Re: [ccp4bb] Input from the community for panel session: Crystallography is Dead! Long Live Crystallography!

[Alexandre Ourjoumtsev]

Happy New Year to everybody ! Health and peace ! 

Hi, Nicholas, 

Actually, the title : “Crystallography is Dead. Long Live Crystallography!” 
made me laugh. As you can find in Wikipedia : 

[ https://en.wikipedia.org/wiki/The_king_is_dead,_long_live_the_king! | 
https://en.wikipedia.org/wiki/The_king_is_dead,_long_live_the_king! ] 

" The phrase "The king is dead, long live the king!" was first declared upon 
the death of King [ https://en.wikipedia.org/wiki/Charles_VI_of_France | 
Charles VI ] in 1422, proclaiming his son [ 
https://en.wikipedia.org/wiki/Charles_VII_of_France | Charles VII ] (shown 
above) king of France." 
It is well known (also as confirmed by Wikipedia), that the king dead (Charles 
VI in that case) was "known for his mental illness". 

In that sense, I would feel myself, say, uncomfortable joining crystallography 
to the category of "dead kings". 

Have a great meeting ! 

Sacha Urzhumtsev 

- Le 2 Jan 24, à 11:56, Nicholas Pearce 
<8ea5c90b8e5a-dmarc-requ...@jiscmail.ac.uk> a écrit : 

> Hello, and happy new year!

> Tomorrow evening, we will have a panel discussion at the CCP4 study weekend
> about the future of crystallography, called “Crystallography is Dead. Long 
> Live
> Crystallography!” [ [
> https://en.wikipedia.org/wiki/The_king_is_dead,_long_live_the_king |
> https://en.wikipedia.org/wiki/The_king_is_dead,_long_live_the_king ] ].

> Whether you’re attending the CCP4SW or not , we want to hear from the 
> community
> about your thoughts on the subject (see the blurb below), so that we can
> discuss things the community is most interested in!

> if you have a few minutes, please do fill in the form ( all questions are
> optional ): [ https://forms.office.com/e/3K5qSMNpYh |
> https://forms.office.com/e/3K5qSMNpYh ] .

> Thanks, and looking forward to seeing some of you very soon!

> Your friendly neighbourhood scientific organisation team,

> Nicholas Pearce, Helen Ginn, and Clemens Vonrhein

> Blurb:

> In this session, we will discuss the current state and the future of
> crystallographic experiments in the context of structural biology:

> * what are the unconfronted problems that the field still faces?
> * what problems are now essentially solved?
> * where should future method development be focussed?
> * what challenges are emerging from new experimental developments?
> * do new experiments provide new perspectives on old problems?

> Inevitably, this will include discussion of whether these challenges are 
> likely
> to be addressed by the application of recent advances in AI, and, with the
> continued developments in cryoEM, what is crystallography's role as a part of
> the structural biologist's toolbox?

> Panel Chair: Elspeth Garman
> Panel Members: Dave Brown, Arwen Pearson, Ashwin Chari
> Please submit questions for consideration during the panel discussion using 
> the
> form below! and we look forward to seeing you on 3rd Jan!
> Some of the questions are asked mischievously - you are welcome to have some 
> fun
> with your answers! All questions are optional!

> [ https://forms.office.com/e/3K5qSMNpYh | 
> https://forms.office.com/e/3K5qSMNpYh
> ]

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Re: [ccp4bb] quantifying electron density

[Alexandre Ourjoumtsev]

Dear Sriram, dear Jon, 

The sum of values of a map (always calculated at some finite resolution) is not 
the same as a sum of density values. 
In such maps, a contribution of each atom is a function oscillating with the 
distance to the atomic center. 
Even when the height of these ripples is relatively small, surprisingly, the 
sum (integral) of the map values converges very-very slowly (not like for a 
density itself!) with the radius at which you truncate you sum. See for example 
§3.2 and Figs. 3-4 in a our recent article in Acta Cryst D (2022), D78, 
1451-1468. 

So one should be very careful with interpretations of such formally calculated 
sums (again, even when you have F000, absolute scale etc). 

With best wishes, 

Sacha Urzhumtsev 

- Le 29 Juin 23, à 3:10, sriram raghavan  a écrit 
: 

> Dear Pavel,

> I came across an example of calculating "electron_sums_around_atom" in [
> https://github.com/cctbx/cctbx_project/blob/master/cctbx/examples/fft_map_electron_density_around_atom.py
> | cctbx ] . If we don't zero the F000 or if we normalize the density of the
> real-space map by the unit cell volume and the scattering factor of the unit
> cell (F000), we can obtain the value of the density and sum the values of the
> positions of the obtained grid points on the map. This approach will yield the
> electron density sum across the volume, correct?

> Additionally, there is a tool called [
> https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0236894 |
> PDB-EDA ] that performs a similar calculation but not on selected volume.

> Best regards,
> S. Sriram

> On Thu, Jun 29, 2023 at 4:03 AM Pavel Afonine < [ mailto:pafon...@gmail.com |
> pafon...@gmail.com ] > wrote:

>> Hi Jon,
>> not really the answer to your question but.. This may be very tricky to do
>> because what you look at is not an electron density map but its Fourier image
>> of finite resolution phased by crystal model (that has errors), plus
>> experimental errors, and missing F000 (which is not measured as part of your
>> diffraction experiment). So.. if such a software exists I'd be very cautious
>> interpreting the results you get from it!
>> Pavel

>> On Wed, Jun 28, 2023 at 9:16 AM Hughes, Jonathan < [
>> mailto:jon.hug...@bot3.bio.uni-giessen.de | 
>> jon.hug...@bot3.bio.uni-giessen.de
>> ] > wrote:

>>> hello everyone,
>>> is there software that can use an electron density map to quantify the 
>>> number of
>>> electrons in a selected volume somewhere in a protein?
>>> cheers
>>> jon

>>> --
>>> Professor Jon Hughes, BSc, PhD
>>> Department of Physics
>>> Free University of Berlin
>>> Arnimallee 14
>>> 14195 Berlin
>>> Germany
>>> mobile: (+49/0)1757929098
>>> email: [ mailto:lv...@posteo.de | lv...@posteo.de ]
>>> homepage:
>>> [ http://www.uni-giessen.de/fbz/fb08/Inst/pflphys |
>>> http://www.uni-giessen.de/fbz/fb08/Inst/pflphys ]
>>> Sent without the use of Apple products

>>> 

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> --
> With Regards

> S.Sriram

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Re: [ccp4bb] Updated pbd metrics and other small things

[Alexandre Ourjoumtsev]

Dear Rafael, 

if 15 years ago are better than 20, do you mean the article 

Urzhumtsev, Afonine & Adams (2009) 
" On the use of logarithmic scales for analysis of diffraction data ". Acta 
Cryst., D65 , 1283-1291 ? 

There are some numbers and also some analytic inter / extrapolations. 

With best wishes, 

Sacha Urzhumtsev 

- Le 2 Avr 23, à 14:38, Rafael Marques  a écrit 
: 

> Hi folks,

> I was wondering if someone has the link of that page where we could check the
> graphs “resolution vs R-value” and “r-value vs r-free”. The ones that I found
> are outdated by let’s say 20 years.

> Off topic. If you guys have some examples of diffraction patterns of Neutron 
> and
> Electron scattering, could you please send me? I am preparing a presentation
> and a single google search has been really misleading.

> Best wishes

> Rafael Marques da Silva

> PhD Student – Structural Biology

> University of Leicester

> Mestre em Física Biomolecular

> Universidade de São Paulo

> Bacharel em Ciências Biológicas

> Universidade Federal de São Carlos

> phone: +55 16 99766-0021

> "A sorte acompanha uma mente bem treinada"

> 



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Re: [ccp4bb] Future Diffraction Methods

[Alexandre Ourjoumtsev]

Hi, everybody, hi, Nukri and Pavel ! 

I fully agree with Pavel that, if the speakers are not exceptional, if they are 
(as usually) concentrated on their specific and narrow problems, 
cross-discipline meetings make us lost quite fast, they are annoying and 
useless. Richard Feynmann had the same experience, according to his books :-) 

At such meetings, people need to have a common point. However, it may be a 
point different from the SUBJECT of the research. This may be common TOOLS. And 
this indeed may lead to new ideas and results, maybe great ones. 

There is a many-years positive experience of such meetings in Pushchino in 
80ths (both of you know this place; for other readers of this post - this was 
indeed a great place !). Closer to our community, as I remember, Paul Adams and 
John Spence organized such kind of meetings about 20 years ago in US. I guess I 
know practical results from both these groups of meetings. Some 
Crystallographic Computing Schools also try to act a little bit "around the 
tools". 

Why do not we think specifically in THIS direction (which is actually what 
Nukri said, right? and somehow not so far from the previous GRC?) ? 
This is hard but feasible. But indeed hard :-( 

Best regards to everybody, 
and many thanks to James for raising the problem ! 

Sacha Urzhumtsev 

- Le 30 Jan 23, à 2:38, Nukri Sanishvili  a écrit : 

> Hi Pavel,
> Your description of the current status is exactly correct. And that's exactly
> what I am proposing to change or, more accurately, try to change. By seeking
> out and bringing together people who do complementary and collaborative work,
> so they can set an example for others.
> This, of course, isn't meant in place of more narrowly defined topical 
> meetings
> and conferences but to be in addition to those.
> James asked the community if we had new ideas and this is a new-ish approach I
> was suggesting.
> Don't get me wrong - I myself will happily continue my efforts in more 
> narrowly
> defined meetings.
> Best wishes,
> Nukri

> On Sun, Jan 29, 2023 at 6:44 PM Pavel Afonine < [ mailto:pafon...@gmail.com |
> pafon...@gmail.com ] > wrote:

>> Nukri,

>> IMO, the idea of cross-discipline meetings is great conceptually, at least 
>> for
>> reasons you pointed out, but utopical in practice. When we attend our
>> field-specific meetings we meet colleagues we know, we talk to collaborators
>> from the past or find new ones, we have things in common that we can talk 
>> about
>> to forge something new, we meet authors of papers we were excited to read, 
>> and
>> so on, and so on.
>> I once attended a meeting of some chemistry society, well, which is not too 
>> far
>> from what we are doing, really, as interpreting atomic models is essentially
>> putting your chemistry knowledge into production. And, at that meeting I felt
>> like I'm alone in a dark forest.
>> Now, I imagine, if you bring two (or more) groups of people to your meeting 
>> from
>> two different domains, well, I guess you will end up having two bubbles of
>> people clustered by their field of interest.

>> Same disclaimer goes here as yours -- no offence to any one, just thinking 
>> out
>> loud...

>> All the best!
>> Pavel

>> On Sun, Jan 29, 2023 at 6:09 AM Nukri Sanishvili < [ 
>> mailto:sannu...@gmail.com |
>> sannu...@gmail.com ] > wrote:

>>> Hi James,
>>> This meeting has indeed been one of the best ones by its format, content, 
>>> and
>>> atmosphere. Many thanks to all the organizers and attendees of the past.
>>> Nevertheless, it is not surprising that it was cancelled, given the trends 
>>> in
>>> structural biology research. Straightforward evolutionary pressure to adapt 
>>> or
>>> else...

>>> Throughout my career I was always amazed (dare I say, annoyed?) how 
>>> scientists
>>> from different fields, or even the same field but different methods, speak
>>> different languages. How little they understand each other, become 
>>> entrenched
>>> in their own methods and how much of the collaboration/cooperation
>>> opportunities are wasted.

>>> IMO, having a conference on "Complementary Methods in Structural Biology" 
>>> with
>>> the emphasis on complementarity and not on individual methods, would be a 
>>> great
>>> benefit in the long run. Hopefully it would give good examples to young
>>> researchers to help them develop a collaborative mindset.

>>> If I offended anyone, it was not intentional, I promise, and apologize in
>>> advance.
>>> Best wishes to all and best of luck to all who continue the effort for the
>>> benefit of the whole community.
>>> Nukri

>>> On Fri, Dec 16, 2022 at 4:11 PM James Holton < [ mailto:jmhol...@lbl.gov |
>>> jmhol...@lbl.gov ] > wrote:

 I want to thank everyone who attended the 2022 Gordon Research
 Conference and Gordon Research Seminar on Diffraction Methods in
 Structural Biology, as well as all those who contributed to these great
 gatherings in the past. It was an outstanding meeting if I do say so

Re: [ccp4bb] Validation of structure prediction

[Alexandre Ourjoumtsev]

Hi, James, hi, everybody, 

somehow relevant to your, James, comments : 

>>> MPscore=0.426∗ln(1+clashscore)+0.33∗ln(1+max(0,rota_out−1))+0.25∗ln(1+max(0,rama_iffy−2))+0.5
>>>  
>>> I.E. What if we could train an AI to predict Rfree by looking at the 
>>> coordinates? 

if somebody missed, there is a couple of papers talking about a single / triple 
measure(s) of model quality : 

Shao et al ., 2017, Structure, 25, 458 

Brzezinski et al ., 2020, The FEBS Journal, 287, 2685 

Best regards, 

Sacha Urzhumtsev 

- Le 13 Jan 22, à 19:40, James Holton  a écrit : 

> Agree with Pavel.

> Something I think worth adding is a reminder that the MolProbity score only
> looks at bad clashes, ramachandran and rotamer outliers.

> MPscore=0.426∗ln(1+clashscore)+0.33∗ln(1+max(0,rota_out−1))+0.25∗ln(1+max(0,rama_iffy−2))+0.5

> It pays no attention whatsoever to twisted peptide bonds, C-beta deviations,
> and, for that matter, bond lengths and bond angles. If you tweak your weights
> right you can get excellent MP scores, but horrible "geometry" in the
> traditional bonds-and-angles sense. The logic behind this kind of validation 
> is
> that normally nonbonds and torsions are much softer than bond and angle
> restraints and therefore fertile ground for detecting problems. Thus far, I am
> not aware of any "Grand Unified Score" that combines all geometric
> considerations, but perhaps it is time for one?

> Tristan's trivial solution aside, it is actually very hard to make all the
> "geometry" ideal for a real-world fold, and especially difficult to do without
> also screwing up the agreement with density (R factor). I would argue that if
> you don't have an R factor then you should get one, but I am interested in
> opinions about alternatives.

> I.E. What if we could train an AI to predict Rfree by looking at the
> coordinates?

> -James Holton
> MAD Scientist

> On 12/21/2021 9:25 AM, Pavel Afonine wrote:

>> Hi Reza,

>> If you think about it this way... Validation is making sure that the model 
>> makes
>> sense, data make sense and model-to-data fit make sense, then the answer to
>> your question is obvious: in your case you do not have experimental data (at
>> least in a way we used to think of it) and so then of these three validation
>> items you only have one, which, for example, means you don’t have to report
>> things like R-factors or completeness in high-resolution shell.

>> Really, the geometry of an alpha helix does not depend on how you determined 
>> it:
>> using X-rays or cryo-EM or something else! So, most (if not all) model
>> validation tools still apply.

>> Pavel

>> On Mon, Dec 20, 2021 at 8:10 AM Reza Khayat < [ mailto:rkha...@ccny.cuny.edu 
>> |
>> rkha...@ccny.cuny.edu ] > wrote:

>>> Hi,

>>> Can anyone suggest how to validate a predicted structure? Something similar 
>>> to
>>> wwPDB validation without the need for refinement statistics. I realize this 
>>> is
>>> a strange question given that the geometry of the model is anticipated to be
>>> fine if the structure was predicted by a server that minimizes the geometry 
>>> to
>>> improve its statistics. Nonetheless, the journal has asked me for such a
>>> report. Thanks.

>>> Best wishes,

>>> Reza

>>> Reza Khayat, PhD
>>> Associate Professor
>>> City College of New York
>>> Department of Chemistry and Biochemistry
>>> New York, NY 10031

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Re: [ccp4bb] criteria to set resolution limit

[Alexandre Ourjoumtsev]

Dear Tom, 

there are a couple of papers (essentially the first one) with a relevant 
discussion. 

Urzhumtseva_2013_ActaCryst_D69_1921-1934 
Urzhumtseva_2015_J.Applied Cryst_48_589-597 

If you wish I may send you the files (off list). 

With best regards, 

Sacha Urzhumtsev 

- Le 13 Sep 21, à 4:42, Peat, Tom (Manufacturing, Clayton) 
 a écrit : 

> Thanks to Petr and Ian for their thoughtful replies.

> One worry I have is that as a community we continue to debate what is the
> 'proper' or 'correct' way to measure resolution which I think is quite
> confusing to those that are early in their crystallographic (or general
> structural biology) careers. It is the scientific method to argue (sometimes 
> ad
> nauseum) about what constitutes the best data, the best methods, etc. so this
> isn't really a surprise to those that have been around a while. But it might 
> be
> nice to have a set of criteria which most people in the field agree to and 
> then
> these are updated on a regular basis as we move forward as a field. Not that 
> we
> will ever get 100% agreement to anything, as that is just unrealistic (and
> there are many posts to this BB already to show that). What I was thinking was
> a set of standards that are reasonable and that when broken (not all at once,
> but one standard at a time), one needs to explain why instead of just hoping
> that a reviewer (or other scientist looking at the data) just misses it. From
> various posts, it seems that people generally agree that CC1/2 is a good
> criteria, that Rpim and Rfree are pretty good criteria, that I/sigI is
> reasonable at some level and that completeness and multiplicity (or 
> redundancy)
> are important as well. These are not all independent (Rpim clearly depends on
> the multiplicity/redundancy, etc) but having some kind of standard set of
> numbers to judge one's own data by as a first pass might be helpful (and I
> believe the original question was basically, what do a I report as the
> resolution?)
> Just to throw some numbers out as an example: CC1/2 at 0.3 (or 30% depending 
> on
> your reporting style), I/sigI at 1.0, completeness at 75% in the last
> resolution bin and multiplicity/redundancy at least 3.0 throughout (and in the
> last shell). Nothing magical in these numbers, but if you feel that your data
> are really good but the completeness isn't there, you just explain why, or
> something to that effect. I believe this is one of the reasons we always have 
> a
> table 1 in our publications and that there is no one number that really gives
> us that sense of assurance that the model and data are good (or in my own
> experience, good enough).

> I guess what I am trying to 'solve' is the issue I come across regularly in
> reviewing papers: the authors are very interested in the biology of their
> system and spend a lot of time explaining what the system is, why it is
> important, etc (all great stuff) and then fill in the table with a set of
> numbers that makes me then wonder why they believe their own models? Often 
> very
> low completeness, low redundancy/ multiplicity, CC1/2 which varies from 0.99+
> to almost zero, all in order to make the reported resolution sound good (and
> crazy numbers of decimal places- reporting a resolution of 1.39623 AA with 15%
> completeness could more realistically be reported at 1.40 AA or 1.50 AA with
> 50% completeness and I don't think the actual interpretation/ electron density
> would change significantly). If it was then stated explicitly in the
> manuscript, for example, that paired refinement was done or that difference
> maps were calculated (or FEM or Polder or ?) at various resolutions which then
> showed the area of interest more clearly, the readers and reviewers might be
> more assured that the authors weren't just reporting a semi-random number as
> 'the resolution'. Numbers in the table that are clearly (?) a bit relaxed, if
> actually explained in the paper, would then make more sense. We as a community
> have gone somewhat this direction with the validation criteria given for
> deposited structures, which is a start, but it hasn't really tackled the 
> thorny
> question of 'what is my resolution?'

> As Ian mentioned, some programs and some criteria depend on relatively high
> completeness in the data in the way they are calculated (CC1/2 is perfect when
> all data are set to zero). If a program 'fills in' data that are missing, then
> that one will also be subject to issues when the data are very incomplete. One
> can always call on people to 'get better data' and of course it would always 
> be
> fantastic if each data set was complete, had high CC1/2 and multiplicity/
> redundancy, but then this isn't very realistic either.

> Thanks again for the considered replies to the previous post, and if this 
> sounds
> like a rant, it probably is.

> cheers, tom

> Tom Peat, PhD
> Proteins Group
> Biomedical Program, CSIRO
> 343 Royal Parade
> Parkville, VIC, 3052
> +613 9662 

Re: [ccp4bb] B-factors very high

[Alexandre Ourjoumtsev]

Dear Eleanor, 

You are absolutely right. 
However, in Polygon, you could compare the models selected by resolution, by 
size, etc. 

I use this occasion to wish you and others a happy New Year ! 

Sacha Urzhumtsev 

- Le 4 Jan 21, à 15:44, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> a écrit : 

> That polygon is not very useful I dont think. The statistics need to be given
> separately for structures solved at given resolutions.
> Eleanor



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Re: [ccp4bb] real real-space-refinement

[Alexandre Ourjoumtsev]

Dear Thierry, 

- Le 31 Juil 20, à 21:58, Fischmann, Thierry 
<22f7fda0a875-dmarc-requ...@jiscmail.ac.uk> a écrit : 

> Jim wrote:

> “ technically, not in Phenix either. The real-space refinement in Phenix 
> simply
> picks peaks in the density and then pulls nearby atoms toward them. . Like a
> black hole gobbling up nearby planets (snip)”

> Do you have a reference to support this assertion

The methodology of the "dirty but very fast" real space refinement in Phenix is 
described in detail in the article : 

Afonine, P.V.et al. (2018) 
"Real-space refinement in PHENIX for cryo-EM and crystallography". Acta Cryst 
., D 74 , 531-544. 

The articel contains also arguments for such kind of procedure, its advantages 
(the principal goal and advantage is a very high speed) and obvious limitations 
(one of them mentioned by James). 

> Hopefully someone from the Phenix team will give some clarifications. But the
> statement above indicates that Phenix is capable of performing real space
> refinement by some other means than the “black hole approach”

Sorry, here I cannot comment. 

Best regards, 

Sacha Urzhumtsev 



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Re: [ccp4bb] How to compare between electron density maps?

[Alexandre Ourjoumtsev]

Dear Murpholino, 

there is a couple of articles addressing specifically this issue : 

Urzhumtsev, A., Afonine, P.V., Lunin, V.Y., Terwilliger, T.C., Adams, P.D. 
(2014) " Metrics for comparison of crystallographic maps ". Acta Cryst., D70 , 
2593-2606 
Urzhumtseva, L., Urzhumtsev, A. (2016) "COMPaRS: stand-alone program for map 
comparison using quantile rang scaling". J. Appl. Cryst., 49 , 2270-2275. 

Best regards, 

Sacha Urzhumtsev 

- Le 12 Mai 20, à 0:18, Murpholino Peligro  a écrit 
: 

> I want to compare electron density features of map A from protein A and map B
> from protein B...

> Because each map has a different rmsd level...

> ...what is the best way to compare electron density between maps?

> Is there a way to normalize maps or something like that?

> Thanks



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Re: [ccp4bb] Overrefinement considerations and Refmac5.

[Alexandre Ourjoumtsev]

Thank you, Bernhard, for poining out this nice paper by Ian, one more that I 
missed previously. 

Best regards, 

Sacha Urzhumtsev 

- Le 6 Mar 20, à 19:15, Bernhard Rupp  a écrit : 

> In addition to Sacha’s work there are a few older papers by Ian Tickle & Cie.
> (summarized in BMC) and a figure of the empirical distributions

> [
> http://www.ruppweb.org/Garland/gallery/Ch12/pages/Biomolecular_Crystallography_Fig_12-24.htm
> |
> http://www.ruppweb.org/Garland/gallery/Ch12/pages/Biomolecular_Crystallography_Fig_12-24.htm
> ]

> which are broad and – as mentioned - the actual delta values are context
> dependent.

> Best, BR

> From: CCP4 bulletin board  On Behalf Of Andrew Leslie
> Sent: Friday, March 6, 2020 08:52
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Overrefinement considerations and Refmac5.

> I would like to add a small caveat to Eleanor’s rule about a 3% difference 
> being
> too low for a structure refined against 3Å data.

> If the 3Å data is for a structure that has already been solved at much higher
> resolution (e.g. 2Å) and the only difference for the 3Å dataset is a different
> ligand (say) and the structure is solved by molecular replacement using the
> high resolution structure as a model, in those circumstances it is possible
> (and quite acceptable) to have a much lower difference between Rwork and Rfree
> than one might expect, even at low as 3-4%.

> Andrew

>> On 6 Mar 2020, at 15:22, Eleanor Dodson < [
>> mailto:176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk |
>> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk ] > wrote:

>> You dont give the data resolution - that is very important..

>> I hate this rule bound approach to Rfree - R differences.. but as a guide

>> No non-crystallographic symmetry.

>> 1A data - you would expect them to be almost equal

>> 3A data - I would expect a difference of at least 10% - once had the 
>> pleasure of
>> sendng a paper back as unreasonable when the data was only to 3A and the r
>> factors differed by 3%

>> Pseudo-symmetry and non-crystallographic symmetry can make things more
>> complicated.

>> Ideally reflections related by such symmetry should match - either set 
>> belong to
>> the Rfree set, or working set.

>> The best way to get a low Rfactor and a high Rfree is to have virtually no
>> geometric restraints. ie have a very high weighting term.

>> The auto selection works pretty well in my experience..

>> Not really an answer but some ideas..

>> Eleanor

>> On Fri, 6 Mar 2020 at 13:32, M T < [ mailto:michel...@gmail.com |
>> michel...@gmail.com ] > wrote:

>>> Dear BBers,

>>> I am trying to refine a structure using COOT and Refmac5 and I have some
>>> concerns about overrefinement and x-ray term weight in Refmac5, based on the
>>> fact that during refinement to let R factor to drift too far from Rfree is 
>>> not
>>> good...

>>> So... First question about that : what is too far ? I have some values in 
>>> mind
>>> like 6% of difference is OK, 10% is not... But is there a relation in 
>>> between
>>> resolution of the structure and this difference? Should it be higher at 
>>> lower
>>> resolution, or always around 6-7% independently of the resolution?

>>> Second question is, ok, I have a too big difference, lets say 9-10%... What
>>> could be the reason of that and on what to play to reduce this difference?

>>> One way I choose is to look at the x-ray term weight (even if I am totally 
>>> sure
>>> that Refmac5 is doing things better than me), because I saw that the final 
>>> rms
>>> on BondLength were to constraint (I have in mind that this value should 
>>> stays
>>> in between 0.02 and 0.01).

>>> So I looked into Refmac log to know where was the starting point and I found
>>> 8.75.

>>> Then I tried several tests and here are the results:

>>> *

>>> R factor


>>> Rfree


>>> BondLength

>>> BondAngle

>>> ChirVolume


>>> Auto weighting and experimental sigmas boxes checked


>>> 0.1932


>>> 0.2886

>>> 0.0072

>>> 1.6426

>>> 0.1184


>>> Weighting term at 4 and experimental sigmas box checked


>>> 0.1780


>>> 0.3159

>>> 0.1047

>>> 8.1929

>>> 0.5937


>>> Weighting term at 4


>>> 0.1792


>>> 0.3143

>>> 0.1008

>>> 7.8200

>>> 0.5667


>>> Weighting term at 15 and experimental sigmas box checked


>>> 0.1783


>>> 0.3272

>>> 0.2020

>>> 1.6569

>>> 0.9745


>>> Weighting term at 15


>>> 0.1801


>>> 0.3279

>>> 0.2022

>>> 12.5748

>>> 0.9792


>>> Weighting term at 8.75


>>> 0.1790


>>> 0.3235

>>> 0.1545

>>> 10.5118

>>> 0.7909


>>> Auto weighting box checked


>>> 0.1948


>>> 0.2880

>>> 0.0076

>>> 1.6308

>>> 0.1176


>>> Refinement Parameters

>>> 

>>> So like nothing looks satisfying I decided to ask my questions here...

>>> What do you recommend to fix my problem, which is a too large difference 
>>> between
>>> R and Rfree?

>>> Thank you for answers.

>>> To unsubscribe from the CCP4BB list, click the following 

Re: [ccp4bb] Overrefinement considerations and Refmac5.

[Alexandre Ourjoumtsev]

Dear Eleanor, dear Michel (?), 

A while ago we statistically analysed the distribution of R, Rfree and of their 
difference as a function of the logarithm of resolution (Urzhumtsev et al., 
2009, Acta Cryst, D65, 1283-1291). 
In this log-scale, the mode values for all three are nearly linear functions 
(see Figs. 4 and 5 and equations (11) and (12) ). 

At 3A resolution, indeed, 3% difference is too small but anyhow 10% seems to be 
not common; just from pure statistics, its mode is rather closer to 5%. At 1A, 
the mode of Rfree-R distribution is near 2%. 

With best wishes, 

Sacha Urzhumtsev 

- Le 6 Mar 20, à 16:22, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> a écrit : 

> You dont give the data resolution - that is very important..
> I hate this rule bound approach to Rfree - R differences.. but as a guide
> No non-crystallographic symmetry.
> 1A data - you would expect them to be almost equal
> 3A data - I would expect a difference of at least 10% - once had the pleasure 
> of
> sendng a paper back as unreasonable when the data was only to 3A and the r
> factors differed by 3%

> Pseudo-symmetry and non-crystallographic symmetry can make things more
> complicated.
> Ideally reflections related by such symmetry should match - either set belong 
> to
> the Rfree set, or working set.

> The best way to get a low Rfactor and a high Rfree is to have virtually no
> geometric restraints. ie have a very high weighting term.
> The auto selection works pretty well in my experience..

> Not really an answer but some ideas..
> Eleanor

> On Fri, 6 Mar 2020 at 13:32, M T < [ mailto:michel...@gmail.com |
> michel...@gmail.com ] > wrote:

>> Dear BBers,

>> I am trying to refine a structure using COOT and Refmac5 and I have some
>> concerns about overrefinement and x-ray term weight in Refmac5, based on the
>> fact that during refinement to let R factor to drift too far from Rfree is 
>> not
>> good...

>> So... First question about that : what is too far ? I have some values in 
>> mind
>> like 6% of difference is OK, 10% is not... But is there a relation in between
>> resolution of the structure and this difference? Should it be higher at lower
>> resolution, or always around 6-7% independently of the resolution?

>> Second question is, ok, I have a too big difference, lets say 9-10%... What
>> could be the reason of that and on what to play to reduce this difference?

>> One way I choose is to look at the x-ray term weight (even if I am totally 
>> sure
>> that Refmac5 is doing things better than me), because I saw that the final 
>> rms
>> on BondLength were to constraint (I have in mind that this value should stays
>> in between 0.02 and 0.01).
>> So I looked into Refmac log to know where was the starting point and I found
>> 8.75.
>> Then I tried several tests and here are the results:
>>  
>> *

>> R factor



>> RfreeBondLength

>>  BondAngle



>> ChirVolume



>> Auto weighting and experimental sigmas boxes checked

>> 0.1932   0.2886

>>  0.0072

>>  1.6426



>> 0.1184



>> Weighting term at 4 and experimental sigmas box checked

>> 0.1780   0.3159

>>  0.1047

>>  8.1929



>> 0.5937



>> Weighting term at 4

>> 0.1792   0.3143

>>  0.1008

>>  7.8200



>> 0.5667



>> Weighting term at 15 and experimental sigmas box checked

>> 0.1783   0.3272

>>  0.2020

>>  1.6569



>> 0.9745



>> Weighting term at 15

>> 0.1801   0.3279

>>  0.2022

>>  12.5748



>> 0.9792



>> Weighting term at 8.75

>> 0.1790   0.3235

>>  0.1545

>>  10.5118



>> 0.7909



>> Auto weighting box checked

>> 0.1948   0.2880

>>  0.0076

>>  1.6308



>> 0.1176

>> Refinement Parameters

>> So like nothing looks satisfying I decided to ask my questions here...

>> What do you recommend to fix my problem, which is a too large difference 
>> between
>> R and Rfree?

>> Thank you for answers.

>> To unsubscribe from the CCP4BB list, click the following link:
>> [ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 |
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 ]
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Re: [ccp4bb] Figure of merit in refinement

[Alexandre Ourjoumtsev]

Thank you, Eleanor, for an important reminder : 

obviously, one more recent and relevant paper is that by Read and McCoy (Acta 
Cryst, D, 2016) 

[ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784668/ | 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784668/ ] 

With best wishes, 

Sacha 

- Le 3 Oct 19, à 12:07, Eleanor Dodson  a écrit 
: 

> The maths for estimating the FOM during refinement in REFMAC is given in some
> detail in the original paper.

> However the assessment uses estimates of the observation standard uncertainly,
> and SigmaA - the estimate of the resolution dependent error due to coordinate
> errors and missing atoms -
> and both these terms can be inaccurate.

> Randy Read et al has suggested ways of improving the SigmaA estimates, and
> better data processing SHOULD help with the measurement errors..

> So - beware but that is amn outline of the teheory
> Eleanor

> Refinement of macromolecular structures by the Maximum likelihood method.
> G.N.Murshudov, A.A.Vagin, E.J.Dodson,(1997) Acta crystallogr. D53, 240-255



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Re: [ccp4bb] Figure of merit in refinement

[Alexandre Ourjoumtsev]

Dear Andre, 

I would strongly advice you to look at the article by Lunin and Skovoroda (Acta 
Cryst, A, 1995) that addresses exactly your question: 

[ https://scripts.iucr.org/cgi-bin/paper?vs0124 | 
https://scripts.iucr.org/cgi-bin/paper?vs0124 ] 

The authors remind a very important point that after model refinement ML phase 
errors are strongly underestimated if using all reflections, as that was done 
in the original works (see references in the article). While the same ML 
estimates work perfectly for unrefined models, that's not the case for refined 
ones, as was observed yet in the beginning of 80ths. 
These authors show then that using the test-set of reflections (the same as for 
R-free) is crucial to get the correct phase error estimates and respective FOMs 
for all cases, as this is implemented now in modern refinement programs. See 
also the article by Pannu & Read (Acta Cryst, A, 1996) 

[ https://onlinelibrary.wiley.com/doi/pdf/10.1107/S0108767396004370 | 
https://onlinelibrary.wiley.com/doi/pdf/10.1107/S0108767396004370 ] 

A more recent important article on this topic is that by Praznikar and Turk 
(Acta Cryst, D, 2009) 

[ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257616/ | 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257616/ ] 

who discuss what can be done if a statistically significant test set of 
reflections is not available. 

I hope this helps you. 

With best wishes, 

Sacha Urzhumtsev 

- Le 3 Oct 19, à 2:17, Andre LB Ambrosio  a écrit : 

> Dear Jonathan, many thanks for this. I will have a look at it right away.
> With best wishes,
> Andre.

> On Wed, Oct 2, 2019, 7:51 PM Jonathan Cooper < [ mailto:bogba...@yahoo.co.uk |
> bogba...@yahoo.co.uk ] > wrote:

>> This is a very good place to start:

>> [ https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html |
>> https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html ]

>> Also recommend this one:

>> [ https://doi.org/10.1107/S0108767386099622 |
>> https://doi.org/10.1107/S0108767386099622 ]

>> and Main, P. (1979) Acta Cryst. A35, 779-85 - the maths in this one are a bit
>> easier!

>> On Wednesday, 2 October 2019, 22:47:56 BST, Andre LB Ambrosio < [
>> mailto:an...@ifsc.usp.br | an...@ifsc.usp.br ] > wrote:

>> Dear all,

>> How is the phase error estimated for any given reflection, specifically in 
>> the
>> context of model refinement? In terms of math I mean.

>> How useful is FOM in assessing the phase quality, when not for initial
>> experimental phases?

>> Many thank in advance,

>> Andre.

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Re: [ccp4bb] resolution

[Alexandre Ourjoumtsev]

Dear Graeme, 

Right, but you are talking about weights that reflect the data quality and say 
nothing about that of the starting model ; however refinement is a comparison 
of a model with data. 

The higher resolution of the data, the more sensitive they to model 
imperfections. 
Refinement targets are sums over reflections, and each refinement term is a 
function with multiple minima; the higher the resoluion, the more frequent 
these minima. 

If the starting model is too far from the answer, a presence of high-resolution 
data prevents the refinement from moving the model as far as necessary; it is 
trapped by multiple local minima of the crystallographic functions that include 
such high-resolution terms. Removing such terms removes or at least attenuate 
the intermediate local minima and improves the convergence. One does not care 
about the statistices but about convergence (" the model stops improving" 
further than with these data). Increaing the resolution step-by-step was the 
standard refinement strategy till the end of 90ths. 

Right, using ML-based targets introduced weights based on comparison of Fmodel 
with Fobs and allowed to do such attenuation in a "soft way". This was great 
and indeed replaced the "before-ML refinement strategy". However, such an 
artificial cut-off of highest-resolution data (temporary, at early refinement 
stages) can be useful in some situations even now and can improve convergence 
even with the modern tools. First cycles of a rigid-body refinement can be an 
example. 

Another reason for a (temporary) removing of higher-resolution data is a heavy 
(systematic) incompleteness of data in the higher-resolution shells. 

With best regards, 

Sacha 

- Le 5 Juil 19, à 8:05, graeme.win...@diamond.ac.uk 
 a écrit : 

> Pavel,

> Please correct if wrong, but I thought most refinement programs used the 
> weights
> e.g. sig(I/F) with I/F so would not really have a hard cut off anyway? You’re
> just making the stats worse but the model should stay ~ the same (unless you
> have outliers in there)

> Clearly there will be a point where the model stops improving, which is the
> “true” limit…

> Cheers Graeme

> On 5 Jul 2019, at 06:49, Pavel Afonine
> mailto:pafon...@gmail.com>> wrote:

> Hi Sam Tang,

> Sorry for a naive question. Is there any circumstances where one may wish to
> refine to a lower resolution? For example if one has a dataset processed to 2
> A, is there any good reasons for he/she to refine to only, say 2.5 A?

> yes, certainly. For example, when information content in the data can justify
> it.. Randy Read can comment on this more! Also instead of a hard cutoff using 
> a
> smooth weight based attenuation may be even better. AFAIK, no refinement
> program can do this smartly currently.
> Pavel

> 

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Re: [ccp4bb] Table 1 successor in 3D?

[Alexandre Ourjoumtsev]

Dear Bernhard and Gerard, 

congratulations for nice results that both you (and Gerard team) have been 
contributed and published ! 

Just a nice occasion to remind (and slightly correct Bernhard's message in that 
article) that the 'efficient resolution' that we suggested (2013) is NOT a 
single global number but exactly what Bernhard is saying : this number may 
vary, and sometimes drastically, from one direction to another, and our program 
gives the minimal - maximal - mean values as well as a histogram of its 
distribution and a list of major outliers (see some examples in Urzhumtseva et 
al., 2013, Acta Cryst D69 , 1921-1934, and especially in J. Appl. Cryst., 48 , 
589-597 ). Obviously, full 3D- STARANISO- views of various data quality metrics 
are much more spectacular ! 

Best regards, 

Sacha Urzhumtsev 

- Le 1 Juin 18, à 18:30, Gerard Bricogne  a écrit : 

> Dear all,

> Bernhard Rupp has just published a "Perspective" article in
> Structure, accessible in electronic form at

> https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2

> in which part of his general argument revolves around an example
> (given as Figure 1) that he produced by means of the STARANISO server
> at
> http://staraniso.globalphasing.org/ .



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Re: [ccp4bb] looking for a link between diffraction resolution and order within the crystal

[Alexandre Ourjoumtsev]

Dear Vincent, 

first, certainly, you can continue to a higher resolutions distinguishing 
further details : 

3.3 A - nucleic acid pairs 
 
1.2 A - atomic details 
0.9 A - deformation density 
(by the way, there was a relevant work, I think, by E.Blanc and G.Bricogne 
beginning of 2000, about some crucial high-resolution cut-offs). 

Second, a convenient scale for this detail analysis is logarithmic (we 
discussed this a few years ago in Acta Crsyt D); the limits you are talking 
about become more or less uniform in this scale. 

Third, at low resolution the situation is not at all so simple as you wrote. 
For example, images at 10-12 A may show neither "more ordered envelopes" nor 
"secondary structure elements" but only a "big mess". This is really the "worse 
resolution" to work with. I can send / give you off-list some illustrations. 

Best regards, 

Sacha Urzhumtsev 

- Le 28 Nov 17, à 15:44, vincent Chaptal  a écrit 
: 

> Hi,

> I've been searching but can't find what I am looking for so I thought I ask
> specialists.

> I am curious about the link between resolution limits of reflections on the
> detector, and what features are ordered in real space.
> I saw the great movie by James Holton on resolution and features in the 
> electron
> density map, but I am looking for something more general.
> I am thinking that a reflection on the detector originates from something
> ordered within the crystal. The level of order would be different at different
> resolution.

> If you can help me fill the void in this phrase:
> I see spots at __A resolution, therefore I know that _ features are 
> ordered
> in my crystal.

> intuitively, I would build the following scale:
> 20A : the envelope is ordered
> 10A: a finer envelope is ordered
> 6A: alpha helices are ordered
> 4-5A: beta sheets are ordered and some residues
> 3-4A: residues start to be ordered
> >3A: more and more order.

> Has this been described somewhere? I would appreciate any comments and
> reevaluation of this scale.

> Thank you in advance.
> All the best
> Vincent

> --

> Vincent Chaptal, PhD

> Institut de Biologie et Chimie des Protéines

> Drug Resistance and Membrane Proteins Laboratory

> 7 passage du Vercors

> 69007 LYON

> FRANCE

> +33 4 37 65 29 01

> http://www.ibcp.fr

Re: [ccp4bb] efresol download?

[Alexandre Ourjoumtsev]

Dear Johan 

one more copy :-) 
Yes, you can get it from 

http://www-ibmc.u-strasbg.fr/spip-arn/spip.php?rubrique2=en 

Sorry for inconvenience and answering so late... 
Luca, Daniel and Pavel, many thanks for your help ! 

Sacha Urzhumtsev 

- Le 26 Oct 17, à 18:50, Hattne, Johan  a écrit : 

> Thanks a lot, Luca, Pavel, and Daniel! I now have sufficiently many copies to
> last me well into 2020!

> // Cheers; Johan

> > On Oct 26, 2017, at 11:58, Bonsor, Daniel  wrote:

> > Is this not it?

> > http://www-ibmc.u-strasbg.fr/spip-arn/rubrique257?lang=en

> > At the bottom of the page.


> > Daniel A Bonsor PhD.
> > Sundberg Lab
> > Institute of Human Virology
> > University of Maryland, Baltimore
> > 725 W Lombard Street N370
> > Baltimore
> > Maryland
> > MD 21201
> > Tel: (410) 706-7457


>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel
> > Afonine
> > Sent: Thursday, October 26, 2017 11:54 AM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] efresol download?

> > Johan,

>> core functionality described in that paper is implemented in cctbx. Re the
> > stand-alone program -- I'm cc'ing to the author.

> > Pavel

> > On Thu, Oct 26, 2017 at 8:39 AM, Hattne, Johan  
> > wrote:
> > Dear all;

>> Would anybody know where I can find efresol (as detailed in
>> http://dx.doi.org/10.1107/S0907444913016673) these days? Googling lead me to 
>> a
>> 2014 post
>> (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1406=ccp4bb===155751),
> > but those links result in 403 Forbidden as of right now.

> > // Best wishes; Johan


> > Research Specialist @ Gonen Lab
> > 
> > Janelia Research Campus * 19700 Helix Drive
> > Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

> Research Specialist @ Gonen Lab
> 
> Janelia Research Campus * 19700 Helix Drive
> Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

Re: [ccp4bb] efresol download?

[Alexandre Ourjoumtsev]

Dear Johan 

one more copy :-) 
Yes, you can get it from 

http://www-ibmc.u-strasbg.fr/spip-arn/spip.php?rubrique2=en 

Sorry for inconvenience... 
Luca, Daniel and Pavel, m 

- Le 26 Oct 17, à 17:39, Hattne, Johan  a écrit : 

> Dear all;

> Would anybody know where I can find efresol (as detailed in
> http://dx.doi.org/10.1107/S0907444913016673) these days? Googling lead me to a
> 2014 post
> (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1406=ccp4bb===155751),
> but those links result in 403 Forbidden as of right now.

> // Best wishes; Johan

> Research Specialist @ Gonen Lab
> 
> Janelia Research Campus * 19700 Helix Drive
> Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

[Alexandre Ourjoumtsev]

Dear Khoa Pham, 

the question of a formal definition of en "effective" resolution and its 
variability with space direction is discussed in 

a) Urzhumtseva, L., Klaholz, B.P., Urzhumtsev, A. (2013) " On effective and 
optical resolution of diffraction data sets". Acta Cryst., D69 , 1921-1934. 
b) Urzhumtseva, L., Urzhumtsev, A. (2015) "A program to calculate effective 
resolution". J. Appl. Cryst., 48 , 589-597. 

U 
With best regatrds, 

Sacha Urzhumtsev 

- Le 18 Juin 17, à 15:42, Khoa Pham  a écrit : 

> Dear Gerard,

> Thank you so much for the very interesting discussions and the recommendation 
> of
> using STARANISO. I will submit my data to STARANISO server and keep you
> updated.

> Sincerely,

> Khoa Pham

[ccp4bb] sorry for spamming

[Alexandre OURJOUMTSEV]

Dear all,


sorry for spamming your mail boxes - there is a bug in our system.


Best regards,


Sacha

Re: [ccp4bb] wavelet application in CCP4

[Alexandre OURJOUMTSEV]

Dear Charles,


if you are interested in applications of wavelets to macromolecular 
crystallography problems, you may look also at a slightly earlier publication 
by Vladimir Lunin in


 Acta Cryst (2000) A56, 73-84

"Fixed-scale wavelet-type approximation of periodic density distributions."


Best regards,


Sacha Urzhumtsev




De : CCP4 bulletin board  de la part de CPMAS Chen 

Envoyé : lundi 28 novembre 2016 17:16
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] wavelet application in CCP4

Dear, All

I happen to see this paper,

Low-resolution phase extension using wavelet analysis.
Main 
P1,
 Wilson 
J

However, I did not see any application in current structure refinement 
softwares. Maybe I overlooked this function in CCP4/phenix etc?

Also, I did not see much references to this paper?

Could anyone give me some heads-up?

Thanks!

Charles

--

***

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

**

Re: [ccp4bb] wavelet application in CCP4

[Alexandre OURJOUMTSEV]

Dear Charles,


if you are interested in applications of wavelets to macromolecular 
crystallography, you may look also at a slightly earlier publication by 
Vladimir Lunin


Acta Cryst. (2000). 
A56, 73-84
https://doi.org/10.1107/S0108767399011277
Fixed-scale wavelet-type approximation of periodic density 
distributions
V. Y. 
Lunin


Best regards,


Sacha Urzhumtsev



De : CCP4 bulletin board  de la part de CPMAS Chen 

Envoyé : lundi 28 novembre 2016 17:16
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] wavelet application in CCP4

Dear, All

I happen to see this paper,

Low-resolution phase extension using wavelet analysis.
Main 
P1,
 Wilson 
J

However, I did not see any application in current structure refinement 
softwares. Maybe I overlooked this function in CCP4/phenix etc?

Also, I did not see much references to this paper?

Could anyone give me some heads-up?

Thanks!

Charles

--

***

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

**

Re: [ccp4bb] wavelet application in CCP4

[Alexandre OURJOUMTSEV]

Dear Charles,


if you are interested in applications of wavelets to macromolecular 
crystallography, you may look also at a slightly earlier publication by 
Vladimir Lunin


Acta Cryst. (2000). 
A56, 73-84
https://doi.org/10.1107/S0108767399011277
Fixed-scale wavelet-type approximation of periodic density 
distributions
V. Y. 
Lunin


Best regards,


Sacha Urzhumtsev



De : CCP4 bulletin board  de la part de CPMAS Chen 

Envoyé : lundi 28 novembre 2016 17:16
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] wavelet application in CCP4

Dear, All

I happen to see this paper,

Low-resolution phase extension using wavelet analysis.
Main 
P1,
 Wilson 
J

However, I did not see any application in current structure refinement 
softwares. Maybe I overlooked this function in CCP4/phenix etc?

Also, I did not see much references to this paper?

Could anyone give me some heads-up?

Thanks!

Charles

--

***

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

**

Re: [ccp4bb] MR phasing using Negative Stain EM reconstruction

[Alexandre OURJOUMTSEV]

Dear Pascal,

A while ago when I did  my tests on MR at a very low resolution, I did it both 
with “shaped” envelopes and with the “flat” ones. It did work for both (with 
simulated data, which is obviously not the same as the experimental), but MR 
with the “shaped” models was more robust.

Some traces of this are in the article in Acta Cryst D51 (1995) 888-895.

Best regards,

Sacha Urzhumtsev


De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Pascal 
Egea
Envoyé : mardi 25 octobre 2016 03:49
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] MR phasing using Negative Stain EM reconstruction

Dear All,

I would like to know if it is possible to use a low resolution EM 
reconstruction of a complex obtained in negative stain EM (not cryo EM) to help 
molecular replacement in a 4.5A resolution X-ray diffraction data set of the 
same complex
I am aware of the possibility of using low resolution cryoEM maps for MR as 
described in the review from Jackson et al in Nature Protocols but I was 
wondering if there is an intrinsically impossibility for negative stain 
reconstructions.

Any thoughts or advice will be greatly appreciated.

Best,

--
Pascal F. Egea, PhD
Assistant Professor
UCLA, David Geffen School of Medicine
Department of Biological Chemistry
Boyer Hall room 356
611 Charles E Young Drive East
Los Angeles CA 90095
office (310)-983-3515
lab  (310)-983-3516
email pegea at mednet.ucla.edu

Re: [ccp4bb] phenix installtion problem

[Alexandre OURJOUMTSEV]

Dear Weifei,

I am neither in the Phenix nor in the CCP4 teams so I let me remark that it 
does not look reasonable, just a few minutes after Tom Terwilliger's mail :

I'll answer you on the Phenix BB as you've asked specific questions about 
Phenix tools.

sending your mail (see below) asking explicitly phenix questions again through 
the CCP4bb. I do not think that you disturb, you should not sorry for this, 
the BB are for this, but we need to follow the rules.

I ask everybody to respect both ccp4 and phenix teams, who assures a lot of 
service and help for our community, and send your requests properly (for your 
own benefit), through the BB concerned.

My another request (luckily not applicable to the Weifei mail)  is that people 
always sign properly their mails and give their name when asking their 
questions : ccp4, phenix teams and other experts answer you openly and this 
looks quite weird seeing anonymous requests. Again, this is for your own 
benefit, for your better integration into the research community.

With best regards,

Sacha Urzhumtsev




De : CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK de la part de ChenWeiFei 
weife...@outlook.com
Envoyé : vendredi 26 juin 2015 15:05
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] phenix installtion problem

Dear all,
Sorry to disturb you.
I have install Phenix to my computer Centos 7.0.
When I want to use it I need to
cd /usr/local/phenix-1.9-1692/
and
 . /usr/local/phenix-1.9-1692/phenix_env.sh
then type phenix in the command line every time.
I wish to use phenix in every terminate window and just type phenix.
Some told me use export PATH to do it but I don't know how to do it.
I am new to linux(centos)
Thank you so much!
Best,
Weifei

Re: [ccp4bb] MOLREP self-rotation matrix

[Alexandre OURJOUMTSEV]

Re: [ccp4bb] MOLREP self-rotation matrix

[Alexandre OURJOUMTSEV]

Sorry for a bug with the previous (empty) mail . Here is the message :

Dear Chen,


there is a very old program CONVROT (Urzhumtseva  Urzhumtsev, 1997, 
J.Appl.Cryst) that you can dowload from


http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Sites.html


(or if you want I can send you a copy off-list).


It converts any kind of angles (rotation description) to any other kind of 
rotation descriptions including the matrices.


If you have difficulties to install it as a whole GUI program, for your 
particular problem you may use only the main fortran program convrot.for.


A new python version will come soon I hope.


Best regards,


Sacha Urzhumtsev



De : CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK de la part de Chen Zhao 
c.z...@yale.edu
Envoyé : mardi 19 mai 2015 16:11
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] MOLREP self-rotation matrix

Hi Eleanor,

Thank you so much for your test! However, I am not starting with a PDB file. 
What I am doing self-RF on is just the Patterson map. So my problem is to 
convert the output Euler angles to orthogonal matrix.

Thanks a lot for your time,
Chen

On Tue, May 19, 2015 at 5:26 AM, Eleanor Dodson 
eleanor.dod...@york.ac.ukmailto:eleanor.dod...@york.ac.uk wrote:
Actually it is pretty easy:

Here is the log of pdbset

[ccp4@roo job_55]$ pdbset xyzin part.pdb
...

  Logical name: XYZIN  File name: part.pdb
  PDB file is being opened on unit 1 for INPUT.

  MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE


 RF  RO

0.016   0.009  -0.000  -0.000   61.922 -30.961   0.000  -0.000
   -0.000   0.019  -0.000   0.0000.000  53.626   0.000   0.000
0.000  -0.000   0.004   0.0000.000   0.000 248.752  -0.000
   -0.000   0.000  -0.000   1.000   -0.000   0.000  -0.000   1.000

rota euler 10 20 30
 Data line--- rota euler 10 20 30
end
 Data line--- end

  Logical name: XYZOUT  File name: XYZOUT
  PDB file is being opened on unit 2 for OUTPUT.


 Coordinates will be transformed as follows:

   (   0.714610 -0.613092  0.336824 ) ( x ) ( 0.000 )
   (   0.633718  0.771281  0.059391 ) ( y )  +  ( 0.000 )
   (  -0.296198  0.171010  0.939693 ) ( z ) ( 0.000 )



Of course you still have to worry about the orthogonalisation code used for the 
SELFROT search.

polarrfn tells you what is chosen

For triclinic, orthorhombic ext the choice is usually

Z || c*   X || a   and Y chosen to make an orthogonal set


But for monoclinic it is often set

Z || b*   X || a  and Y chosen to make an orthogonal set

Eleanor



On 18 May 2015 at 18:57, Chen Zhao c.z...@yale.edumailto:c.z...@yale.edu 
wrote:
Sorry for the spaming... Just want to correct that I plan to say covert the 
MOLREP self-RF Euler angle to RESOLVE (not SOLVE) orthogonal matrix...

On Mon, May 18, 2015 at 1:44 PM, Chen Zhao 
c.z...@yale.edumailto:c.z...@yale.edu wrote:
I got some answers from the previous thread: 
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36578.htmlhttps://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_ccp4bb-40jiscmail.ac.uk_msg36578.htmld=AwMFaQc=-dg2m7zWuuDZ0MUcV7Sdqwr=uV9bK9zAIvRZlk7q6-YllAm=7kauOiFgNMhDGRtA1PkMFhKOYJHao8bdY2NU84DO36Us=LWP0S_qlKqdAsniO09EK3o72dfTWMQ42_JzTShSCZvQe=

But I just want to make sure what I am doing...

Thanks a lot,
Chen

On Mon, May 18, 2015 at 1:36 PM, Chen Zhao 
c.z...@yale.edumailto:c.z...@yale.edu wrote:
Hi Eleanor,

Yeah, the relationship of the XYZ with the unit cell axes is tricky too. 
Although I can get some clues by looking at the position of the 
crystallographic symmetry axes on the XY plane, it is better if I could find a 
definite answer...

Thank you,
Chen

On Mon, May 18, 2015 at 1:24 PM, Eleanor Dodson 
eleanor.dod...@york.ac.ukmailto:eleanor.dod...@york.ac.uk wrote:
Hmm - there are programs which give you the matrix associated with Eulerian or 
Polar angles. I think one is pdbset..

Or there is documentation in polarrfn or rotmat which describes how to do it..

But remember there are conventions about which axes correspond to the 
orthogonal X Y Z axes used to define the angles

Eleanor


On 18 May 2015 at 17:04, Chen Zhao c.z...@yale.edumailto:c.z...@yale.edu 
wrote:
Hi all,

I am now trying to convert the NCS axis expressed by theta, phi, chi (or alpha, 
beta, gamma) from MOLREP to an orthogonal matrix in order to feed into SOLVE. 
Would anybody suggest me a correct way to do it?

Thank you so much in advance!

Best,
Chen

Re: [ccp4bb] crystal anisotropy measurement?

[Alexandre OURJOUMTSEV]

Dear Cosmo,

you may calculate effective resolution of your data set along different 
directions using the program EFRESOL (article in press in J.Appl.Cryst., the 
method is described by Urzhumtseva et al., 2013, Acta Cryst D69, 1921-1934). 
You can download the program from 
http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Sites.html or I can send it to 
you off list.

Good luck !

Sacha Urzhumtsev


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Cosmo Z Buffalo 
[cbuff...@ucsd.edu]
Envoyé : mardi 17 février 2015 19:55
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] crystal anisotropy measurement?

Hi all,
I have a anisotropic crystal with cell dimensions of 78, 78  345.  Is there a 
method for quantitatively measuring the the anisotropy of my diffraction data 
and a way to compare my data to that of similarly anisotropic crystals?
-Cosmo

Re: [ccp4bb] Bulk solvent correction in Phaser MR LF

[Alexandre OURJOUMTSEV]

Hi, Bernhard,

ok, sure, you are right ! Nevertheless, I would not be so desperate and 
categorical: you are right , at my knowledge also, there is currently NO known 
algorithm to take into account the flat mask bulk solvent contribution at the 
rotation step (maybe I am wrong?), however this does not mean it is impossible. 
The question is should it be done at all ?
 When do you the rotation search, you need to use mostly the highest 
resolution data, and it may be rather useful to remove the low-resolution data 
(see the tests described in Acta Cryst D51, 888-895, 1995; however, it looks 
like in practice nobody uses variable resolution for different MR steps). When 
you work at low resolution with envelopes, you do not care about bulk solvent 
correction since all this results indeed in a scale coefficient.
 There is a tiny (but not unusual) situation when one wants to do MR at the 
worse resolution of 9-12 A (worse in the sense that the maps show neither 
(already) molecular envelope nor (yet) clear structure. Suppose we could solve 
the MR problem - what we do then since the maps are so poor ? It is worthy in 
this case artificially lower the resolution ? I do not know...

However, I agree, you question is fully valid and is interesting.


All the best ,

Sacha

De : hofkristall...@gmail.commailto:hofkristall...@gmail.com 
[hofkristall...@gmail.com]
Envoyé : mercredi 4 février 2015 14:09
À : Alexandre OURJOUMTSEV; CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Objet : RE: [ccp4bb] Bulk solvent correction in Phaser MR LF
Hi Sacha,

I was imprecise. With unplaced I meant 'neither rotated nor translated'.
Once you become post-rotationally SF based, you can in fact compute a F(env)
whole inclusion should improve the TF score.

What is not evident to me is how to use a mask and compute the Fs  if the 
orientation
(rotation) is yet to be determined?

Thx, BR

Re: [ccp4bb] proton scattering by X-rays

[Alexandre OURJOUMTSEV]

Dear Jacob,

there was a nice small computation project by Anne Bochow published in the CCP4 
Newsletters (2005), 

http://www.ccp4.ac.uk/newsletters/newsletter42/content.html,  communication 
9,

illustrating how strong and how confusing the ripples may be indeed; if you 
want I may send it you off list the corresponding pdf file. Please make a look 
the figures, they are very impressive. And Pavel just commented how to 
distinguish such the ripples from the peaks for the deformation bond density. 

With best regards,

Sacha Urzhumtsev


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Keller, Jacob 
[kell...@janelia.hhmi.org]
Envoyé : jeudi 5 février 2015 21:53
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] proton scattering by X-rays

What about the bogey of Fourier truncation ripples--I have heard many have been 
fooled by the into thinking they were seeing orbitals. How does one tell the 
difference?

JPK

Re: [ccp4bb] Bulk solvent correction in Phaser MR LF

[Alexandre OURJOUMTSEV]

Dear Bernhard,

For the unplaced model, it can only be a Babinet model to improve the scaling,

This is not fully true, and the flat mask correction can be used as well. 
Please look :

Fokine, A.  Urzhumtsev, A.G. (2002) On the use of low resolution data for 
translation search in molecular replacement. Acta Cryst., A58, 72-74

Fokine, A., Capitani, G., Grütter, M.G.  Urzhumtsev, A. (2003) Bulk-solvent 
correction for fast translation search in molecular replacement: service 
programs for AMoRe and CNS. J. Appl.Cryst., 36, 352-355.

Best regards,

Sacha Urzhumtsev


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Bernhard Rupp 
(Hofkristallrat a.D.) [hofkristall...@gmail.com]
Envoyé : mardi 3 février 2015 14:49
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Bulk solvent correction in Phaser MR LF

Hi Fellows,

I cannot find the proper reference for the implementation of bulk solvent 
corrections in the
Phaser Molecular replacement likelihood functions.  For the unplaced model, it 
can only be a Babinet model to improve the scaling, and I believe that is 
implemented via a
Babinet rescaled function for sigma A including the coordinate error.

Can anybody help me where to find that?
Thx, BR

Re: [ccp4bb] phase shift vs non-isomorphism

[Alexandre OURJOUMTSEV]

Dear Phil,

Gerard Bricogne pointed out a long time ago that the clearest comparison 
between two sets of phases is the complex correlation coefficient between two 
best structure factors ( m F exp(i phi) ) - this is equivalent to map 
correlation, but can be analysed in resolution bins.

I'm not sure whether there are programs which calculate this, though it's 
straightforward, and I've had various jiffy programs in the past (which I've 
probably lost)

A while ago this was formally reported, including technical details, by Lunin  
Lunina (1996), Acta Cryst., A52, 365-368, and they had at that moment some 
fortran program. In particular, this algorithm makes a key part of the 
low-resolution direct phasing approaches.

With best regards,

Sacha Urzhumtsev

Re: [ccp4bb] Fwd: question about calculating electrostatic potentials

[Alexandre OURJOUMTSEV]

Dear Constance,

your question means that you want to know the so-called quantile rank 
corresponding to the cut-off levels you have chosen (see the article in Acta 
Cryst D, D70, 2593-2606 (2014) that is talking specially about this).

To rescale from sigma's into percentile ranks, you may use either the 
corresponding phenix option (map comparison) or using a separate python program 
that I will send you by a separate mail, out of bb.

With best wishes,

Sacha


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Constance 
Jeffery [cjeff...@uic.edu]
Envoyé : dimanche 30 novembre 2014 21:26
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Fwd: question about calculating electrostatic potentials

Dear CCP4 users,
I have a question about protein electrostatic surfaces.  We used Pymol to 
calculate electrostatic surfaces of several protein structures.  Is there a way 
to calculate the percent of surface that is red, or the area of surface that is 
red, so that we can quantitatively compare these structures?

Thanks,
Connie

[ccp4bb] are mathematician scientists ?! (previously Free Reflections as Percent and not a Number)

[Alexandre OURJOUMTSEV]

Dear Tim,

as you know I avoid making public comments and prefer enjoying the comments 
done by others, however this time is hard to resist :-)

I was surprised by your mail : do you mean that mathematicians are NOT 
SCIENTISTS ?! Do you mean that they are nasty persons who fight against normal 
biologists, do not let them developing new techniques and prevent them from 
achieving their holy goals ? 

I think (hope) all of us are a sort natürphilosophes (is it a right term in 
German ? estestvoispytatel' = естествоиспытатель in Russian), all of us 
trying to solve the same Global Problems, looking on them from different sides 
and applying the best of our individual knowledge. This diversity is a force of 
our community, and there is a very nice article by Kathleen Lonsdale dated by 
September 1953 (!!! more than 60 year ago! ) in Acta Cryst, 6, 874-875, 
entitled The training of modern crystallographers. She is talking exactly 
about chemists, biochemists, physicists, geologists, engineers or 
mathematicians (we can make this list much longer); a short and excellent 
text. 

Each of us has a center of gravity of individual knowledge in different 
domains, and professional points of view  are useful to contribute into 
development of the respective parts of our Global Project (not only Global 
Phasing :-). Then I see nothing wrong if an expert in methods (Pavel in this 
case; I think he deserves this word) gives a general point of view to a person 
who wants to improve crystallographic methods because without such general 
points of view (usually based on a profound experience of many other experts) 
the improvements we are waiting for may not come or will come with a pain 
(cannot resist from citing Arthur Conan Doyle: All refinement is through 
sorrow). 

I hope that it was just an unfortunate phrase in your mail and that everybody 
understands what exactly you had in mind :-) During my life I was lucky seeing 
fantastic collaborative projects of biologists and mathematicians.

With best regards,

Sacha Urzhumtsev

Prof. of Universities of Lorraine and of Strasbourg


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Tim Gruene 
[t...@shelx.uni-ac.gwdg.de]
Envoyé : samedi 29 novembre 2014 11:16
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] Free Reflections as Percent and not a Number

Hi Pavel,

I think your email highlights one of the differences between us and one
of the reasons for this discussion:

I am a scientist, not a mathematician - I want to improve
crystallographic methods because people who solve crystal structures
want an answer to a biological or chemical or physical question rather
than because they enjoy watching the realisation of a mathematical
definition. I like Ken Follett's definition of a physicist, for whom
reality is a poor approximation to theory, but the motivation for my
research runs the other way round.

Cheers,
Tim

On 11/29/2014 05:12 AM, Pavel Afonine wrote:
 Hi Tim,

 your examples are valid and valuable, and clearly exemplify existing
 problems, limitations as well as common misconceptions.

 However, if you follow mathematics and strict definitions thereof, then
 crystallographic structure refinement is nothing but an optimization
 problem that, fundamentally, to be defined requires: a) definition of model
 parameterization, b) definition of a function that relates experimental
 data and model parameters, and c) definition of a method that changes model
 parameters in a such a way that optimizes (most of the time minimizes) the
 chosen (at step b) function.

 Please don't think that I've just made up or invented these a)-b)-c)
 steps above.. In fact, this has been published, for example, in
 *Acta Cryst.* (1985). A*41*, 327-333,
 and then reiterated using modern jargon, for example, in
 *Acta Cryst.* (2012). D*68*, 352-367.

 (I say for example above just to stick to the context and also point out
 that you can find more examples in crystallographic literature as well as
 in totally different disciplines such as economics, aerospace science etc.)

 Anyways, once all the above (a-b-c) are set and defined, then your only
 goal is as simple as finding the global minimum of the function that you
 have chosen to optimize.

 Anything else beyond that are either technical details or various
 inefficiencies related to improper model parameterization, improper target
 choice or using limited optimization tool.

 All the best,
 Pavel


 On Fri, Nov 28, 2014 at 11:40 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de
 wrote:

 Dear Pavel,

 there is a beautiful paper called 'Where freedom is given, liberties are
 taken' by Kleywegt and Jones, but also a wide variety of articles that
 (fortunately) fought hard for the introduction of Rfree to the
 (macro-)crystallographic community.

 In there is mentioned the threading of an amino acid chain backwards
 into the density achieving (by refinement) a lower R-value than the
 original one. 

Re: [ccp4bb] are mathematician scientists ?!

[Alexandre OURJOUMTSEV]

Dear Tim,

sure - no any problem . It was a nice occasion to talk about our 
complementarity (and make a publicity of some excellent old papers) !

With best regards, be well !

Sacha

PS : I am even less English native speaker


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Tim Gruene 
[t...@shelx.uni-ac.gwdg.de]
Envoyé : samedi 29 novembre 2014 14:38
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] are mathematician scientists ?! (previously Free 
Reflections as Percent and not a Number)

Dear Sasha,

I was taught that 'scientist' was best translated into German as
'Naturwissenschaftler' rather than the general term 'Wissenschaftler'.
Mathematicians were philosophers and e.g. economy belongs maybe to
humanities. I thought this distinction was also made at the Imperial
College were my English learned at school settled further.

I am not a native speaker, if I am wrong I would like to apolgise - I
meant no offense.

Best,
Tim

Re: [ccp4bb] Treating Missing Reflections as Zero or Fcalc

[Alexandre OURJOUMTSEV]

Dear Gregg and Tim,

Thank you for an interesting discussion and data.

It may be useful to point out, in particular for other readers of the CCP4bb, 
that there are a couple of relevant issues (the role of a few missed 
reflections on a quality of images and the choice of the cut-off level when 
analyzing / comparing the density) addressed by our recent article in Acta 
Cryst D (2014) 2593-2606.

  It gives also an example showing that excluding the “test-set” 
reflections from the map calculations (as it should be for a proper 
validation), even chosen randomly and uniformly, is a more risky business than 
it is usually thought; at least with 10% test set the changes may be 
significant.

With best regards,

Sacha Urzhumtsev

De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Gregg 
Crichlow
Envoyé : vendredi 28 novembre 2014 11:53
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] Treating Missing Reflections as Zero or Fcalc

Dear Tim,
 Thank you for your quick review of the map, and your reply.  Actually, I 
always check every water molecule manually one by one before finalizing my 
structures because I know that automated algorithms often get them wrong, and 
also often place waters in ligand density.  I'm away from home and away from a 
graphics computer, and it will be some hours before I can log in remotely to 
check this again, but judging from the residues on the perimeter of the screen 
shot you sent, it looks as if the view you are showing is of the pore that is 
through the center of the homotrimer (the trimer is doughnut shaped). The 
trimer essentially has a three-fold non-crystallographic symmetry axis down the 
center of the pore, which is a very narrow pore, often filled with water. (The 
pore isn't the active site).

However, the final maps were calculated with CNS as I recall (it was 
almost 7 years ago when I was actually doing the refinement) in order to 
visualize both overlapping ligands. I mention that because I noticed a long 
time ago that when displaying CNS maps in Coot, the sigma level is represented 
by the e/A3 contour. I discovered this when seeing a contour difference between 
CNS maps displayed in O and Coot. Then when I displayed them in PyMol, they 
matched the O maps. However, when I displayed the CNS maps in Coot at 1 e/A3, 
then they looked like the 1 sigma CNS maps in O and PyMol.  Many probably know 
about this already, but I just want to make sure that you are looking at the 
sigma level you think you have.  That looks like a Coot screen shot you are 
showing, and this peculiar way Coot handles CNS contours may explain why you 
see that extra ligand in that screen shot, but not in your EDS server maps.

...and yes, I do want to get more experience using shelxl myself!
Gregg

On Fri, Nov 28, 2014 at 4:32 AM, Tim Gruene 
t...@shelx.uni-ac.gwdg.demailto:t...@shelx.uni-ac.gwdg.de wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Gregg,

your post raised my curiosity and I look at the map after a round of
refinement with shelxl.
I thought you might be interested in two observations:

1) shelxl refines the occupancy of the 1Q1 ligand to 60% rather than
78% (I don't think shelxl fills in missing reflections)

2) the second observation is the reason why I am posting this
publicly, because it illustrates the danger of automatic water
placement to hover out important information: there is strong
difference density for another ligand as you can see in the attached
screenshot (the Met on the left is residue A2 in the deposited PDB
file. The water network that was build instead has too high B-values
compared to the surround protein structures.

I assume you used an automated procedure to place these waters - the
map from the EDS sever looks very different on does not reveal an
extra ligand.

Once you model this extra ligand you should further decrease the noise
level and might get an even better indication of the two overlapping
ligands.

Did I mention I like shelxl ;-) (NB: these are 1.55A data!)

Best regards,
Tim

On 11/28/2014 06:22 AM, Gregg Crichlow wrote:
 My fault for not changing the thread subject! I'm sorry! Greetings
 to ccp4bb readers! This is a long-delayed reply to requests that I
 received after I posted an observation on the ccp4bb almost three
 years ago. (I think it was early 2012). The paper had not yet been
 published (pending finalization of experiments unrelated to
 structural biology) and so I was not free to distribute any of the
 structure factors to those who were interested.  The paper now has
 been published, and the coordinates and structure factors have been
 released. The following is the peculiarity that made this of
 interest.

 I refined a structure with 1.55 A data of a homotrimeric protein
 bound to an inhibitor. Although the inhibitor added to the enzyme
 contained a five-membered ring, the inhibitor we observed in two of
 the three active sites had the ring opened. We therefore discovered
 

Re: [ccp4bb] hi - history of protein crystallization (should be : conversion of euler angles)

[Alexandre OURJOUMTSEV]

Dear Vijay

Sorry for further troubles with the program.
Could you send me (in a PRIVATE mail, out of CCP4bb) the tcl file that you 
prepared using my template ?

With best wishes,

Sacha Urzhumtsev


De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de vijay 
srivastava
Envoyé : vendredi 25 juillet 2014 10:59
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] hi - history of protein crystallization

Dear Dr. Sacha,

it is giving following error after typing the command
…

Re: [ccp4bb] Hi - euler angles conversion

[Alexandre OURJOUMTSEV]

Dear Vijay,

(sorry, it looks like my previous mail went being unfinished).

There is a program developed in purpose for this goal :

Urzhumtseva, L.M., Urzhumtsev, A.G. (1997) Tcl/Tk based programs. II. CONVROT: 
program to recalculate different rotation descriptions. J.Appl. Cryst., 30, 
402-410

There are a fortran command-line version and a tcl/tk GUI version which can be 
download from

http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Sites.html#

or directly from

http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/convrot/Convrot.html

If you have problems to download them or have more questions on this subject or 
about the program please write me directly to sa...@igbmc.fr  .

With best wishes,

Sacha Urzhumtsev


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de vijay srivastava 
[vijaytec...@yahoo.co.in]
Envoyé : lundi 21 juillet 2014 06:01
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Hi

Dear All,

Is there is any program to convert euler angles into theta, phi and kappa?

regards

Vijay

[ccp4bb] efresol (effective resolution ) : updated version

[Alexandre OURJOUMTSEV]

Dear All,

Sorry for spamming.
Thanking to the criticism and advices from a number of recent testers (in 
particular, Mark van Raaij, Oleg Sobolev, Pavel Afonine), we produced an 
updated version (version 2.3) of the program EFRESOL to calculate the effective 
and optical resolutions and the anisotropy ratio for a data set of an arbitrary 
completeness, as it was recently discussed in the ccp4bb. The new version seems 
to be stable over various computers and systems. A few 'bugs' have been also 
fixed.
This version can be free taken from :
http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/efresol/Efresol.html
http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Sites.html
We used the same occasion to update the program FOBSCOM (Urzhumtseva  
Urzhumtsev, J.Appl.Cryst., 2011) which allows one to visualize a diffraction 
data set and to numerically characterize the regions of missed reflections. The 
new version can be free downloaded from
http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/fobscom/Fobscom.html

With best wishes,

Sacha Urzhumtsev
(IGBMC, Strasbourg ; Universite de Lorraine, Nancy)

[ccp4bb] GUI program to calculate effective resolution of a data set

[Alexandre OURJOUMTSEV]

Dear All,

Recently, there was a ccp4bb conversation concerning the definition of a ‘real’ 
(effective) resolution of (incomplete) diffraction data sets. I am happy to 
announce that a corresponding GUI program EFRESOL is available now and you may 
download it from the Web site:

http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/efresol/Efresol.html
http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Sites.html

The method is described in L.Urzhumtseva, B.P.Klaholz, A.Urzhumtsev (2013) Acta 
Cryst., D69, 1921-1934.
We would like to thank Joel Bard, Tom Peat, Rajan Prabu and especially Boaz 
Shaanan for testing the original version of the program.

With best wishes,

Sacha Urzhumtsev

[ccp4bb] effective resolution : programs

[Alexandre OURJOUMTSEV]

Dear Boaz,

yes, sure, there is the original fortran program to run it through a command 
line, and there is also a GUI (python) version. I'll send it to you off-list. 
There are a few imperfections and a minor bug that we noted, and we hope to 
fix them next days, but the program is operational and you can try it.

With best wishes,

Sacha

De : Boaz Shaanan [bshaa...@bgu.ac.il]
Envoyé : samedi 19 avril 2014 17:28
À : Alexandre OURJOUMTSEV; CCP4BB@JISCMAIL.AC.UK
Objet : RE: [ccp4bb] crystallographic confusion

...
Have the criteria that you propose for determining the effective resolution 
been implemented in any program or crystallographic suite in way that we can 
read in a data set and get out the effective resolution based on your criteria?

  Cheers,

  Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710






From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Alexandre 
OURJOUMTSEV [sa...@igbmc.fr]
Sent: Saturday, April 19, 2014 12:41 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] crystallographic confusion

Dear Dale, dear Kay,

last year, we discussed this kind of problems (Urzhumtseva et al., 2013, Acta 
Cryst., D69, 1921-1934).
Our approach does not tell you where to cut your data and which reflections to 
accept / reject but as soon as you have your set of reflections, you calculate 
very formally and very strictly the effective resolution of ANY diffraction 
data set, with ANY completeness, with ANY composition of measured / missed 
reflections.  For a complete data set, d_effective coincides with the d_high 
value but is different for incomplete data sets. The article contains a number 
of examples.

With this approach, the discussion of the completeness of the 
highest-resolution shell becomes irrelevant; one can simply cite the effective 
resolution. I hope this can help.

With best regards,

Sacha Urzhumtsev


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Dale Tronrud 
[de...@daletronrud.com]
Envoyé : samedi 19 avril 2014 03:20
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] crystallographic confusion

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1


   I see no problem with saying that the model was refined against every
spot on the detector that the data reduction program said was observed
(and I realize there is argument about this) but declare that the
resolution of the model is a number based on the traditional criteria.


Dale Tronrud

Re: [ccp4bb] crystallographic confusion

[Alexandre OURJOUMTSEV]

Dear Dale, dear Kay,

last year, we discussed this kind of problems (Urzhumtseva et al., 2013, Acta 
Cryst., D69, 1921-1934).
Our approach does not tell you where to cut your data and which reflections to 
accept / reject but as soon as you have your set of reflections, you calculate 
very formally and very strictly the effective resolution of ANY diffraction 
data set, with ANY completeness, with ANY composition of measured / missed 
reflections.  For a complete data set, d_effective coincides with the d_high 
value but is different for incomplete data sets. The article contains a number 
of examples.

With this approach, the discussion of the completeness of the 
highest-resolution shell becomes irrelevant; one can simply cite the effective 
resolution. I hope this can help.

With best regards,

Sacha Urzhumtsev


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Dale Tronrud 
[de...@daletronrud.com]
Envoyé : samedi 19 avril 2014 03:20
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] crystallographic confusion

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1


   I see no problem with saying that the model was refined against every
spot on the detector that the data reduction program said was observed
(and I realize there is argument about this) but declare that the
resolution of the model is a number based on the traditional criteria.


Dale Tronrud

Re: [ccp4bb] difference between polar angle and eulerian angle

[Alexandre OURJOUMTSEV]

Dear Ed,

It looks like the problem is not yet closed, so I'll add my remarks. 
In addition to very detailed comments by Ian, Tim and others, it might be 
useful to look our article in J.Appl.Cryst (1997), 30, 402-410, which addresses 
exactly these confusing points: what is rotated, what is fixed, in which 
direction rotated, polar angles vs Euler angles, etc... Maybe not so detailed 
as you wish but may help. Some tables may be also useful (unfortunately, there 
is one mistyping in Table 2, if I remember).

With best wishes,

Sacha Urzhumtsev

De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Edward A. Berry 
[ber...@upstate.edu]
Envoyé : mardi 1 avril 2014 01:12
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] difference between polar angle and eulerian angle

Dear Tim, Ian,
Tim Gruene wrote:
 [...]
 Actually it does not depend - the rotation matrices are a representation

Re: [ccp4bb] which space group?!?

[Alexandre OURJOUMTSEV]

Dear Jürgen, dear Katherine,

Sorry for a late reaction.

In our article in Acta Cryst., 2009, D65, 1283-1291 (Section 4) we show an 
accurate distribution of the most frequent R, Rfree, Rfree-R  as a practically 
linear function of the Log(resolution) , and not that of the resolution itself, 
and give the corresponding equations. Also we look for the min/max and the 
dispersion of R/ Rfree values around these most frequent values.

Best regards,

Sacha

From: Bosch, Juergen [jubo...@jhsph.edu]
Sent: Tuesday, July 23, 2013 2:23 PM
To: Katherine Donovan
Subject: Re: [ccp4bb] post to ccp4bb
Hi Katherine,

As a rule of thumb you should expect R values around your resolution/10 so in 
the low to mid 20 - 18/23 sound reasonable for that resolution.

How many molecules in the asu do you have in each case ?

Jürgen

[ccp4bb] RE : [ccp4bb] Envelope Phasing.

[Alexandre OURJOUMTSEV]

Dear David,

I would remind that the molecular-replacement positionning of molecular 
envelopes and some methodological features (in comparison with a conventional 
MR) of this have been discussed in : 

Urzhumtsev  Podjarny (1995). On the Solution of the Molecular Replacement 
Problem at Very Low Resolution: Application to Large Complexes. Acta Cryst. 
D51, 888-895. 

Concerning the practical results, at my knowlegde, this was the first step in 
the ribosome phasing by Nenad Ban in 1999 (while the envelope was from EM and 
not from SAXS, but this shall not make a difference).

Best regards,

Sacha Urzhumtsev


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de David Briggs 
[drdavidcbri...@gmail.com]
Date d'envoi : lundi 12 mars 2012 21:10
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Envelope Phasing.

Hi CCP4bb,

I would like to ask about envelope phasing - specifically with SAXS data.

There are papers (1) and tutorials (2) describing how this might be
done, but I have also found comments on the ccp4bb, such as this one
(http://www.proteincrystallography.org/ccp4bb/message11690.html) which
are somewhat less optimistic.

I get the impression from my reading around that SAXS envelope phasing
is somewhat difficult to do unless you have some NCS you can use to
help the phase extension process. Does anybody have any
opinions/evidence/examples/anecdotes/tips about how SAXS envelope
phasing can be done successfully?

Cheers,

Dave

(1) - eg - http://scripts.iucr.org/cgi-bin/paper?dz5081
(2) - eg - 
http://www.phaser.cimr.cam.ac.uk/index.php/Using_Electron_Density_as_a_Model


David C. Briggs PhD
Father, Structural Biologist and Sceptic

University of Manchester E-mail:
david.c.bri...@manchester.ac.uk

Webs : http://flavors.me/xtaldave
Twitter: @xtaldave
Skype: DocDCB

Re: [ccp4bb] proper or improper ncs?

[Alexandre OURJOUMTSEV]

Hi, everybody,

In addition to all comments, just as a pleasure to remind an old-fashion no 
computer way to calculate the rotation angle. The trace of a rotation matrix 
(the sum of its diagonal elements) is always equal to 2*cos(kappa)+1. Calculate 
it yourself for kappa = 180° and compare with the trace of the Francis's matrix.

ROTA 1:   -0.5444   -0.22020.8094
ROTA 2:0.8330   -0.02780.5526
ROTA 3:   -0.09910.97510.1985

One can easily reject (still without a computer) other crystallographic 
angles.

Best regards,

Sasha Urzhumtsev


-Message d'origine-
De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Ian Tickle
Envoyé : mardi 21 février 2012 15:13
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] proper or improper ncs?

Francis,

It's very easy to spot a 2-fold rotation or screw because the matrix must be 
symmetric (or nearly so)**.  Your matrix very obviously is not (i,e, A12 ne 
A21, A13 ne A31 etc).

** Proof:

 A rotation matrix is orthogonal, which implies inverse = transpose: A^-1 = A~.

A 2-fold rotation is proper which implies AA = I or A^-1 = A.

Take these together and you get A = A~ i.e. A is symmetric.

Surprising how many people aren't aware of this!

Cheers

-- Iann

On 21 February 2012 13:47, Francis E Reyes francis.re...@colorado.edu wrote:
 Hi all

 This structure has the following ncs (output via 
 phenix.simple_ncs_from_pdb) OPERATOR 1
 CENTER:   18.3443  -55.4605   23.0986

 ROTA 1:    1.    0.    0.
 ROTA 2:    0.    1.    0.
 ROTA 3:    0.    0.    1.
 TRANS:     0.    0.    0.

 OPERATOR 2
 CENTER:   37.0405  -23.8676  -14.9388

 ROTA 1:   -0.5444   -0.2202    0.8094
 ROTA 2:    0.8330   -0.0278    0.5526
 ROTA 3:   -0.0991    0.9751    0.1985
 TRANS:    45.3456  -78.7231   53.0085


 It looks two-foldish but I'm not sure if it's proper or improper. (I'm trying 
 to rationalize the lack of peaks on the self rotation maps).


 Any help would be appreciated.

 F



 -
 Francis E. Reyes M.Sc.
 215 UCB
 University of Colorado at Boulder

Re: [ccp4bb] atomic scattering factors in REFMAC

[Alexandre OURJOUMTSEV]

Dear all,

Just as a historic reminder, I feel necessary to mention a key article on 
refinement, written by R.Aragwal (1978) in Acta Cryst A, where he used 1- and 
2-gaussian atomic factors (obviously, less precise that 4 gaussians + constant 
but allowed him at that moment to accelerate as much as possible the 
calculations).

With best regards,

Sacha Urzhumtsev


De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Pavel 
Afonine
Envoyé : jeudi 3 novembre 2011 04:40
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] atomic scattering factors in REFMAC

Continuing on the subject, as far as I know there are at least three flavors of 
form-factors currently used in refinement programs:

4 gaussian plus const:
International Tables for Crystallography (1992)

5 gaussian plus const:
D. Waasmaier  A. Kirfel. Acta Cryst. (1995). A51, 416-431. New analytical 
scattering-factor functions for free atoms and ions

n-gaussian (n determined dynamically)
Grosse-Kunstleve RW, Sauter NK  Adams PD. Newsletter of the IUCr Commission on 
Crystallographic Computing 2004, 3:22-31. cctbx news

All three are available in PHENIX (the 3rd is used by default), and I presume 
the first one is used in CNS and Refmac, if I remember correctly (the authors 
of respective programs please correct me).

Pavel

Re: [ccp4bb] HOLE CHANNEL

[Alexandre OURJOUMTSEV]

Dear Dave,

I afraid that this program is not maintained for many-many years

“An algorithm to find channels and cavities within protein crystals (CHANNEL)”: 
Oleg S. Kisljuk, Galina S. Kachalova and Nadejda Ph. Lanina ; J. Mol. Graphics, 
1994, vol12


knowing that the principal programming power Oleg Kisljuk left his researches 
in structural biology about at the time of that publication.

Galina Kachalova just recently stopped working in Hamburg so maybe somebody of 
her ex-colleagues knows her personal mail (if this may help).



Best wishes,



Sacha Urzhumtsev

[ccp4bb] RE : [ccp4bb] consistently missing eletron density

[Alexandre OURJOUMTSEV]

Dear Huiming,

as Pavel said, to get a reasonable map you need to collect either 
higher-resolution data (that you do not have because of your crystal) or 
low-resolution data. Working with only intermediate-resolution data may give 
you ugly maps even when your phases are perfect.

As an example, you may look Figs.3 and 7 in Urzhumtsev (1991), Acta Cryst. A47, 
794-801 (other examples like this may be suggested).

Best regards,

Sacha Urzhumtsev


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Huiming Li 
[huimin...@hotmail.com]
Date d'envoi : vendredi 12 août 2011 19:32
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] consistently missing eletron density

Dear All,

   I am working on a structure using several sets of data collected between 5 
to 6 angstroms. I have never worked with such low resolution before.  I was 
able to get pretty good TFZ between 10 and 16, and the electron density looks 
overall pretty good. However, among the three data sets I have processed so 
far, a large chunk of density is missing in all of them around the same area of 
the protein (largely beta sheet). Is this a manifestation of some intrinsic 
problems of the crystal, the data, or the protein? Is there a proper procedure 
I can take to get this density back to make the map a bit more pleasing to view?

Thanks,

Huiming Li, Ph.D.
Immune Disease Institute
Children's Hospital Boston

Re: [ccp4bb] Same protein, different molecule numbers per ASU

[Alexandre OURJOUMTSEV]

Dear Ferrol,

Could you let us know the unit cell parameters for both these crystals ? (did I 
miss them somewhere in your previous mails?).  I wonder if in fact this is not 
the same packing with minor variation.

Sacha

De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de ferrol 
shariff
Envoyé : dimanche 10 juillet 2011 10:10
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Same protein, different molecule numbers per ASU

Hello and good day to everyone! :)

I have some general questions on crystallography work. I hope you don't mind 
giving me some ideas.

I have solved my lipase protein both ground-grown crystals and space-grown 
crystals with good resolutions (1.4A and 2.2A). They are the same protein from 
the same source, same purification methods, and produced crystals from the same 
crystallization conditions (except the gravity part).

From the data, it shows that both of them belong to the same space group 
P212121. But they have different number of molecule per asymmetric unit. 
Ground crystal= 1 molecule/ASU, Space crystal= 2 molecules/ASU. At the moment 
i have problem explaining this issue. Is it normal to have such results? Same 
protein with different number of molecule/ASU?

I've been trying to get some references on this matter but so far i don't 
really get anything that can directly explain it. Furthermore, do i need to 
relate this with the gravity effect?

I hope you don't mind sharing some experiences on crystallography especially 
regarding this matter.

Thank you very much

--
FAIROLNIZA

Re: [ccp4bb] Citations in supplementary material

[Alexandre OURJOUMTSEV]

Thank you, Victor !

It is my many-years complain, and I tried to point it out orally at a 
number of conferences many times concerning both the publications and 
presenting results in posters. Very-very often we see a structure as given 
with no comments which (often very multiple and sophisticate!) computer and 
theoretical tools were exploited to obtain it. After this there is no surprise 
that :

- developers of methods are poorly supported except of a few big factories 
(my impression; maybe I'm wrong ?)

- scientific administration believes that in crystallography already 
everything is done, that it is no more a science but a pure routine

Obviously, there are barriers beyond which citation are useless, but at least 
some basic references must be always done.
 
I think that the group leaders should play the major role to correct the 
situation described by Victor, to make always proper citations and to stop 
cutting the branch on which we all together are sitting on.

With best wishes,

Sacha Urzhumtsev

 

-Message d'origine-
De : CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] De la part de Victor 
Lamzin
Envoyé : mercredi 17 novembre 2010 17:06
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Citations in supplementary material

Dear All,

I would like to bring to your attention the recent Editorial in Acta 
Cryst D (http://journals.iucr.org/d/issues/2010/12/00/issconts.html), 
which highlights the long-standing issue of under-citation of papers 
published in the IUCr journals. The Editorial, having looked at the 
papers published in 2009 in Nature, Science, Cell and PNAS, concluded:

'almost half of all references to publications in IUCr journals end up 
being published in the supplementary material only... Not only does this 
mean that the impact factor of IUCr journals should be higher, but also 
that the real overall numbers of citations of methods papers are much 
higher than what is reported, for instance, by the Web of Science'

Although this topic may seem to concern mostly methods developers, I 
think the whole research community will only benefit from more fair 
credit that we all give to our colleagues via referencing their 
publications. What do you think?

Victor

Re: [ccp4bb] diverging Rcryst and Rfree

[Alexandre OURJOUMTSEV]

Dear Rakesh, dear Artem,

Since the initial question is not precise (which kind of comments are 
expected?)  I may mention that the most frequent values of R, Rfree and DeltaR 
(that is asked about) are given in our work published in 2009 in Acta Cryst., 
D65, 1283-1291. Interestingly, they are practically linear functions of 
log(resolution). The plots show also the statistics of deviation from these 
lines.

Best regards,

Sacha Urzhumtsev
Universities of Strasbourg  Nancy


De : CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] De la part de Artem 
Evdokimov
Envoyé : mardi 26 octobre 2010 03:36
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] diverging Rcryst and Rfree

http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg04677.html

as well as some notes in the older posts :)

As a very basic rule of thumb, Rfree-Rwork tends to be around Rmerge for the 
dataset for refinements that are not overfitted.

Artem
On Mon, Oct 25, 2010 at 4:10 PM, Rakesh Joshi 
rjo...@purdue.edumailto:rjo...@purdue.edu wrote:
Hi all,

Can anyone comment, in general, on diverging Rcryst and Rfree values(say7%) for
structures with kind of low resolutions(2.5-2.9 angstroms)?

Thanks
RJ

Re: [ccp4bb] Babinet solvent correction / comment for imperfect models

[Alexandre OURJOUMTSEV]

Dear all,

Sorry to come back late, when the discussion is over, with one more remark 
relevant to the bulk solvent modeling.
I've just got a comment by a colleague of mine, Adam Ben-Shem, who kindly 
agreed that I post his message (below) to CCP4bb.

 I think he is completely right saying that the models we discussed were 
relevant to the well-solved structures and practically complete atomic models. 
In the process of structure solution the situation may be different, as he saw 
in his own practice (in particular when solving 80S ribosome).

With best regards,
Sacha Urzhumtsev
Universities of Strasbourg  Nancy

== message by Adam Ben-Shem 

I think the discussion of bulk solvent correction should be divided into three 
parts.
Part one - bulk solvent correction for the final model. In this case, the 
physical meaning of the mask model is clear and this is obviously the right 
way to apply the correction.

Part two - bulk solvent correction of partial models. These can be models with 
large flexible domains or models coming from bad maps where building is a very 
iterative process. In these cases the physical meaning of the mask model that 
Pavel is so worried about vanishes. In some extreme cases I can imagine that 
Babinet bulk solvent correction would be better than the mask model. As I 
told you before I suggest a better solution for these cases and that is to 
calculate the mask for the mask model using density modification.

Part three - density modification following refinement. From my own experience, 
for very partial models, phases and FOMs for this procedure should come from 
model alone (without bulk solvent) and let density modification define bulk 
solvent for itself. Bulk solvent correction is still important for the 
refinement process to produce the best model but then the input to density 
modification process should not include bulk solvent correction (and in 
very-very partial models  FOMs should be calculated by old SIGMAA program over 
all reflections and not by refinement program using R-free reflections alone).

Adam

[ccp4bb] RE : [ccp4bb] Babinet solvent correction [WAS: R-free flag problem]

[Alexandre OURJOUMTSEV]

Dear Ethan,

Just answering your last remarks,

very many years ago I've done tests (unpublished) where I tried to estimate the 
magnitudes Fbulk and PHASES Pbulk for the reflections due to bulk solvent. It 
came out that :
- for high-resolution reflections the magnitudes are small (everybody knows) 
and phases are irrelevant to phases of F(atomic model)
- for very low resolution reflections  Fbulk are practically proportional to 
F(atomic model), and the phases are different by pi (as everybody knows), as it 
should be from the Babinet principle; so it works well here, say at resolution 
lower than 20 A (the tests were done with a middle-size protein experimental 
data)
- however for reflections of the intermediate resolution say, 10-15A, Fbulk are 
already comparable in size with F(atomic model) but Pbulk are irrelevant to 
PHASES(atomic model); That means that at such intemediate resolution generating 
Fbulk, Pbulk by the Babinet principle is not a good idea.

Obviously, my tests were not exhaustive, imperfect etc. However I think the 
results seem to be logical.

Also working much later with Andrey Fokine we saw quite physical values for the 
parameters of a flat-mask model while for the Babinet-based  bulk-solvent model 
Glykos  Kokkinidis (Acta Cryst D, 2000 ? I do not remember by hard) did not 
see and system. This also makes an indirect point for the flat-mask model.

In that sens, the flat-mask model uses a more advanced information. Again, I 
think nobody claims that this model is perfect ; I hope a better model may be 
suggested with time.

Best regards,

Sacha Urzhumtsev

[ccp4bb] Re : Re: [ccp4bb] How to make fft-map more physically meaningful?

[Alexandre OURJOUMTSEV]

Dear Hailiang,As James said, the hermitian symmetry of Fourier coefficients, 
F(h)=F*(-h), that is known in diffraction theory as the Friedel's law, is an 
equivalent of the condition that the corresponding function (electron density) 
is a real function.I think if you need further information you can make a look 
into some basic textbook or write me (or to somebody on your choice :-) a 
direct personal mail; I am not sure if we need to bother the whole community by 
further details of this discussion. You can write and send to CCP4bb the resume 
afterall if you want.Best regards,SachaDe: James Holton jmhol...@lbl.gov 
Uhh.  No.  You will only get imaginary electron  density if your structure 
factors violate Friedel's law.  I am not aware of  map calculation codes that 
do this (on purpose).  Yes, I think Fourier synthesis at a finite resolution 
range  will generate some negative, or more generally imaginary values in real 
 space (hope I am right again:).