure the one patient many times, but this is 
not always possible.

I find that Jaynes book on Probability Theory[2] is THE definitive guide on how 
to teach it. For the less mathematically inclined, Chapter 1, which is freely 
available[3] online as a PDF is very readable and eye-opening.

[1] Jaynes, E. T., 1989, `Clearing up Mysteries - The Original Goal, ' in 
Maximum-Entropy and Bayesian Methods, J. Skilling (ed.), Kluwer, Dordrecht, p. 
1;

[2] http://www.amazon.com/Probability-Theory-Logic-Science-Vol/dp/0521592712

[3] http://bayes.wustl.edu/etj/prob/book.pdf


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Colin Nave
Sent: April-27-10 4:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Help with Bayes's theorem

 
This is quite a good one as well
http://www.inference.phy.cam.ac.uk/mackay/pope.html

I recall the pope analysis followed on from a Nature article covering
the O J Simpson example (also covered in the NY times link).

Sean Eddy who is an author on the above link wrote what I regard as an
excellent intro to Bayesian statistics
ftp://selab.janelia.org/pub/publications/Eddy-ATG3/Eddy-ATG3-reprint.pdf
Colin

 -Original Message-
 From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On 
 Behalf Of Jim Pflugrath
 Sent: 26 April 2010 20:30
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] Help with Bayes's theorem
 
 I thought some of you would enjoy a little conditional 
 probability discussion found in the NY Times today, since 
 this is a big part of crystallography nowadays.  I'm always 
 on the lookout for good ways to teach Bayes's theorem.
 
 http://opinionator.blogs.nytimes.com/2010/04/25/chances-are/
 
 Jim 
 

Re: [ccp4bb] Crystallographic computing platform recommendations?

[Michel Fodje]

On Tue, 2008-11-18 at 09:40 -0500, James M. Vergis wrote:

 2) Graphics Cards:
 I like the Nvidia cards since they provide linux drivers.  ATI also does
 now.  I would say the only thing I don't like about them is when you do a
 kernel update you have to remake the driver.

I would just add that for those using Fedora, you can avoid having to
remake the driver by using the RPMFusion repositories to install the
Nvidia drivers. This way updating the kernel automatically installs the
corresponding Nvidia kernel module.  The same applies to AMD/ATI
drivers.

[ccp4bb] Beamtime available at the CLS - invitation for requests

[Michel Fodje]

Dear Crystallographers,

Beamline 08ID-1 (CMCF1) at the Canadian Light Source (CLS) is accepting
user beamtime requests for the period November 6 - December 18, 2008.
Detailed information about the beamline can be found on our web pages
http://www.lightsource.ca/experimental/cmcf.php ,
http://ex.lightsource.ca/cmcf/index.htm.

Currently, new users can gain direct access to CMCF through a Letter of
Intent (LOI). To become a new user,
- Please login to https://user.lightsource.ca and click on Complete New
User Registration Now. Upon completion you will be sent your username
and password. 
- Upon receipt of your username, please complete the on-line Letter of
Intent proposal, available at https://user.lightsource.ca 
- Select My Proposals; Select Create Other Proposal, General tab:
select Letter of Intent for Type of Application Beamline Tab:
select 08ID-1 (CMCF)
Please contact the beamline staff if you need assistance in the LOI
submission. 

If you have a current active LOI proposal with CLS, please inform us on
the number of shifts you are requesting and the type of experiment you
are planning. We will contact you shortly afterwards with a confirmation
of your shifts. 

Shifts will be assigned on a first-come, first-served basis. Please note
however, that CMCF will be switching over to a peer-reviewed proposal
system in the new year. 



.
Michel N. Fodje
Staff Scientist, Experimental Facilities
Canadian Light Source, Inc.
University of Saskatchewan
Phone: (306) 657-3758
Fax:   (306) 657-3535 

Re: [ccp4bb] XDS and overlaps

[Michel Fodje]

I should add that inspecting the average three-dimensional profiles in
INTEGRATE.LP could give you an indication if you have overlaps or not.
The profiles look like slices through a 3D  unimodal gaussian. If you
have overlaps it will be revealed by bi-/multi-modal features. However,
these are average profiles so a small number of overlaps may not be
apparent. 

/Michel


On Wed, 2008-02-20 at 14:54 -0800, Engin Ozkan wrote:

 Hi everyone,
 
 I have been recently relying on XDS quite a bit, but at the same time 
 worrying about how XDS treats overlaps.  We had one dataset that both 
 HKL2000 and Mosflm would show to have severe overlaps, as expected due 
 to unit cell parameters and the unfortunate crystal orientation in the 
 loop. We always ended up with completeness percentages in the 70's.
 
 XDS can find the same lattice, index and scale the data, but yields a 
 100% complete mtz (and a nice structure). Without the HKL/Mosflm-like 
 GUI, it is difficult to assess the fate of the overlapped observations 
 in XDS. What I could see with VIEW was that some observations were being 
 divided into several ovals, probably different reflections, but I'm not 
 very certain.
 
 So, the basic question is, how does XDS treat overlaps?  I could not 
 find in the documentation an answer to this question; the single mention 
 of overlaps I could find tells me that XDS can recognize overlaps, but 
 does not tell me if it rejects them, or divvies them up into separate 
 reflections, and if that is the case, how does it divide them, and how 
 reliable is that? Depending on how it divides the overlaps, could that 
 affect commonly-used intensity stats and distributions?
 
 Thanks,
 
 Engin

Re: [ccp4bb] Questions about diffraction

[Michel Fodje]

  1. In every description of Braggs' law I've seen, the in-coming waves
  have to be in phase. Why is that? Given that the sources used for
  diffraction studies are mostly non-coherent.
 
 Think of Bragg's Law as explaining what happens to a single photon
 that is probabilistically scattered by every atom in the lattice.
 It's perfectly coherent with itself.
Why does the photon not diffract at all angles then, since one 'part' of
the photon will never have a different phase from another 'part'? If you
are correct that it is a single photon diffracting, it would suggest
that at some point the photon is in-coherent with itself thus the need
to have a diffraction condition for specific angles.

It would make more sense to me in such a case, if we interpreted Braggs'
law as the condition under which the photon keeps it's 'internal
coherence but instead we talk of constructive and destructive
interference! 

 This idea should be no stranger than textbook illustrations of the
 result of sending a single particle through a narrow slit or pinhole.
 The interference effects follow the expected predictions even for
 illumination by one particle at a time.

The mathematics works but doesn't necessarily mean the current
interpretation of the mathematics has any resemblance to what actually
happens in reality. 

Re: [ccp4bb] Questions about diffraction

[Michel Fodje]

 For every direction where there is destructive interference and a
 loss of energy there is a direction where there is constructive
 interference that piles up energy.  If you integrate over all
directions
 energy is conserved.

For the total integrated energy to be conserved, energy will have to be
created in certain directions to compensate for the loss in other
directions. So in a direction in which the condition is met, the total
will have to be more than the sum of the waves in that direction.

How about considering the possibility that all photons coming into the
sample are diffracted -- just in different directions. So that what is
happening is not constructive and destructive interference but a kind
sorting of the photons based on a certain property of the photons, maybe
the phase.

Re: [ccp4bb] Questions about diffraction

[Michel Fodje]

 You are just using the coherent fraction of the beam.
My point is that Braggs' law as currently understood does not preclude
the diffraction from waves which were non-coherent before hitting the
sample

 It is not clear at all how you arrive to that condition. By definition, if
 two waves are non coherent, you cannot define a phase difference. The
 phase difference is continuosly changing at random with non coherent waves.
if the phase difference between two waves is y, the extra distance the
second wave has to travel to again be in phase is  y*lambda/2pi
if this distance is the same as the 2dsin(theta), the diffraction
condition will also be met.

My understanding is that coherence has to do with the phase not the
wavelength. Only when the wavelengths are also different will the phase
difference be changing continuously. No?

   You do not annihilate energy with interferences, you just spread it
 differently. Apart for conservation of energy, Thermodynamics is seldom
 involved in these considerations.
My point is that destructive interference implies that energy is
destroyed which does not make sense. If as you say the energy is simply
spread differently, what would be the mechanism/geometry of this
spreading? 


 A complete lack of coherence leads simply to adding intensities of the two
 waves.

On the contrary. complete lack of coherence leads to destructive
interference. No? Perfect coherence leads to the amplitudes adding up.

Re: [ccp4bb] Questions about diffraction

[Michel Fodje]

Would it be taking it too far to suggest that one could go all the way
and consider that each electron diffracts not as groups in a plane but
as individual electrons and a photon impinging on an electron with with
a specific phase will be diffracted in a specific direction. However the
lattice arrangement of the electrons will statistically accumulate
photons which impinged on electrons on a specific family of planes in
one direction at the detector. Such that the crystal is a phase sorter.

In which case diffraction is not based on constructive or destructive
interference but on conservation of some property of the photon, such as
angular momentum? IANAM either.

 
On Fri, 2007-08-24 at 15:36 -0700, James Stroud wrote:
 Without resorting to a circular argument? You are asking too much.
 
 However, this probability distribution is perfectly described by 
 considering a component wave model wherein coherence of the component 
 waves correlates with peaks in the probability distribution--i.e. 
 Bragg's Law.
 
 IANAM (I am not a mathematician), but, if pressed, I would posit that 
 one could decompose the fun description just a little bit and consider 
 the lattice not as *groups* of reflecting planes, but as individual 
 planes. In such a case, each single reflecting plane would contribute a 
 probability distribution with an angular dependence. The total 
 probability distribution would then be the sum of the probability 
 distributions for every plane in the lattice.
 
 Your next question might be, what's the probability distribution for a 
 single plane. Well, I would imagine that it has a maximum where the 
 angle of incidence equals the angle of reflection and that the phase of 
 a component probability distributions is spatially (i.e. angularly) 
 directly related to the phase of the originating photon.
 
 The sum distribution of the reflected photon takes into account the 
 angular phase dependence of its components and so one gets positive and 
 negative interference between component distributions.
 
 James
 
 Jacob Keller wrote:
  Yes, but why should the directions of diffraction conditions be most 
  probable (one of your premises)?
 
  ==Original message text===
  On Fri, 24 Aug 2007 4:54:53 pm CDT James Stroud wrote:
  
  Here's a fun way to think of it:
  
  A photon hits a crystal and will diffract off in a certain direction 
  with the same energy as the original photon. The direction is subject to 
  a probability distribution based on the lattice, with angles at the 
  diffraction conditions being most likely and the broadness of the peaks 
  in the distribution arising from imperfections in the lattice. The 
  photon propagates as this probability distribution and then is forced to 
  select from the distribution because we stuck a detector up. The 
  diffraction pattern we observe is the sum of many such photons 
  interacting with the crystal.
 
 

Re: [ccp4bb] The CCP4 license is ambiguous

[Michel Fodje]

On Tue, 2007-07-03 at 10:54 -0700, Ethan Merritt wrote:

 Not at all.  Consider all those users of GPL programs running on Windows.
 The developers of cygwin, mplayer, etc have no right to  redistribute
 Windows itself.

Programs running under windows are not derivative works of Windows
otherwise software developers will require a license from Microsoft to
develop windows software. Simply linking to system libraries does not
make a program a derivative as far as the GPL is concerned. The only
thing the GPL requires is that the users of the software receive the
same rights to the software that you received

 They do have the same rights.  They can use it, modify it, and
 redistribute it.  They may or may not be permitted to distribute
 3rd party libraries with it, but that was true of the original
 distributor also.   

The specific rights that must be transferred with the software are:
1 -  The freedom to run the program, for any purpose (freedom 0)
2 -  The freedom to study how the program works, and adapt it to your
needs (freedom 1). Access to the source code is a precondition for
this. 
3 -  The freedom to redistribute copies so you can help your neighbor
(freedom 2). 
4 - The freedom to improve the program, and release your improvements to
the public, so that the whole community benefits (freedom 3). Access to
the source code is a precondition for this.

If you distribute software that, in whole or in part does not convey all
those freedoms, it is a violation of the GPL if you use GPL code in it.
Unless of course you are the original author of all the GPL code, in
which case it does not make sense to distribute it under the GPL.
Distributing sofware under the GPL license implies that the recipients
receive all those rights.

 Well, there is of course one respect in which the rights are different.
 The original author retains the copyright itself, and consequently
 the right to issue other non-exclusive licenses.  The recipient
 of GPL code does not obtain a right to re-license.

The GPL (CopyLeft)  is only concerned about the 4 freedoms (rights) of
users mentioned above. The rights of the author are taken care of by
copyright law.

/Michel

Re: [ccp4bb] The CCP4 license is ambiguous

[Michel Fodje]

On Tue, 2007-07-03 at 12:34 -0700, Ethan Merritt wrote:
 Yes. That is a more complete statement of rights under the GPL.
 Please note, however, that the source code to which you are
 guaranteed access is the source code to the GPL-ed program itself,
 not to pieces of the operating environment it runs in.
And what do you mean by 'operating environment'?  In my own
understanding, the CCP4 libraries are not an 'operating environment'.
Linux/Windows/OSX and compiler run-time libraries are operating
environments. If you distribute the program to Linux/Windows users, you
don't need to distribute Linux to them for your program to be useful.
But if you don't distribute CCP4 libraries with your program, the
program is not useful.

 This is an overstatement, or could be mis-read as an overstatement.
 You can distribute a mixture of GPL and non-GPL code together.
Yes you can distribute GPL programs as part of COLLECTIVE works which
also include non-GPL compatible programs. But the terms you apply over
the whole of the collective work must be compatible with the GPL. The
GPL says the following:

These requirements apply to the modified work as a whole. If
identifiable sections of that work are not derived from the
Program, and can be reasonably considered independent and
separate works in themselves, then this License, and its terms,
do not apply to those sections when you distribute them as
SEPARATE WORKS. But when you distribute the same sections as
part of a whole which is a work based on the Program, the
distribution of the whole must be on the terms of this License,
whose permissions for other licensees extend to the entire
whole, and thus to each and every part regardless of who wrote
it.

Thus, it is not the intent of this section to claim rights or
contest your rights to work written entirely by you; rather, the
intent is to exercise the right to control the distribution of
derivative or collective works based on the Program.

In addition, mere aggregation of another work not based on the
Program with the Program (or with a work based on the Program)
on a volume of a storage or distribution medium does not bring
the other work under the scope of this License.

Sounds clear to me.

/Michel

Re: [ccp4bb] Highest shell standards

[Michel Fodje]

You are probably referring to the following works:

Caliandro et al, Acta Cryst. D61 (2005) 556-565
and Caliandro et al, Acta Cryst. D61 (2005) 1080-1087

in which they used density modification to calculate phases for
unmeasured reflections, and used the phases to extend the resolution by
calculating rough estimates unmeasured amplitudes. Using this technique
they actually could improve the electron density.

If I'm not mistaken, George Sheldrick has implemented this Free Lunch
algorithm in SHELXE.

/Michel

On Fri, 2007-03-23 at 08:05 -0800, Edward Berry wrote:
 If instead you allow the missing F's
 to float, calculating them on each cycle from the previous map
 using the fillin option, someone has shown (don't have the
 reference handy at the moment) that the F's tend toward the true F's
 (in the case that they weren't really missing but omitted as part
 of the test).
 
 Ed