Re: [ccp4bb] Add secondary structure definition into an alphafold PDB

[Harry Powell - CCP4BB]

Also, of course, you could get the up-to-date version from - 

https://swift.cmbi.umcn.nl/gv/dssp/

Harry

> On 7 Apr 2022, at 09:29, Harry Powell - CCP4BB  
> wrote:
> 
> Hi Ines
> 
> DSSP? (In ccp4 as “mkdssp” in $CBIN)? Should work with any (valid??) PDB file
> 
> “Oldie but goodie”...
> 
> Harry
> 
>> On 7 Apr 2022, at 09:24, Munoz.Ines  wrote:
>> 
>> Dear all,
>> 
>> Is there any program or server that automatically assign the secondary 
>> structure elements into a pdb generated by alpha fold?
>> 
>> Many thanks
>> Inés
>> 
>> 
>> 
>> 
>> Inés G. Muñoz 
>> Head of Crystallography and Protein Engineering Unit
>> Spanish National Cancer Research Centre, CNIO
>> 
>> imu...@cnio.es
>> Phone +34 91 732 8000 (ext. 3020)
>> 
>> Melchor Fernández Almagro, 3
>> 28029 Madrid, Spain
>> www.cnio.es
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> Fb Amigos del CNIO |  Tw @CNIOStopCancer |  Youtube canalcnio
>> 
>> 
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Re: [ccp4bb] Add secondary structure definition into an alphafold PDB

[Harry Powell - CCP4BB]

Hi Ines

DSSP? (In ccp4 as “mkdssp” in $CBIN)? Should work with any (valid??) PDB file

“Oldie but goodie”...

Harry

> On 7 Apr 2022, at 09:24, Munoz.Ines  wrote:
> 
> Dear all,
> 
> Is there any program or server that automatically assign the secondary 
> structure elements into a pdb generated by alpha fold?
> 
> Many thanks
> Inés
> 
> 
> 
> 
> Inés G. Muñoz 
> Head of Crystallography and Protein Engineering Unit
> Spanish National Cancer Research Centre, CNIO
> 
> imu...@cnio.es
> Phone +34 91 732 8000 (ext. 3020)
> 
> Melchor Fernández Almagro, 3
> 28029 Madrid, Spain
> www.cnio.es
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Fb Amigos del CNIO |  Tw @CNIOStopCancer |  Youtube canalcnio
> 
> 
> 
> **ADVERTENCIA LEGAL**: Este correo electrónico, y en su caso los ficheros 
> adjuntos, pueden contener información protegida para el uso exclusivo de su 
> destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo 
> de transmisión por parte de otra persona que no sea el destinatario. Si usted 
> recibe por error este correo, se ruega comunicarlo al remitente y borrar el 
> mensaje recibido.
> De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la 
> protección de los datos personales de las personas físicas, la información 
> personal que nos pueda facilitar a través de este correo electrónico quedará 
> registrada por la Fundación CNIO con la finalidad de tramitar el objeto del 
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> encuentra legitimado por ser necesario para gestionar el objeto del presente 
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> Fernandez Almagro 3, 28029 (Madrid). Podrá ponerse en contacto con el 
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Re: [ccp4bb] Coot 1

[Harry Powell - CCP4BB]

Isn’t that what we all say every year on the day after March finishes?

Harry

> On 1 Apr 2022, at 23:46, Paul Emsley  wrote:
> 
> That, for the record, is more or less what Ralf said 18 years ago.
> On 01/04/2022 23:38, Pavel Afonine wrote:
>> It's April 1st today, isn't it? -;)
>> 
>> 
>> On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley  wrote:
>> Coot 1
>> 
>> 18 years after the release of Coot 0 it's time that I actually released 
>> Coot 1.
>> 
> 
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Re: [ccp4bb] ligand binds to one molecule

[Harry Powell - CCP4BB]

Hi folks

Just my two ha’porth; if you go back to one of the first two structures 
determined by protein crystallography, haemoglobin (horse?) has multiple oxygen 
binding sites) which are potentially different (the binding of oxygen ion one 
affects the binding in the other - “allostery”). I’m not sure if the two sites 
are distinguishable in any 3D structures, but the possiblility would be there. 
No doubt experts on this BB would be able to expand on this or tell me that I’m 
wrong…

My answer to the OP would be along the lines of “I wouldn’t be surprised by 
this at all”...

Harry

> On 6 Mar 2022, at 18:02, Dom Bellini - MRC LMB  
> wrote:
> 
> I dont think it is necessary to prove what others have said so far, but if 
> you would like some concrete evidence to support those statements:
> 
> we cocrystallized a protein together with a small peptide, producing a 
> crystal with for molecules in the AU but only one promoter showed clear 
> density for the bound peptide (crystal contacts played a part in this); then 
> the construct was shorten a bit and cocrystallized in a different space group 
> still, by chance, with 4 molecules in the AU, but this time we could clearly 
> see the peptide bound to all 4 copies. So indeed each protomer in the AU can 
> be affected differently in the way they bind a ligand, depending on all 
> causes (and perhaps even more) that people have already mentioned.
> 
> BW,
> 
> D
> 
> On 06/03/2022 12:38, David J. Schuller wrote:
>> I think it would be a mistake to generalize. 
>> I have seen a situation in which 1 of 4 sites was occupied, the ligand was 
>> not included in the crystallization solution(which means it must have been 
>> bound beforehand) and the site participated in crystal contacts. I do not 
>> doubt that examples of the opposite causality exist. And the data I used to 
>> make my conclusions in my own example came from outside the structure itself.
>> 
>> ===
>>  All Things Serve the Beam
>>  ===
>>  David J. Schuller
>>  modern man in a post-modern world
>>  MacCHESS, Cornell University
>>  schul...@cornell.edu
>> From: CCP4 bulletin board  on behalf of Palm, 
>> Gottfried 
>> Sent: Sunday, March 6, 2022 4:10 AM
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Subject: Re: [ccp4bb] ligand binds to one molecule
>>  
>> Dear all, 
>>   I don't think, there is much to add to the statement of Bernhard or James 
>> that different protomers in the asymmetric unit (must) have some difference 
>> in there contacts and therefore often in their conformation. What it doesn't 
>> answer is a chicken or the egg question: 
>> do the different environments in the crystal allow or force different 
>> conformations (e.g. open or closed loops) and/or different (active) site 
>> occupancies or
>> do different states in an oligomer allow or force crystallization only in a 
>> packing and space group with multiple states?
>> Latter could be due to an anti-cooperative binding to a dimer. We have seen 
>> this in the dimeric Tet repressor: wt binds the ligand (a tetracycline) in 
>> each monomer of the dimer with one chain in the asymmetric unit, but some of 
>> the mutants bind only one ligand per dimer (confirmed by ITC, Biochimica et 
>> Biophysica Acta, 2020). Despite the same packing, this forces reduction of 
>> space group symmetry from I422 to P422 (omitting screws). 
>> From the crystal structures alone, I think, one cannot prove what comes 
>> first. From my gut feeling, in most cases multiple states in solution force 
>> multiple states in the crystal - in other words - I tend to say, multiple 
>> states in the crystal are "real" in the sense they also occur in solution. 
>> Does somebody want to comment on this?
>> Greetings
>>   Gottfried
>> 
>> 
>> Am Sonntag, den 06-03-2022 um 00:40 schrieb Bernhard Rupp:
>> As you stated, you have multiple protomers in the asymmetric unit, where 
>> they are free from 
>> crystallographic symmetry constraints. Generally that means different local 
>> environment for
>> each protomer. Inspecting the sites in the different protomers (frequently 
>> related by various 
>> non-crystallographic symmetry operations) often can reveal plausible reasons 
>> for different occupancies. One hydrogen bond more or less for example can 
>> mean a 
>> difference of 4 orders of magnitude in Kd.
>> 
>> Best, BR
>> 
>> -Original Message-
>> From: CCP4 bulletin board  On Behalf Of 
>> Sent: Saturday, March 5, 2022 12:01
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] ligand binds to one molecule
>> 
>> Hello all,
>> 
>> In homo-dimeric or homo-oligomeric protein crystal structures, what would be 
>> the reason for having a ligand (chemical compound or fragment) binds to one 
>> molecule and 

Re: [ccp4bb] CCTBX current reference?

[Harry Powell - CCP4BB]

Hi folks

I am reliably informed that this is the right reference - many thanks to Nick 
Sauter for sending it to me off-board - 

> New Python-based methods for data processing.
> Sauter NK, Hattne J, Grosse-Kunstleve RW, Echols N.
> Acta Crystallogr D Biol Crystallogr 69, 1274-82. (1 Jul 2013)

Harry

> On 21 Feb 2022, at 10:04, Harry Powell - CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi
> 
> Is this _really_ the most recent reference for cctbx?
> 
> Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W. & Adams, P. D. 
> (2002). J. Appl. Cryst. 35, 126–136. 
> 
> (from one of Dorothee Liebschner’s recent papers)?
> 
> Harry
> 
>> On 21 Feb 2022, at 09:44, Harry Powell - CCP4BB 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Hi
>> 
>> I didn’t find this in a couple of minutes searching so I thought I’d ask - 
>> what’s the current literature reference for the cctbx toolkit?
>> 
>> Harry
>> 
>> 
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> 
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Re: [ccp4bb] CCTBX current reference?

[Harry Powell - CCP4BB]

Hi

Is this _really_ the most recent reference for cctbx?

Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W. & Adams, P. D. (2002). 
J. Appl. Cryst. 35, 126–136. 

(from one of Dorothee Liebschner’s recent papers)?

Harry

> On 21 Feb 2022, at 09:44, Harry Powell - CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi
> 
> I didn’t find this in a couple of minutes searching so I thought I’d ask - 
> what’s the current literature reference for the cctbx toolkit?
> 
> Harry
> 
> 
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[ccp4bb] CCTBX current reference?

[Harry Powell - CCP4BB]

Hi

I didn’t find this in a couple of minutes searching so I thought I’d ask - 
what’s the current literature reference for the cctbx toolkit?

Harry


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Re: [ccp4bb] OFF_TOPIC: Should you be worried about BPA from plastics? Yes, if you store alkaline reagents in polycarbonate bottles!

[Harry Powell - CCP4BB]

Hi

Last year there were a few reports in the chemical press (e.g. 
https://doi.org/10.1039/D1SC02708E, and references therein) of studies of glass 
catalysing reactions  - it seems that it isn’t as benign as one might imagine. 
Of course, this will not be news to the old chemical hands on this BB...

Harry

> On 31 Jan 2022, at 10:09, Artem Evdokimov  wrote:
> 
> Interesting note - and a reminder that alkaline solutions are tricky :) By 
> personal preference, HDPE bottles are probably the best for storing strongly 
> alkaline solutions (XLPE also is very good, but harder to get lab-grade 
> bottles).
> 
> Here's a handy chart for plastic vs stuff resistance. Note that HDPE is "E" 
> whereas PC (polycarbonate) is "N".
> 
> https://www.calpaclab.com/chemical-compatibility-charts/
> 
> Glass is not recommended for alkali storage, although there are some glass 
> products that have A1 or better alkali resistance rating. They can get pretty 
> esoteric, especially if one requires near-complete passivity towards strongly 
> alkaline solutions.
> 
> Artem
> 
> - Cosmic Cats approve of this message
> 
> 
> On Sun, Jan 30, 2022 at 1:02 PM Edward Berry  wrote:
> After using the same reagents for the Lowry assay and seeing the color yield 
> in the standard curve gradually decreasing year by year, we decided to make 
> new reagents last year. Sure enough the color yield was restored, but in the 
> next assay a few weeks later the blank was unusually high. after a month the 
> blank read nearly 1 AU.
> 
> The problem was, we stored the alkaline reagent (NaOH + Na2CO3)in a 
> polycarbonate bottle. I like polycarbonate because it is transparent and hard 
> like glass, but lighter and less breakable. But polycarbonate is a polyester 
> of Bis-phenol A with carbonic acid. Apparently the high pH slowly hydrolyzes 
> the ester linkages, or the plastic retains some monomers that slowly leach 
> out, and (duh!) bis-phenol A gives a positive reaction with the 
> Folin-Ciocalto phenol reagent.
> 
> 
> 
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Re: [ccp4bb] [ccp4bb] A "funny" thing related to AlphaFold2 ....

[Harry Powell - CCP4BB]

Hi Jon

Just checked an mmCIF file for one of the AlphaFold models - the model number 
is “1”, no sign of a model 0 that I can see…

A quick “sed” script could sort them all out…

Harry

> On 10 Nov 2021, at 12:22, Jon Agirre  wrote:
> 
> It might be, because the mmCIF versions work fine with MG.
> 
> On Wed, 10 Nov 2021 at 12:16, Harry Powell - CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi folks
> 
> Been a while, but I’ve been doing some work on checking that some files are 
> valid PDB files and went back to the documentation; as far as I can work out, 
> the best solution to this is John Walker’s, because “MODEL 0” is not allowed 
> in the standard (maybe it is for mmCIF…) - 
> 
> > On 27 Aug 2021, at 16:39, John R. Walker  wrote:
> > 
> > I just change MODEL 0 to MODEL 1 then it works fine.
> > 
> > John
> 
> As far as I can see (from a small sample of the 150,000 AlphaFold models, 
> soon to be a few more...) all the PDB files downloadable from 
> alphafold.ebi.ac.uk are non-conformant. The documentation on PDB files that I 
> have been able to find easily says - 
> 
> > Details 
> > 
> > * This record is used only when more than one model appears in an entry. 
> > Generally, it is 
> > employed only for NMR structures. The chemical connectivity should be the 
> > same for each model. 
> > ATOM, HETATM, SIGATM, SIGUIJ, ANISOU, and TER records for each model 
> > structure are 
> > interspersed as needed between MODEL and ENDMDL records. 
> > 
> > * The numbering of models is sequential beginning with 1. 
> 
> Harry 
> 
> > 
> > On Fri, Aug 27, 2021 at 11:03 AM Schreuder, Herman /DE 
> >  wrote:
> > Dear Nick,
> > 
> >  
> > 
> > I had just looked at a pdb downloaded from the alphafold server without 
> > problems. However, then I realized that I had looked at the alphafold model 
> > after I had it superimposed on my own structure. Loading the alphafoldmodel 
> > directly in coot failed for me as well.
> > 
> >  
> > 
> > By looking into the pdb file, I discovered that the alphafold file has a 
> > “MODEL” record just before the coordinates and an “ENDMDL” record after the 
> > coordinates. After deleting these two records, the alphafold pdb loads fine.
> > 
> >  
> > 
> > Hope this helps,
> > 
> > Herman
> > 
> >  
> > 
> > Von: CCP4 bulletin board  Im Auftrag von Nicholas 
> > Keep
> > Gesendet: Freitag, 27. August 2021 16:51
> > An: CCP4BB@JISCMAIL.AC.UK
> > Betreff: Re: [ccp4bb] A "funny" thing related to AlphaFold2 
> > 
> >  
> > 
> > Has anyone made use of an Alpha Fold PDB as opposed to CIF.  On the half 
> > dozen or so I have tried to read into CCP4mg or coot the PDB has always 
> > failed but the CIF is fine.  I can then write out a PDB if I want.
> > 
> > I could add to the conspiracy theories that this is EBI trying to 
> > normalise use of CIF format, but I suspect it is something much more 
> > mundane, that should be addressed.
> > 
> > Best wishes
> > 
> > Nick
> > 
> > -- 
> > NOTE NEW PHONE NUMBER JULY 2020
> > 
> > I do not work Mondays. For urgent business on a Monday contact Clare 
> > Woodward (Director of Operations) or Gillian Forrester (Deputy Dean)
> > 
> > Prof Nicholas H. Keep
> > Executive Dean of School of Science
> > Professor of Biomolecular Science
> > Crystallography, Institute for Structural and Molecular Biology,
> > Department of Biological Sciences
> > Birkbeck, University of London,
> > Malet Street,
> > Bloomsbury
> > LONDON
> > WC1E 7HX
> > 
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Re: [ccp4bb] [ccp4bb] A "funny" thing related to AlphaFold2 ....

[Harry Powell - CCP4BB]

Hi folks

Been a while, but I’ve been doing some work on checking that some files are 
valid PDB files and went back to the documentation; as far as I can work out, 
the best solution to this is John Walker’s, because “MODEL 0” is not allowed in 
the standard (maybe it is for mmCIF…) - 

> On 27 Aug 2021, at 16:39, John R. Walker  wrote:
> 
> I just change MODEL 0 to MODEL 1 then it works fine.
> 
> John

As far as I can see (from a small sample of the 150,000 AlphaFold models, soon 
to be a few more...) all the PDB files downloadable from alphafold.ebi.ac.uk 
are non-conformant. The documentation on PDB files that I have been able to 
find easily says - 

> Details 
> 
> * This record is used only when more than one model appears in an entry. 
> Generally, it is 
> employed only for NMR structures. The chemical connectivity should be the 
> same for each model. 
> ATOM, HETATM, SIGATM, SIGUIJ, ANISOU, and TER records for each model 
> structure are 
> interspersed as needed between MODEL and ENDMDL records. 
> 
> * The numbering of models is sequential beginning with 1. 

Harry 

> 
> On Fri, Aug 27, 2021 at 11:03 AM Schreuder, Herman /DE 
>  wrote:
> Dear Nick,
> 
>  
> 
> I had just looked at a pdb downloaded from the alphafold server without 
> problems. However, then I realized that I had looked at the alphafold model 
> after I had it superimposed on my own structure. Loading the alphafoldmodel 
> directly in coot failed for me as well.
> 
>  
> 
> By looking into the pdb file, I discovered that the alphafold file has a 
> “MODEL” record just before the coordinates and an “ENDMDL” record after the 
> coordinates. After deleting these two records, the alphafold pdb loads fine.
> 
>  
> 
> Hope this helps,
> 
> Herman
> 
>  
> 
> Von: CCP4 bulletin board  Im Auftrag von Nicholas Keep
> Gesendet: Freitag, 27. August 2021 16:51
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] A "funny" thing related to AlphaFold2 
> 
>  
> 
> Has anyone made use of an Alpha Fold PDB as opposed to CIF.  On the half 
> dozen or so I have tried to read into CCP4mg or coot the PDB has always 
> failed but the CIF is fine.  I can then write out a PDB if I want.
> 
> I could add to the conspiracy theories that this is EBI trying to 
> normalise use of CIF format, but I suspect it is something much more 
> mundane, that should be addressed.
> 
> Best wishes
> 
> Nick
> 
> -- 
> NOTE NEW PHONE NUMBER JULY 2020
> 
> I do not work Mondays. For urgent business on a Monday contact Clare Woodward 
> (Director of Operations) or Gillian Forrester (Deputy Dean)
> 
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> Executive Dean of School of Science
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> Crystallography, Institute for Structural and Molecular Biology,
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> Malet Street,
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> 
> Office G54a
> 
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> office)
> 
> If you want to access me in person you have to come to the crystallography 
> entrance
> and ring me or the department office from the internal phone by the door
> 
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Re: [ccp4bb] biomolecular NMR for IDPs

[Harry Powell - CCP4BB]

Hi

Forgive me if I’ve missed something, but I can’t find a way to run AlphaFold 
without installing it locally - in which case I need a reasonable GPU.

On the other hand, RoseTTAFold does pretty much the same thing and is available 
via David Baker’s web server - upload your sequence and sit back and wait. The 
overall models that come out are very similar to those from AlphaFold (not 
_quite_ as good…) but are generally available wihtout having to install the 
software and maybe invest in a good GPU (DeepMind doesn’t have to worry about 
the cost or hassle of such things).


https://www.bakerlab.org/index.php/2021/07/15/accurate-protein-structure-prediction-accessible/
 (see the link at the bottom of the page just next to Minkyung Baek’s photo)

On the third hand, both AlphaFold and RoseTTAFold are very good at finding 
models for proteins that have good order at the secondary structure level. I 
don’t know much about IDPs, but I thought that they were intrinsically 
disordered because they lack 3D structure. Secondary structure is most 
certainly three dimensional…

Just another two ha’porth.

Harry

> On 17 Aug 2021, at 16:59, George Sheldrick  wrote:
> 
> 
> 
> 
> As Joel has suggested before, alphafold on an IDP would be interesting and 
> would seem like a zero-cost starting point - perhaps one you have tried 
> already.
> 
> 
> Sent from ProtonMail mobile
> 
> 
> 
>  Original Message 
> On 15 Aug 2021, 15:53, Scott Horowitz < scott.horow...@du.edu> wrote:
> 
> Hi Sorin,
> 
> I hate to say it, but this is a really tough and expensive one. Solving a 
> true conformational ensemble of one IDP of decent size (~>70 residues) at 
> something like decent resolution is hard, and not that many labs actually do 
> it (it's usually a different set of NMR techniques than solving folding 
> proteins, and that knowledge is even somewhat specialized even within the NMR 
> community). Solving a co-structural ensemble of two IDPs that bind is even 
> harder, and I'm hard pressed to remember a single case right now where it's 
> been done (probably has, but very rarely). Assuming they express really well 
> and produce decent spectra, it is in theory doable, but I'd assume multiple 
> years of work by a very good student or postdoc from a lab that specializes 
> in this and many thousands of dollars (I'd very roughly assume ~$10k in 
> materials costs alone) would be required for that co-structure.
> 
> The SAXS route is certainly less expensive and faster if it works and gets 
> you the info you need, but it certainly will be low-res. I'm not as familiar 
> with it, but if you can differentially label the proteins, the neutron 
> equivalent of SAXS might also help with the co-structural ensemble to 
> differentiate which protein is where in the resulting blob.
> 
> Scott
> 
> Scott Horowitz, Ph.D.
> Assistant Professor
> Department of Chemistry & Biochemistry
> Knoebel Institute for Healthy Aging
> University of Denver
>  
> ECS Building
> 2155 E. Wesley Ave
> Denver, CO 80208
> Phone: 303-871-4326
> Fax: 303-871-7915
> Zoom Room: https://udenver.zoom.us/my/scotthorowitz
> Email: scott.horow...@du.edu
> Office: Room 561   Lab: Room 505
> 
> From: CCP4 bulletin board  on behalf of Roopa Thapar 
> <070a21fba45f-dmarc-requ...@jiscmail.ac.uk>
> Sent: Sunday, August 15, 2021 8:20 AM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [EXTERNAL] Re: [ccp4bb] biomolecular NMR for IDPs
>  
> [External Email From]: owner-ccp...@jiscmail.ac.uk
> 
> 
> Hello Sorin,
> 
> 
> 1. The cost of getting NMR data on the IDPs you propose depends upon the 
> expression levels of the protein/s as you will need to label with 15N and 13C 
> - and depending upon your overall yields per liter of E.coli culture, this 
> can add up.  In addition you will need to run triple resonance experiments - 
> so you should look into the hourly charge to access the NMR spectrometers 
> where you are located.  Moreover, you need to account for time required for 
> optimization of solution conditions to collect the NMR data as the sample 
> needs to be homogenous (as in no aggregation) at millimolar or hundreds of 
> micromolar concentration.   As Ethan Merritt suggested, it would be a good 
> idea to use SAXS first as it requires very little sample, no isotope 
> labeling, and you can try to narrow down the solution conditions that would 
> be best suited for NMR.  The Kratky plots, Rg values under different solution 
> conditions can give very useful information about conformational states and 
> ensembles populated by IDPs.  However, although NMR tends to be more 
> expensive than other techniques but is perfect for IDPs as you point out you 
> can get residue specific information.  A combined NMR/SAXS approach has 
> proven to be very useful to validate computational models.
> 
> 2. In general, CROs are much more expensive particularly for generating 
> isotopically labeled samples - it is cost-prohibitive for academic labs.  
> 

Re: [ccp4bb] biomolecular NMR for IDPs

[Harry Powell - CCP4BB]

Hi

Just my two ha’porth.

I’m currently involved in a project where my collaborators are investigating 
the interactions between protein pairs (both hetero and homo) - they 
specifically asked me _not_ to give them any models from ensembles (actually, 
they said “no NMR structures because they are ensembles") - because (unless 
they try their “docking” with every member of the ensemble) they have no idea 
which member of the ensemble they should use for their studies. If you don't 
actually know how the different parts of a protein are oriented with respect to 
itself, how can you know how they will be disposed to another protein?

Which is not to say you shouldn’t try (or even that I’m right) - what it does 
indicate is that if you include ensembles (from any source) you are going to 
make your life harder and also possibly cast doubt on the results.

Harry


> On 15 Aug 2021, at 14:57, Krieger, James M  wrote:
> 
> It is possible to get an ensemble for an intrinsically disordered segment 
> from NMR. We did this in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4008819/
> 
> Best wishes 
> James 
> 
>> On Aug 15, 2021, at 14:48, Jon Cooper 
>> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Hello, my numpty-level understanding is that being intrinsically disorder 
>> and giving high-resolution structural data are mutually exclusive. I will 
>> re-read your e-mails. Hope this helps. Cheers, Jon.C.
>> 
>> 
>> Sent from ProtonMail mobile
>> 
>> 
>> 
>>  Original Message 
>> On 15 Aug 2021, 09:16, Sorin Draga < sor.dr...@gmail.com> wrote:
>> 
>> Hello Ethan, 
>> 
>> Thank you for the suggestions. I should have mentioned in my initial post 
>> that my intention is to first conduct a high throughput virtual screening on 
>> these proteins, thus I would need high "resolution" of the structures which 
>> SAXS could not provide, as far as I understand.
>> SAXS/SAS might become useful at a later stage, when I have a small number of 
>> potential inhibitors identified.
>> 
>> Kind regards,
>> 
>> Sorin
>> 
>> On Sat, Aug 14, 2021 at 5:55 PM Ethan A Merritt  wrote:
>> It is possible that you could address some of your questions
>> more quickly and much more cheaply by small-angle scattering,
>> either light (SAS) or X-ray (SAXS).
>> 
>> I would suggest looking into those avenues first.
>> 
>> If you have well behaved (i.e. non-aggregating) purified proein
>> and access to synchrotron beam time (easily requested),
>> a series of SAXS experiments could probably be conducted in one day.
>> I don't want to oversell SAXS, I'm not really an enthusiast.
>> But this case, categorizing the interaction of two poorly ordered proteins
>> in solution and in particular the facilitation or disruption of this
>> interaction by small molecules, should be well within its scope.
>> 
>> best
>> 
>> Ethan
>> 
>> On Saturday, 14 August 2021 14:12:40 PDT Sorin Draga wrote:
>> > Hello everyone,
>> > 
>> > I do realize that this is not a NMR focused group, but I do hope that there
>> > are a few spectroscopists lurking around that could possibly answer a few
>> > questions (I am more of a modeler/computationalist):
>> > 
>> > The problem: I have two intrinsically disordered proteins that are known to
>> > interact (let's call them 1 and 2). I would like to get structural
>> > information (a conformational ensemble) for 1 and for the "complex" (1+2).
>> > Further down the line (depending on whether this is possible) I would also
>> > like to evaluate potential small molecule inhibitors for the said complex.
>> > Both 1 and 2 are <200 aminoacids long.
>> > 
>> > The questions:
>> > 
>> > 1. Could the cost of determining the "structure" for 1 and 1+2 be
>> > estimated? To be more precise, I am looking for a ball-park figure on how
>> > much a NMR measurement would cost in this case.
>> > 2. Could anyone recommend a good group/CRO that could provide such a
>> > service and not have an astronomical cost?
>> > 3. Any other suggestions/thoughts that you think might be worth mentioning
>> > (minimum quantity of protein necessary, purity, type of NMR etc)
>> > 
>> > Many thanks for your help and time!
>> > 
>> > Cheers!
>> > 
>> > Sorin
>> > 
>> > 
>> > 
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> > 
>> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>> > list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
>> > https://www.jiscmail.ac.uk/policyandsecurity/
>> > 
>> 
>> 
>> -- 
>> Ethan A Merritt
>> Biomolecular Structure Center,  K-428 Health Sciences Bldg
>> MS 357742,   University of Washington, Seattle 98195-7742
>> 
>> 
>> 
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Re: [ccp4bb] AI papers in experimental macromolecular structure determination

[Harry Powell - CCP4BB]

Hi folks

This is probably a good time to mention that both Melanie and Andrea will be 
giving presentations at the IUCr in Prague in a couple of weeks or so in the 
Commission for Crystallographic Computing session chaired by Rita Giordano - 

MS-73 Machine learning in biological and structural sciences 
Friday 20th August 2021 10:20 - 12:45

Harry

> On 4 Aug 2021, at 10:11, Vollmar, Melanie (DLSLtd,RAL,LSCI) 
> <64fe7ccc6b4d-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> I don't have a list to add here, as my review on the topic awaits feedback on 
> the corrections (self-advertisement ) but perhaps we should consider that 
> machine learning and AI are two different beasts. Admittingly, I don't always 
> make a proper distinction either.
> 
> Surely, many of us get their heads around machine learning, which usually 
> covers so called shallow learners that firmly sit in well-known concepts of 
> statistics. This type of machine learning doesn't require many resources and 
> is accessible to almost anyone with an average laptop. Plenty of software in 
> MX and EM use these tools and no-one every thinks about them.
> 
> I think, Andrea, perhaps, was looking more into the direction of AI (based on 
> so many cryo-EM references listed , where this is a standard tool), which 
> requires a lot more understanding and thought as well as resources and would 
> appear to many as a magic black box. This type of machine learning has only 
> recently taken off due to huge leaps in hardware development, which many of 
> us can't afford to buy, unless it is provided through some shared resource. 
> Having said that, an average graphics card GPU is often a good start. And if 
> one isn't the book reading kind (usually due to lack of time), there are lots 
> of good blogs, videos and other online resources to get one into the basics.
> 
> The papers that should clearly be added, are those for protein structure 
> prediction, as, in a way, they determine a structure, albeit with a different 
> kind of experiment:
> 
> https://science.sciencemag.org/content/early/2021/07/19/science.abj8754
> https://www.nature.com/articles/s41586-021-03819-2
> 
> Cheers
> 
> M
> From: CCP4 bulletin board  on behalf of Nave, Colin 
> (DLSLtd,RAL,LSCI) <64fdcfc6624b-dmarc-requ...@jiscmail.ac.uk>
> Sent: 04 August 2021 09:34
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] AI papers in experimental macromolecular structure 
> determination
>  
> Bernhard
> What qualifies? Good question. 
> There are plenty of books on AI/machine learning but, as always, it is more 
> efficient/lazier to read reviews than the books themselves. I think the 
> London Review of Books allows limited access to its articles so most should 
> be able to read this
> https://www.lrb.co.uk/the-paper/v43/n02/paul-taylor/insanely-complicated-hopelessly-inadequate?referrer=https%3A%2F%2Fwww.google.com%2F
> It might be interesting (though perhaps not useful)  to classify the examples 
> for macromolecular structure determination in to categories such as GOFAI 
> etc. However, this particular term is rather pejorative as it would mean 
> describing the developers as old fashioned!
> 
> Colin
> 
> 
> 
> 
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Bernhard Rupp
> Sent: 03 August 2021 21:00
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] AI papers in experimental macromolecular structure 
> determination
> 
> Maybe we should get to the root of this - what qualifies as machine learning 
> and what not?
> 
> Do nonparametric predictors such as KDE qualify?
> 
> https://www.ruppweb.org/mattprob/default.html
> 
> Happy toa dd to the confusion.
> 
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Tim Gruene
> Sent: Tuesday, August 3, 2021 11:59
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] AI papers in experimental macromolecular structure 
> determination
> 
> Hello Andrea,
> 
> profile fitting, like it is done in mosflm
> (https://doi.org/10.1107/S090744499900846X) or evalccd, or ... probably also 
> qualify as AI/machine learning.
> 
> Best wishes,
> Tim
> 
> On Tue, 3 Aug 2021 11:43:06 +
> "Thorn, Dr. Andrea"  wrote:
> 
> > Dear colleagues,
> > I have compiled a list of papers that cover the application of 
> > AI/machine learning methods in single-crystal structure determination 
> > (mostly macromolecular crystallography) and single-particle Cryo-EM.
> > The draft list is attached below.
> > 
> > If I missed any papers, please let me know. I will send the final list 
> > back here, for the benefit of all who are interested in the topic.
> > 
> > Best wishes,
> > 
> > 
> > Andrea.
> > 
> > 
> > __
> > General:
> > - Gopalakrishnan, V., Livingston, G., Hennessy, D., Buchanan, B. & 
> > Rosenberg, J. M. (2004). Acta Cryst D. 60, 1705–1716.
> > - Morris, R. J. (2004). Acta Cryst D. 60, 2133–2143.
> > 
> > Micrograph preparation:
> > - (2020). Journal of Structural Biology. 210, 107498.
> > 

[ccp4bb] interesting paper...

[Harry Powell - CCP4BB]

Readers of this BB may be interested in the following paper from DeepMind - 

https://www.nature.com/articles/s41586-021-03819-2_reference.pdf

referenced from 

https://www.nature.com/articles/s41586-021-03819-2

Of course, you should never just open a link contained in an e-mail…

Harry


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Re: [ccp4bb] Lowering R factor from small molecule structure

[Harry Powell - CCP4BB]

I’d have to say that Phil is possibly one of the small molecule 
crystallographers who could probably sort this out in a flash - hence my last 
suggestion…

Harry

> On 4 Jun 2021, at 14:40, Phil Jeffrey  wrote:
> 
> Unlike macromolecular crystallography, small molecule crystallography is 
> infrequently starved for data.  So it makes no sense at all to extend your 
> data to e.g. I/sigI of 1.0 amd Rmeas > 80% unless you want your R1 to be >10% 
> for no good reason or utility, which is what was behind my suggestion - test 
> to see if the data cutoff is an issue.  Also about the fastest test you can 
> do in SHELXL.
> 
> > Yes, ANIS and adding hydrogens (in SHELXL) are good things to do - with 
> > 0.8Å data most small molecule crystallographers would do this as a first 
> > step after fitting all the non-H atoms.
> 
> Actually, adding AnisoB's and hydrogens too soon will mess up your disorder 
> modeling, so blanket statements like that work for well-behaved structures 
> but not so much for more challenging ones.
> 
> e.g. in one of the the four structures I've done this week, one had 
> significant main-molecule disorder so that comes ahead of adding hydrogens, 
> and refining unrestrained anisoB (as is the default) for disordered atoms is 
> asking for trouble.  It's not as cookie-cutter as you represent, and I stick 
> to all my suggestions.
> 
> Phil Jeffrey
> Princeton
> 
> On 6/4/21 4:27 AM, Harry Powell - CCP4BB wrote:
>> Hi
>> Yes, ANIS and adding hydrogens (in SHELXL) are good things to do - with 0.8Å 
>> data most small molecule crystallographers would do this as a first step 
>> after fitting all the non-H atoms.
>> One thing I can’t agree with is to cut the resolution of your data _unless_ 
>> you have a very, very good reason to do so. Normal small molecule 
>> refinements will use data to ~0.8Å and not use a cut-off based on resolution 
>> or I/sig(I). A good dataset will often go to higher resolution and small 
>> molecule crystallographers will be very happy to use these data (unless, as 
>> I say, they have a very good reason not to), and would certainly have to 
>> “explain to the referees” why they didn’t if they ignored a systematic chunk.
>> Something else that you might not have thought of - have you actually told 
>> SHELXL what the reflection data are - i.e., are they F, F^2, intensity? It’s 
>> perfectly possible to solve a small molecule structure by e.g. telling the 
>> program you’re giving it F^2 but actually giving it F, but refinement would 
>> be somewhat less straightforward. SHELXL normally uses F^2 in refinement, 
>> macromolecular programs still normally use F (AFAIK).
>> What programs did you use for processing the diffraction data?
>> Of course, lowering the R factor is not the objective of the exercise - a 
>> lower R-factor is a consequence of having a model that fits the data better.
>> I would be strongly inclined to ask a small molecule crystallographer (or 
>> someone with a strong background in it) to have a look at your data & model 
>> - they could probably give you a definitive answer by return of e-mail.
>> Just my two ha’porth
>> Harry
>>> On 4 Jun 2021, at 03:10, Jon Cooper 
>>> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>>> 
>>> Agreed, ANIS is the command to try.
>>> 
>>> Sent from ProtonMail mobile
>>> 
>>> 
>>> 
>>>  Original Message 
>>> On 3 Jun 2021, 20:18, Philip D. Jeffrey < pjeff...@princeton.edu> wrote:
>>> 
>>> R1 of 17% is bad for small molecule.
>>> 0.8 Å is in the eye of the beholder - if you're using macromolecular 
>>> cutoffs then these might be too aggressive for small molecule-type 
>>> refinement stats - try a more conservative cutoff lie 0.9 and see how that 
>>> changes R1.  However I suspect it's more to do with how your model is 
>>> fitting the data.
>>> 
>>> Have you refined anisotropic Bfactors ?
>>> Have you added hydrogens ?
>>> 
>>> I would suggest non-CCP4 programs like Olex2 or SHELXLE as the interface 
>>> for the refinements - I use the latter and it's somewhat Coot like with 
>>> useful features that are particular to small molecule.  Also PLATON has 
>>> some things (like expand-to-P1 and Squeeze) that, respectively, might be 
>>> useful to explore space group issues and disordered solvent.  PLATON also 
>>> has a means to check for some forms of twinning.
>>> 
>>> Phil Jeffrey
>>> Princeton
>>> From: CCP4 bulletin board  on behalf of Jacob 
>>

Re: [ccp4bb] Lowering R factor from small molecule structure

[Harry Powell - CCP4BB]

Hi

Yes, ANIS and adding hydrogens (in SHELXL) are good things to do - with 0.8Å 
data most small molecule crystallographers would do this as a first step after 
fitting all the non-H atoms.

One thing I can’t agree with is to cut the resolution of your data _unless_ you 
have a very, very good reason to do so. Normal small molecule refinements will 
use data to ~0.8Å and not use a cut-off based on resolution or I/sig(I). A good 
dataset will often go to higher resolution and small molecule crystallographers 
will be very happy to use these data (unless, as I say, they have a very good 
reason not to), and would certainly have to “explain to the referees” why they 
didn’t if they ignored a systematic chunk.

Something else that you might not have thought of - have you actually told 
SHELXL what the reflection data are - i.e., are they F, F^2, intensity? It’s 
perfectly possible to solve a small molecule structure by e.g. telling the 
program you’re giving it F^2 but actually giving it F, but refinement would be 
somewhat less straightforward. SHELXL normally uses F^2 in refinement, 
macromolecular programs still normally use F (AFAIK).

What programs did you use for processing the diffraction data?

Of course, lowering the R factor is not the objective of the exercise - a lower 
R-factor is a consequence of having a model that fits the data better.

I would be strongly inclined to ask a small molecule crystallographer (or 
someone with a strong background in it) to have a look at your data & model - 
they could probably give you a definitive answer by return of e-mail.

Just my two ha’porth

Harry

> On 4 Jun 2021, at 03:10, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Agreed, ANIS is the command to try. 
> 
> Sent from ProtonMail mobile
> 
> 
> 
>  Original Message 
> On 3 Jun 2021, 20:18, Philip D. Jeffrey < pjeff...@princeton.edu> wrote:
> 
> R1 of 17% is bad for small molecule.
> 0.8 Å is in the eye of the beholder - if you're using macromolecular cutoffs 
> then these might be too aggressive for small molecule-type refinement stats - 
> try a more conservative cutoff lie 0.9 and see how that changes R1.  However 
> I suspect it's more to do with how your model is fitting the data.
> 
> Have you refined anisotropic Bfactors ?
> Have you added hydrogens ?
> 
> I would suggest non-CCP4 programs like Olex2 or SHELXLE as the interface for 
> the refinements - I use the latter and it's somewhat Coot like with useful 
> features that are particular to small molecule.  Also PLATON has some things 
> (like expand-to-P1 and Squeeze) that, respectively, might be useful to 
> explore space group issues and disordered solvent.  PLATON also has a means 
> to check for some forms of twinning.
> 
> Phil Jeffrey
> Princeton
> From: CCP4 bulletin board  on behalf of Jacob Summers 
> <60a137e4bf3a-dmarc-requ...@jiscmail.ac.uk>
> Sent: Thursday, June 3, 2021 2:49 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [ccp4bb] Lowering R factor from small molecule structure
>  
> Greetings!
> 
> I am currently trying to reduce the R factor of a cyclic small molecule 
> peptoid in ShelXle. The max resolution of the molecule is 0.8 angstroms. The 
> molecule itself fits the density very well, but there are a few unexplained 
> densities around the molecule which do not seem to be anything in the 
> crystallization conditions. The R1 factor of the refinement is 17.07% but I 
> am unsure how to lower this value. Any ideas on how to better refine this 
> molecule or fill densities to lower the R1 factor? I do not have much 
> experience working with small molecule refinement or with ShelX.
> 
> Thanks so much,
> Jacob Summers
> 
> 
> 
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Re: [ccp4bb] Analysis of NMR ensembles

[Harry Powell - CCP4BB]

This even seems to have a”batch” mode (similar to the well-known homology 
modelling server Phyre2) that might accept a zip file containing multiple PDBs. 
If it does, and if it will take my ~700 PDBs, then that would save me a little 
bit of scripting.

Harry

> On 27 May 2021, at 22:03, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> A bit late, I know, but a bit more googling gave me this site which I don't 
> think has been mentioned so far:
> 
> http://old.protein.bio.unipd.it/mobi/
> 
> Given the pdb code, it is a one click job to get a pdb file with the 
> "B-factors changed to averaged Scaled Distance x 100" and the resulting 
> picture (attached) looks about right, I think/hope.
> 
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
> 
> Sent with ProtonMail Secure Email.
> 
> ‐‐‐ Original Message ‐‐‐
> On Thursday, 27 May 2021 08:48, Harry Powell - CCP4BB 
>  wrote:
> 
>  Hi Jon
> 
>  The RMSD data (also NOEs, chemical shifts, etc) are not in the original 
> PDB so I would have to calculate them - which takes me to my original 
> question!
> 
>  Harry
> 
>   On 26 May 2021, at 17:22, Jon Cooper jon.b.coo...@protonmail.com 
> wrote:
>   Hello Harry,
>   Looking at:
>   http://www.mcgnmr.mcgill.ca/ProtSkin/
>   It says: "If your input is a plain file containing your scalar data 
> to map, such as heteronuclear NOE or chemical shift differences, ensure the 
> first column in your file contains residue numbers and the second column 
> contains the values to map, then click the Browse button to retrieve this 
> file and select "Plain list of scores"
>   If you can get the residue number and rmsd data into columns in a 
> file, it should map them onto a pdb file for one monomer as pseudo-B-factors.
>   HTH, Jon.C.
>   Sent from ProtonMail mobile
>    Original Message 
>   On 26 May 2021, 16:51, Harry Powell - CCP4BB  
> hrp-ccp...@virginmedia.com wrote:
>   Yes, Jon, but I was hoping I wasn’t the first person to ever want 
> this…
>   Harry
>  
>On 26 May 2021, at 16:34, Jon Cooper 
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk wrote:
>The hard bit is to get the rmsd's into the B-factor column, 
> but it shouldn't stretch you too much, Harry ;-
>    There is ProtSkin on the web which does something similar with 
> sequence alignments.
>Sent from ProtonMail mobile
> Original Message 
>On 26 May 2021, 16:28, Harry Powell - CCP4BB  
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk wrote:
>Hi Jurgen
>NMR structures don’t appear to have B_factors, or at least not 
> meaningful ones (e.g. in 2kv5 they’re all 0.00…).
>thanks for the response, though
>    Harry
>   
> On 26 May 2021, at 16:21, Jurgen Bosch jxb...@case.edu 
> wrote:
> How about color by B-factor and look for the cold areas 
> and hot areas?
> Jürgen
>
>  On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB 
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk wrote:
>  Hi
>  Given that there are plenty of people on this BB who 
> are structural biologists rather than “just” crystallographers, I thought 
> someone here might be able to help.
>  If I have a structure in the PDB (e.g. 2kv5) that is 
> an ensemble of structures that fit the NOEs, is there a tool available that 
> will give me some idea about the bits of the structure that do not vary much 
> (“rigid”) and the bits that are all over the place (“flexible”)?
>  Would superpose or gesamt be a good tool for this? 
> Ideally I’d like something that could add a figure to the B columns in a PDB 
> file so I could see something in QTMG (or PyMol if forced…) or do other 
> useful things with the information.
>  Harry
>  
> 
>  To unsubscribe from the CCP4BB list, click the 
> following link:
>  
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> #

Re: [ccp4bb] Analysis of NMR ensembles

[Harry Powell - CCP4BB]

Cool…

Purely for visualisation this does look like the approved CCP4 way - 



Harry

> On 27 May 2021, at 10:01, Stuart McNicholas 
> <19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Drawing style (right menu in display table) -> Worm scaled by -> Worm
> scaled by NMR variability
> 
> in ccp4mg?
> 
> This changes the size of the worm but not the colour.
> 
> On Thu, 27 May 2021 at 09:56, Harry Powell - CCP4BB
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Anyway, thanks to all those who answered my original question - especially
>> 
>>Tristan: Chimerax (+ his attached script)
>>Michal, Scott: Theseus (https://theobald.brandeis.edu/theseus/)
>>Bernhard: Molmol (https://pubmed.ncbi.nlm.nih.gov/8744573/ )
>>Rasmus CYRANGE (http://www.bpc.uni-frankfurt.de/cyrange.html) and 
>> https://www.ccpn.ac.uk/ (of course…)
>>Andrew (uwmn - not sure if this is buildable on a modern box)
>>Smita: PyMol (not sure if I’m allowed to say that on ccp4bb…)
>> 
>> or I could script it and use Gesamt or Superpose for the superposition if I 
>> wanted to stay in the ccp4 universe and had the time to spare ;-)
>> 
>> Harry
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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> 
> 
> 
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Re: [ccp4bb] Analysis of NMR ensembles

[Harry Powell - CCP4BB]

Anyway, thanks to all those who answered my original question - especially 

Tristan: Chimerax (+ his attached script)
Michal, Scott: Theseus (https://theobald.brandeis.edu/theseus/)
Bernhard: Molmol (https://pubmed.ncbi.nlm.nih.gov/8744573/ )
Rasmus CYRANGE (http://www.bpc.uni-frankfurt.de/cyrange.html) and 
https://www.ccpn.ac.uk/ (of course…)
Andrew (uwmn - not sure if this is buildable on a modern box)
Smita: PyMol (not sure if I’m allowed to say that on ccp4bb…)

or I could script it and use Gesamt or Superpose for the superposition if I 
wanted to stay in the ccp4 universe and had the time to spare ;-)

Harry



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Re: [ccp4bb] Analysis of NMR ensembles

[Harry Powell - CCP4BB]

Hi

This is why I put “rigid” and “flexible” in quotes in my original post - to 
allow people to put whatever interpretation on them that they chose (within 
limits)! 

Of course, it’s always best to try to use the correct terms in a scientific 
discussion, but we all use shorthand; e.g., in crystallography we’re (mostly) 
happy to talk about “reflections” (even Lawrence Bragg did, but spelt it with 
an “x” not “ct”) when we all know that they aren’t specular reflections, which 
is what most people (including physicists) mean by the word…

Harry

> On 26 May 2021, at 22:06, Dale Tronrud  wrote:
> 
> Dear Boaz,
> 
>   We are likely in agreement. "Deficient NOE's for some regions (e.g. loops) 
> arise from their flexibility, ..."  This makes it sound like you agree that 
> these deficiencies in other regions may be caused by properties other than 
> flexibility.
> 
>   As an extreme example, the N-terminal region of a protein may have a broad 
> distribution in the ensemble model either because this region experiences 
> many conformations in solution, or because this peptide was cleaved from the 
> protein at some earlier time and its absence was not recognized by the 
> experimentalist.
> 
> Dale Tronrud
> 
> On 5/26/2021 1:06 PM, Boaz Shaanan wrote:
>> Hi Dale and Cecil,
>> This is quite a circular argument, isn't it? Deficient NOE's for some 
>> regions (e.g. loops) arise from their flexibility, hence they are not as 
>> well resolved as other (e.g. internal ) regions for which the number of NOE 
>> is large. So they are flexible by all accounts and, not surprisingly, align 
>> usually with high B-factor regions in the corresponding crystal structures. 
>> In cases where such flexible regions are held by crystal contacts the 
>> situations would likely be different.
>> 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
>> Fax:   972-8-647-2992 or 972-8-646-1710 /
>> //
>> //
>> /
>> /
>> 
>> *From:* CCP4 bulletin board  on behalf of Dale 
>> Tronrud 
>> *Sent:* Wednesday, May 26, 2021 10:46 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK 
>> *Subject:* Re: [ccp4bb] Analysis of NMR ensembles
>> I agree with Dr Breyton. The variability in an NMR ensemble does not
>> reflect "mobility" but simply "uncertainty" in conformation.  The spread
>> in coordinates in some regions simply reflects the lack of experimental
>> data which could define a single conformation.  There are many reasons
>> why these data are be absent and high mobility is only one.
>> Dale Tronrud
>> On 5/26/2021 8:45 AM, Cécile Breyton wrote:
>>> Hello,
>>> In my understanding of NMR, the loops and terminii that adopt very 
>>> different conformations in the structure ensemble rather reflect the fact 
>>> that for those residues, the number of constraints is lower, thus the 
>>> number of structures that fulfil the constraints is larger A dynamics 
>>> study of the protein will be much more informative.
>>> Cécile
>>> Le 26/05/2021 à 17:29, S. Mohanty a écrit :
>>>> Hi Harry,
>>>> 
>>>> The superpose/overlay of all the structures in PyMol should inform you the 
>>>> rigid part of the protein as well as the flexible part. The rigid part 
>>>> would have very low backbone RMSD or overlay tightly and the flexible part 
>>>> (loops, N-term and C-term etc.) would not superpose tightly. If you check 
>>>> literature, the dynamics of the protein may have been studied through NMR 
>>>> relaxation.
>>>> 
>>>> Smita
>>>> 
>>>> 
>>>> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB 
>>>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>>> 
>>>> 
>>>> Hi
>>>> 
>>>> Given that there are plenty of people on this BB who are structural 
>>>> biologists rather than “just” crystallographers, I thought someone here 
>>>> might be able to help.
>>>> 
>>>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of 
>>>> structures that fit the NOEs, is there a tool available that will give me 
>>>> some idea about the bits of the structure that do not vary much (“rigid”) 
>>>> and the bits that are all over the place (“flexible”)?
>

Re: [ccp4bb] Analysis of NMR ensembles

[Harry Powell - CCP4BB]

Hi Smita

Yes, that’s the kind of analysis I had in mind.

I have > 700 structures to “look” at so something that would say “these 
residues overlay with a small RMSD so this bit is rigid, but these residues 
don’t, so that part is flexible” ~700 times. 

Using an MG program of any kind would just be a sanity check that I’d use on a 
very few structures (probably no more than ~20-30) to make sure I’m happy with 
the results before automating the whole thing.

Harry

> On 26 May 2021, at 16:29, S. Mohanty  wrote:
> 
> Hi Harry,
> 
> The superpose/overlay of all the structures in PyMol should inform you the 
> rigid part of the protein as well as the flexible part. The rigid part would 
> have very low backbone RMSD or overlay tightly and the flexible part (loops, 
> N-term and C-term etc.) would not superpose tightly. If you check literature, 
> the dynamics of the protein may have been studied through NMR relaxation. 
> 
> Smita
> 
> 
> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> 
> Hi
> 
> Given that there are plenty of people on this BB who are structural 
> biologists rather than “just” crystallographers, I thought someone here might 
> be able to help.
> 
> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of 
> structures that fit the NOEs, is there a tool available that will give me 
> some idea about the bits of the structure that do not vary much (“rigid”) and 
> the bits that are all over the place (“flexible”)?
> 
> Would superpose or gesamt be a good tool for this? Ideally I’d like something 
> that could add a figure to the B columns in a PDB file so I could see 
> something in QTMG (or PyMol if forced…) or do other useful things with the 
> information.
> 
> Harry
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> 
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Re: [ccp4bb] Analysis of NMR ensembles

[Harry Powell - CCP4BB]

Hi Jurgen

NMR structures don’t appear to have B_factors, or at least not meaningful ones 
(e.g. in 2kv5 they’re all 0.00…). 

thanks for the response, though

Harry

> On 26 May 2021, at 16:21, Jurgen Bosch  wrote:
> 
> How about color by B-factor and look for the cold areas and hot areas?
> Jürgen 
> 
>> On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Hi
>> 
>> Given that there are plenty of people on this BB who are structural 
>> biologists rather than “just” crystallographers, I thought someone here 
>> might be able to help.
>> 
>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of 
>> structures that fit the NOEs, is there a tool available that will give me 
>> some idea about the bits of the structure that do not vary much (“rigid”) 
>> and the bits that are all over the place (“flexible”)?
>> 
>> Would superpose or gesamt be a good tool for this? Ideally I’d like 
>> something that could add a figure to the B columns in a PDB file so I could 
>> see something in QTMG (or PyMol if forced…) or do other useful things with 
>> the information.
>> 
>> Harry
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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> 
> 
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[ccp4bb] Analysis of NMR ensembles

[Harry Powell - CCP4BB]

Hi

Given that there are plenty of people on this BB who are structural biologists 
rather than “just” crystallographers, I thought someone here might be able to 
help.

If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of structures 
that fit the NOEs, is there a tool available that will give me some idea about 
the bits of the structure that do not vary much (“rigid”) and the bits that are 
all over the place (“flexible”)?

Would superpose or gesamt be a good tool for this? Ideally I’d like something 
that could add a figure to the B columns in a PDB file so I could see something 
in QTMG (or PyMol if forced…) or do other useful things with the information.

Harry


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Re: [ccp4bb] Converting data set to another format?

[Harry Powell - CCP4BB]

Hi Dirk

Converting to a form that Mosflm can read is not too much of a problem - the 
problem arises because Kappa CCD images are not corrected for spatial 
distortions, which can be significant. 

I think you would need a correction table (or similar - maybe “brass plate” 
images if you have them); it’s possible that d*Trek (Jim Pflugrath) might be 
able to convert for you (or even process the images, since it was quite popular 
in the days when Kappa CCDs were around), or Fit2D (Andy Hammersley) might work 
- but I don’t think either program is maintained (the Fit2D website says it was 
last updated in 1997…).

Harry Powell

> On 21 May 2021, at 03:45, Dirk Bussiere 
> <5f8efc77064a-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Dear colleagues,
>  
> I have an old data set collected on a Nonius Kappa CCD (.kcd format).   I 
> would like to convert the frames from the .kcd Nonius format to a format 
> which would allow me to process the data with Mosflm.   Might anyone have 
> suggestions on how to do this?   I am struggling to find a conversion program 
> or route.  Thank you.
>  
> -Dirk
>  
> Dirksen Bussiere, Ph.D., M.B.A.
> Sr. Director/Head, Molecular Pharmacology
> Lilly Research Laboratories
> Eli Lilly and Company
> Lilly Biotechnology Center
> 10290 Campus Point Dr.   E-mail: 
> bussiere_dirk...@lilly.com
> San Diego, CA 92121
>  
>  
> 
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Re: [ccp4bb] ccp4i2 crashes on MacOSX 10.13.6 - High Sierra

[Harry Powell - CCP4BB]

Blimey, I’m surprised I found this about 15 minutes after posting, having spent 
all this week trying to locate it.

It *seems* that I had libs from an openssl installed via Homebrew that the 
openssl supplied with CCP4 found before its own. Deleting those files 
(/usr/local/lib/libssl.1.1.dylib and its link /usr/local/lib/libssl.dylib) 
looks like it’s solved my problem.

Talk about needles in haystacks…

Harry

> On 21 Apr 2021, at 10:42, Harry Powell - CCP4BB  
> wrote:
> 
> Hi folks
> 
> I have an old-ish Mac (Mac Pro, mid-2010, 3.46 6-core Intel Xeon, 32GB RAM) 
> running High Sierra (OSX 10.13.6) - the box will not support newer versions 
> of OSX or MacOS, so I can’t “upgrade” any further on the OS front (well, I 
> could if I really wanted to hack beyond Apple’s recommendations). 
> 
> I’ve been in touch with CCP4 central, but they have been unable to reproduce 
> my issue (over the course of several days), so I though I would ask here…
> 
> Please don’t say “buy a new Mac”...
> 
> It runs the CCP4 programs as per spec if I avoid CCP4I2, e.g. runs DIALS, 
> runs iMosflm, runs QTMG, runs Coot, etc etc etc.
> 
> BUT, if I run ccp4i2 problems soon follow - 
> 
> (1) start iMosflm - I get the “running man” and that’s all. If I try to stop 
> the job with any of the four options, I2 crashes.
> 
> (2) if I have any jobs in the Job list and left click in that window, I2 
> crashes.
> 
> (3) If I run xia2, the job starts and appears to run, but when I leave the 
> xia2 task, I2 crashes.
> 
> (4) Try to run Coot from I2, it never starts.
> 
> I get a whole bunch of errors if I launch a console that indicate there’s an 
> issue with QT and SSL (I won’t bore everyone here with the details) so it’s 
> likely there’s something wrong there.
> 
> Any (useful) ideas?
> 
> Harry
> 
> 



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[ccp4bb] ccp4i2 crashes on MacOSX 10.13.6 - High Sierra

[Harry Powell - CCP4BB]

Hi folks

I have an old-ish Mac (Mac Pro, mid-2010, 3.46 6-core Intel Xeon, 32GB RAM) 
running High Sierra (OSX 10.13.6) - the box will not support newer versions of 
OSX or MacOS, so I can’t “upgrade” any further on the OS front (well, I could 
if I really wanted to hack beyond Apple’s recommendations). 

I’ve been in touch with CCP4 central, but they have been unable to reproduce my 
issue (over the course of several days), so I though I would ask here…

Please don’t say “buy a new Mac”...

It runs the CCP4 programs as per spec if I avoid CCP4I2, e.g. runs DIALS, runs 
iMosflm, runs QTMG, runs Coot, etc etc etc.

BUT, if I run ccp4i2 problems soon follow - 

(1) start iMosflm - I get the “running man” and that’s all. If I try to stop 
the job with any of the four options, I2 crashes.

(2) if I have any jobs in the Job list and left click in that window, I2 
crashes.

(3) If I run xia2, the job starts and appears to run, but when I leave the xia2 
task, I2 crashes.

(4) Try to run Coot from I2, it never starts.

I get a whole bunch of errors if I launch a console that indicate there’s an 
issue with QT and SSL (I won’t bore everyone here with the details) so it’s 
likely there’s something wrong there.

Any (useful) ideas?

Harry



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Re: [ccp4bb] Ice ring data issue

[Harry Powell - CCP4BB]

Hi Alex

Have a look at Auspex - it may be able to help

AUSPEX (www.auspex.de)

Harry

> On 4 Mar 2021, at 15:39, Alexander Brown  
> wrote:
> 
> Hi all,
> I'm struggling with a dataset I have which shows very poor data quality 
> around 3.6A, or exactly where I can see a significant ice ring in the images. 
> I'm trying to use mosflm to process the image files, and I have seen a 
> previous thread on the message board where it is recommended to turn on three 
> tick boxes for ice ring exclusion, but despite this, as I continue through 
> the processing sequence and use aimless, it still flags that the data is 
> affected by an ice ring at that resolution, which you can also see in the 
> quality/resolution graphs. 
> 
> I have even tried making a mask in the moslfm viewer using the mask tool to 
> cover the entire ice ring, but to no avail.
> 
> Finally I did have a go at using EVAL which is mentioned in the original post 
> about ice rings, but it seems it depends on libgfortran3 packages which have 
> now been replaced with libgfortran5 and so I didn't get very far.
> 
> Is there a manual way to mask out certain data, or could there be something 
> with my data that is causing the automatic ice ring resolution not to be as 
> effective?
> 
> Thank you!
> 
> Alex Brown
> 
> PhD Student
> School of Pharmacy
> Biodiscovery Institute (previously Centre for Biomolecular sciences)
> University of Nottingham
> Nottingham
> NG7 2RD 
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Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

[Harry Powell - CCP4BB]

The “something” is what gives them their edge (and which they’ve hinted at, but 
avoided being explicit)…

The main quality score used to distinguish their results is GDT_TS (Global 
Distance Test - Total Score - you can look it up on Wikipedia like I did). 
Although it doesn’t say in Wikipedia, it seems to be normalised to 100 for a 
perfect fit. Alphafold2 was scoring >90+, the best second-placed were ~60-65. 

Some of the superpositions of models from structure solution and AlphaFold2 
looked like the errors in position of main and side chains were <<1Å. 

Since I’m quite new to the field, and haven’t really paid CASP much attention 
in the past I wouldn’t want to comment about past methods. I’ve got a lot to 
learn.

Harry



> On 9 Dec 2020, at 12:35, Bryan Lepore  wrote:
> 
> On Dec 9, 2020, at 07:16, Harry Powell wrote:
>> 
>> ...the important thing is [...] they’ve done something that no-one else has 
>> managed to do as well in spite of years of trying.
> 
> What, precisely, is the “something”?
> 
> Exactly how much better than second place? 
> 
> Was the scoring the same across all years when no-one else managed to do as 
> well?
> 
> -Bryan W. Lepore
> 
> 
> 
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Re: [ccp4bb] AW: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

[Harry Powell - CCP4BB]

Hi

Actually, since Deep Mind is a commercial organization (funded by shareholders 
and people who buy their services), I don’t think they are subject to the same 
rules as academia as regards making their source code public. It would be very 
nice if they would (could?) make their code public, but I don’t see any 
obligation to do so. Their responsibility is primarily to their shareholders 
(you can argue the rights and wrongs of that until the cows come home).

Commercially, they can maintain an advantage through several routes - they can 
publish in patents (so people can see what they’ve done, but not legally 
implement it without a licence), they can keep it all confidential and hope 
that no-one manages to reverse engineer and implement it (at the risk of 
someone else publishing the details and removing their advantage), they can 
publish something that is honest but just misleading enough (or lacking in 
detail) to throw people off the scent, or…

If they can provoke other developers to work out where they have gone wrong and 
produce something that competes with AlphaFold2, that would be great. If they 
can provide something like a web service that allows users to run their method, 
that would be great too, but the important thing is (that unless they had prior 
knowledge of the structures in CASP14) they’ve done something that no-one else 
has managed to do as well in spite of years of trying.

Just my two ha’porth.

Harry

> On 9 Dec 2020, at 10:36, Hughes, Jonathan 
>  wrote:
> 
> i think the answer to all these doubts and questions is quite simple: the 
> AlphaFold2 people must make all details of their methods public (source code) 
> and, as would probably be necessary, open their system for inspection and use 
> by independent experts. isn't that what peer review and reproducibility are 
> all about? those rules date from the time before every tom, dick and 
> henriette could publicize anything they like inside their own zuckerberg 
> bubble. my opinion is that this is a virtual infectious disease that will 
> cause humanity far bigger problems than corona ever will – i just hope i'm 
> wrong!
> 
> best
> 
> jon
> 
>  
> 
> Von: CCP4 bulletin board  Im Auftrag von Mark J van 
> Raaij
> Gesendet: Mittwoch, 9. Dezember 2020 11:14
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and 
> less pipetting (?)
> 
>  
> 
> on the day the news came out, I did wonder if the AlphaFold2 team somehow had 
> access to all the preliminary PDB files sent around via Gmail (which belongs 
> to the same company), but more as a joke/conspirational thought.
> 
> "our" target T1052, was also predicted very well by domains and as a monomer. 
> It will be interesting to see how well future iterations of the method can 
> assemble the complete protein chain and the complete protein chains into the 
> correct heteromer.
> 
>  
> 
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> 
> Section Editor Acta Crystallographica F
> https://journals.iucr.org/f/
> 
>  
> 
> On 9 Dec 2020, at 10:37, Cedric Govaerts  wrote:
> 
>  
> 
> Dear All
> 
>  
> 
> After about 10 (!) years of (very) hard work we solved the structures of our 
> dearest membrane transporter.  Dataset at 2.9 And resolution, fairly 
> anisotropic, experimental phasing, and many long nights with Coot and 
> Buster to achieve model refinement. 
> 
>  
> 
> The experimental structure had a well defined ligand nicely coordinated but 
> also a lipid embedded inside the binding cavity (a complete surprise but 
> biologically relevant) and two detergent molecules well defined 
> (experimental/crystallisation artefact).
> 
>  
> 
> As our paper was accepted basically when CASP organisers were calling for 
> targets I offered my baby to the computing Gods. However we only provided the 
> sequence to CASP, no info regarding any ligand or lipid.
> 
>  
> 
> Less than a month after, the CASP team contacted us and send us the best 
> model.  In fact it was 2 half models as the transporter is a pseudo dimer, 
> with the N-lobe and C-lobe moving relative to each other during transport 
> cycle, thus divided as two domains in CASP.
> 
>  
> 
> The results were breathtaking. 0.7 And RSMD on one half, 0.6 on the other. 
> And yes, group 427 was the superpower (did not know at the time that it was 
> AlphaFold).
> 
>  
> 
> We had long discussions with the CASP team, as -for us- this almost exact 
> modelling was dream-like (or science fiction) and -at some point- we were 
> even suspecting fraud, as our coordinates had travelled over the internet a 
> few times around when interacting with colleagues.  The organisers reassured 
> us that we were not the only target that had been “nailed” so no reason to 
> suspect any wrongdoing.
> 
>  
> 
> To this day I am still baffled and I would be happy to hear from 

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

[Harry Powell - CCP4BB]

Since I didn’t actually read the press release (but “attended" the CASP event 
instead where the results were discussed in a little more detail…) this is news 
to me, but I’d agree that there is some hyperbole there. 

Alphafold2 (it’s probably important to distinguish it from AlphaFold since it’s 
a complete re-write, from what I understand) was the only software that 
reliably gave results that could be used for MR. I don’t know how long it 
actually took to run the modelling for each sequence (building its libraries 
was, shall we say, “time-consuming”), but it may not be a bad way to get an MR 
model if you can get DeepMind to run the modelling for you.

Harry

> On 8 Dec 2020, at 13:04, Ian Tickle  wrote:
> 
> 
> There was a little bit of press-release hype: the release stated "a score of 
> around 90 GDT is informally considered to be competitive with results 
> obtained from experimental methods" and "our latest AlphaFold system achieves 
> a median score of 92.4 GDT overall across all targets. This means that our 
> predictions have an average error (RMSD) of approximately 1.6 Angstroms,".
> 
> Experimental methods achieve an average error of around 0.2 Ang. or better at 
> 2 Ang. resolution, and of course much better at atomic resolution (1 Ang. or 
> better), or around 0.5 Ang. at 3 Ang. resolution.  For ligand-binding studies 
> I would say you need 3 Ang. resolution or better.  1.6 Ang. error is probably 
> equivalent to around 4 Ang. resolution.  No doubt that will improve with time 
> and experience, though I think it will be an uphill struggle to get better 
> than 1 Ang. error, simply because the method can't be better than the data 
> that go into it and 1-1.5 Ang. represents a typical spread of homologous 
> models in the PDB.  So yes very competitive if you're desperate for a MR 
> starting model, but not quite yet there for a refined high-resolution 
> structure.
> 
> Cheers
> 
> -- Ian
> 
> 
> On Tue, 8 Dec 2020 at 12:11, Harry Powell - CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi
> 
> It’s a bit more than science by press release - they took part in CASP14 
> where they were given sequences but no other experimental data, and did 
> significantly better than the other homology modellers (who had access to the 
> same data) when judge by independent analysis. There were things wrong with 
> their structures, sure, but in almost every case they were less wrong than 
> the other modellers (many of whom have been working on this problem for 
> decades).
> 
> It _will_ be more impressive once the methods they used (or equivalents) are 
> implemented by other groups and are available to the “public” (I haven’t 
> found an AlphaFold webserver to submit a sequence to, whereas the other 
> groups in the field do make their methods readily available), but it’s still 
> a step-change in protein structure prediction - it shows it can be done 
> pretty well.
> 
> Michel is right, of course; you can’t have homology modelling without 
> homologous models, which are drawn from the PDB - but the other modellers had 
> the same access to the PDB (just as we all do…).
> 
> Just my two ha’porth.
> 
> Harry
> 
> > On 8 Dec 2020, at 11:33, Goldman, Adrian  wrote:
> > 
> > My impression is that they haven’t published the code, and it is science by 
> > press-release.  If one of us tried it, we would - rightly - get hounded out 
> > of time.
> > 
> > Adrian
> > 
> > 
> > 
> >> On 4 Dec 2020, at 15:57, Michel Fodje  wrote:
> >> 
> >> I think the results from AlphaFold2, although exciting and a breakthrough 
> >> are being exaggerated just a bit.  We know that all the information 
> >> required for the 3D structure is in the sequence. The protein folding 
> >> problem is simply how to go from a sequence to the 3D structure. This is 
> >> not a complex problem in the sense that cells solve it deterministically.  
> >> Thus the problem is due to lack of understanding and not due to 
> >> complexity.  AlphaFold and all the others trying to solve this problem are 
> >> “cheating” in that they are not just using the sequence, they are using 
> >> other sequences like it (multiple-sequence alignments), and they are using 
> >> all the structural information contained in the PDB.  All of this 
> >> information is not used by the cells.   In short, unless AlphaFold2 now 
> >> allows us to understand how exactly a single protein sequence produces a 
> >> particular 3D structure, the protein folding problem is hardly solved in a 
> >> theoretical sense. The only reason we know how well AlphaFold2 did i

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

[Harry Powell - CCP4BB]

Hi

It’s a bit more than science by press release - they took part in CASP14 where 
they were given sequences but no other experimental data, and did significantly 
better than the other homology modellers (who had access to the same data) when 
judge by independent analysis. There were things wrong with their structures, 
sure, but in almost every case they were less wrong than the other modellers 
(many of whom have been working on this problem for decades).

It _will_ be more impressive once the methods they used (or equivalents) are 
implemented by other groups and are available to the “public” (I haven’t found 
an AlphaFold webserver to submit a sequence to, whereas the other groups in the 
field do make their methods readily available), but it’s still a step-change in 
protein structure prediction - it shows it can be done pretty well.

Michel is right, of course; you can’t have homology modelling without 
homologous models, which are drawn from the PDB - but the other modellers had 
the same access to the PDB (just as we all do…).

Just my two ha’porth.

Harry

> On 8 Dec 2020, at 11:33, Goldman, Adrian  wrote:
> 
> My impression is that they haven’t published the code, and it is science by 
> press-release.  If one of us tried it, we would - rightly - get hounded out 
> of time.
> 
> Adrian
> 
> 
> 
>> On 4 Dec 2020, at 15:57, Michel Fodje  wrote:
>> 
>> I think the results from AlphaFold2, although exciting and a breakthrough 
>> are being exaggerated just a bit.  We know that all the information required 
>> for the 3D structure is in the sequence. The protein folding problem is 
>> simply how to go from a sequence to the 3D structure. This is not a complex 
>> problem in the sense that cells solve it deterministically.  Thus the 
>> problem is due to lack of understanding and not due to complexity.  
>> AlphaFold and all the others trying to solve this problem are “cheating” in 
>> that they are not just using the sequence, they are using other sequences 
>> like it (multiple-sequence alignments), and they are using all the 
>> structural information contained in the PDB.  All of this information is not 
>> used by the cells.   In short, unless AlphaFold2 now allows us to understand 
>> how exactly a single protein sequence produces a particular 3D structure, 
>> the protein folding problem is hardly solved in a theoretical sense. The 
>> only reason we know how well AlphaFold2 did is because the structures were 
>> solved and we could compare with the predictions, which means verification 
>> is lacking.
>>  
>> The protein folding problem will be solved when we understand how to go from 
>> a sequence to a structure, and can verify a given structure to be correct 
>> without experimental data. Even if AlphaFold2 got 99% of structures right, 
>> your next interesting target protein might be the 1%. How would you know?   
>> Until then, what AlphaFold2 is telling us right now is that all (most) of 
>> the information present in the sequence that determines the 3D structure can 
>> be gleaned in bits and pieces scattered between homologous sequences, 
>> multiple-sequence alignments, and other protein 3D structures in the PDB.  
>> Deep Learning allows a huge amount of data to be thrown at a problem and the 
>> back-propagation of the networks then allows careful fine-tuning of weights 
>> which determine how relevant different pieces of information are to the 
>> prediction.  The networks used here are humongous and a detailed look at the 
>> weights (if at all feasible) may point us in the right direction.
>>  
>>  
>> From: CCP4 bulletin board  On Behalf Of Nave, Colin 
>> (DLSLtd,RAL,LSCI)
>> Sent: December 4, 2020 9:14 AM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting 
>> (?)
>>  
>> The subject line for Isabel’s email is very good.
>>  
>> I do have a question (more a request) for the more computer scientist 
>> oriented people. I think it is relevant for where this technology will be 
>> going. It comes from trying to understand whether problems addressed by 
>> Alpha are NP, NP hard, NP complete etc. My understanding is that the 
>> previous successes of Alpha were for complete information games such as 
>> Chess and Go. Both the rules and the present position were available to both 
>> sides. The folding problem might be in a different category. It would be 
>> nice if someone could explain the difference (if any) between Go and the 
>> protein folding problem perhaps using the NP type categories.
>>  
>> Colin
>>  
>>  
>>  
>> From: CCP4 bulletin board  On Behalf Of Isabel 
>> Garcia-Saez
>> Sent: 03 December 2020 11:18
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] AlphaFold: more thinking and less pipetting (?)
>>  
>> Dear all,
>>  
>> Just commenting that after the stunning performance of AlphaFold that uses 
>> AI from Google maybe some of us we could dedicate ourselves to the noble art 
>> of gardening, baking, 

Re: [ccp4bb] Apple Silicon / XQuartz / X11 / CCP4

[Harry Powell - CCP4BB]

Hi

To be fair to Apple, the original Rosetta that allowed Power PC executables to 
run on their Intel chipped computers worked really well. I still have a machine 
that can run Snow Leopard (OSX 10.6.8), which uses Rosetta to run a very old 
version of PPC MS Word. The main issue appears to be speed - it’s much slower 
than on a native PPC machine (but actually not noticeably slower than a recent 
Intel version of MS Word running on the same machine under High Sierra).

More seriously, I think some older versions of gcc (e.g. 4+) have been ported 
to run on Apple chips (for IOS devices), but ports of newer versions (e.g. gcc 
10) are not yet available. It’s probably not reasonable to expect Intel to port 
their compilers…

Harry

> On 11 Nov 2020, at 09:25, Winter, Graeme (DLSLtd,RAL,LSCI) 
>  wrote:
> 
> Hi Antony
> 
> In theory (TM) things should just work with Rosetta 2 - how well they work is 
> a matter for some debate and I think there will be a lot of eyes on non-Apple 
> benchmarks of this system. 
> 
> I would guess though that it will be inevitable that we (DIALS, CCP4, the 
> community, …) need to natively support the system eventually as these are 
> pretty popular type machines. Also, I suspect the M2 or whatever will appear 
> in higher end MacBook pro’s could be very interesting
> 
> I’d certainly say ignoring the new architecture would be a poor choice…
> 
> Cheers Graeme
> 
>> On 11 Nov 2020, at 09:21, Antony Oliver  wrote:
>> 
>> Perhaps this is a little too soon, but does anyone know if the new M1 
>> system-on-a-chip will continue to run XQuartz/X11 + the CCP4 program suite + 
>> other crystallography / EM software? Will CCP4 continue to support the 
>> platform?
>> 
>> (a quick check of the GitHub page indicates that there is already an ARM64 
>> implementation of XQuartz)
>> 
>> I am not in a rush to purchase the newly announced computers, but am keen to 
>> understand if we are going to need to future-proof ourselves when the entire 
>> family moves over to the new hardware.
>> 
>> With thanks,
>> 
>> Antony.
>> 
>> 
>> 
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Re: [ccp4bb] how to calculate the volume of a small molecule

[Harry Powell - CCP4BB]

Hi

If it’s just organic, use 18 Å^3 per non-hydrogen - e.g. glucose (C6H12O6) 
occupies around 12*18 ~= 216Å^3. Atoms like S and P add a little more, but for 
mental artihmetic and a quick estimate it doesn’t amount to a hill of beans.

H

> On 5 Nov 2020, at 09:25, vincent Chaptal  wrote:
> 
> Dear Kemin, 
> 
> I use VOIDOO from Upsala. 
> 
> Best
> Vincent
> 
> Le 04/11/2020 à 21:05, Tan, Kemin a écrit :
>> Dear all,
>>  
>> Is there a way to calculate or estimate the volume of a small molecule 
>> within CCP4 or with other programs?
>>  
>> Thanks,
>>  
>> Kemin 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
> 
> -- 
> Vincent Chaptal, PhD
> Director of GdR APPICOM
> Drug Resistance and Membrane Proteins Lab
> 
> MMSB -UMR5086
> 7 passage du Vercors 
> 69007 LYON
> FRANCE
> +33 4 37 65 29 01
> http://www.appicom.cnrs.fr
> http://mmsb.cnrs.fr/en/
> 
> 
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Re: [ccp4bb] saturn 724 query

[Harry Powell - CCP4BB]

Hi 

I haven’t looked at this for a few years, but I can’t see why you couldn’t; as 
far as I remember, Mosflm reads Saturn images okay.

You would probably need to do low and high resolution runs since the detector 
is (I think) only 72mm square.

Best option would be to try with something like cubic insulin or HEWL, which 
you might have on-hand.

Harry

> On 28 Oct 2020, at 10:18, Magnus Alphey 
> <4fbd1ddd2c2f-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi, 
> Does anyone know if a Rigaku Saturn 724 ccd can be used for protein crystal 
> data collection or only for small molecule ?
> Thanks
> Magnus Alphey
> 
> University of St. Andrews
> 
> 
> 
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Re: [ccp4bb] Can anyone hear me?

[Harry Powell - CCP4BB]

Hi Folks

Okay, you can stop replying to me now on this topic - I’ve had several replies 
from people on the BB telling me that they 

(a) have received my message and/or
(b) have noticed that the BB is rather quiet at the moment

So it seems to be working - except that I haven’t even received my own message 
from the BB…

Harry

> On 21 Sep 2020, at 09:47, Harry Powell - CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi folks
> 
> SInce early last week I have had no messages from the BB - and also received 
> a message telling me that I had been unsubscribed automatically because of 
> bounced messages.
> 
> I _should_ have now been resubscribed, but am not getting anything - and the 
> BB is no longer on JISCMAIL’s list of existing BBs.
> 
> Is anyone else out there having issues?
> 
> Harry
> 
> 
> 
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> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
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[ccp4bb] Can anyone hear me?

[Harry Powell - CCP4BB]

Hi folks

SInce early last week I have had no messages from the BB - and also received a 
message telling me that I had been unsubscribed automatically because of 
bounced messages.

I _should_ have now been resubscribed, but am not getting anything - and the BB 
is no longer on JISCMAIL’s list of existing BBs.

Is anyone else out there having issues?

Harry



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Re: [ccp4bb] Problems with iMosflm under CCP4i2

[Harry Powell - CCP4BB]

Hi folks

Thank for the name-check Jon - I haven’t been employed on the Mosflm project 
since 2016, but it’s nice to be remembered.

The place to look for a more definitive answer to the problem is in the 
date-stamped mosflm.lp file (called something like mosflm_202008319_124743.lp) 
which will give more information. It’s also worth looking at the History->Log 
tab in iMosflm (which gives a nice Tektronix 4010 rendering…) which may also 
indicate problems.

The current version of CCP4 is distributed with the current iMosflm version 
(version 7.3.0, built by Charles Ballard on Thursday, May 07 2020 at 16:24) - 
so the first thing I would check is that your installed (and running…) version 
of CCP4 is the latest (use the update manager) - until I updated this morning 
it seemed to be running iMosflm 7.2.2 (which is obsolete and will probably give 
the “…detector type MAR” error).

The second thing I’d do after that is download and run the definitive iMosflm 
from the MRC website:

> https://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver730/introduction.html


and see if the problem persists with that. If it does, the best thing to do 
then is to discuss it with Andrew…

Harry

> On 30 Aug 2020, at 22:43, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Re: "I think MAR is the default detector, so I guess for some reason the 
> image header is not getting read correctly or is missing..."
> 
> Thanks for the proper explanation, Mark. 
> 
> Indeed the manual says:
> 
> "Default: DETECTOR defaults to MAR"
> 
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
> 
> 
> 
> 
> 
>  Original Message 
> On 30 Aug 2020, 18:20, Mark J van Raaij < mjvanra...@cnb.csic.es> wrote:
> 
> Hi Jon,
> I think MAR is the default detector, so I guess for some reason the image 
> header is not getting read correctly or is missing...
> (I wrote this to Yahui also)
> 
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> 
> 
> 
>> On 30 Aug 2020, at 19:16, Jon Cooper 
>> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Apologies, I see that MAR now sell the Pilatus 200K detector, which may 
>> partly explain things.
>> 
>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>> 
>> 
>> 
>> 
>> 
>>  Original Message 
>> On 30 Aug 2020, 18:03, Jon Cooper < 
>> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Hello, have you installed the latest version of ccp4 or could you post the 
>> version number for mosflm that you are using? I know Harry has a penchant 
>> for detectors of all ages: 
>> https://doi.org/10.1080/0889311X.2019.1615483
>> 
>> but I have no idea why mosflm would think yours is one of these as they have 
>> not really been around for some time:
>> 
>> https://1.bp.blogspot.com/-Y3HEe2KTczg/X0rPRm3ffNI/AfQ/EeSLElXobsUG-uIlWpU4BruLO3J6CChjACLcBGAsYHQ/s2048/IMG_1032.JPG
>> 
>> (Picture c/o P. McArdle)
>> 
>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>> 
>> 
>> 
>> 
>> 
>>  Original Message 
>> On 30 Aug 2020, 13:09, Yahui Liu < liuyahui1...@gmail.com> wrote:
>> 
>> Dear CCP4er,
>> I have some problem in loading the data(taken with a Dectris Pilatus 200K 
>> detector) with iMosflm.
>> The iMosflm showed the error message  “Error reading image header. Message 
>> from Mosflm is Incorrect size of image for detector type MAR” first (see the 
>> attachment), and  quit directly.
>> 
>> After that, I got another error in CCP4i2(the second attachment).
>> 
>> Dr.Andrew Leslie was kind and test my data with iMosflm alone, it was 
>> totally fine for him to open my images.  
>> It seems like this only happened when we start iMosflm in CCP4i.
>> 
>> Any one has some suggestions?
>> 
>> 
>> Best
>> Yahui
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
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>> 
>> 
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>> 
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> 
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Re: [ccp4bb] Quote source inquiry [SEC=UNCLASSIFIED]

[Harry Powell - CCP4BB]

 to handle that stuff and success means users just expect good data 
> from good crystals and they get it. If you don't look for problems in the 
> beamlines you don’t find them. I think lot of MX experiments are viable when 
> a beamline has a problem (fluctuating intensity, beam position vibration, 
> structure in the beam etc) but some experiments are more sensitive than 
> others and users may think they just have bad crystals despite pretty 
> diffraction.
> 
> So yes, there are people these days who collect powder data for wavelength 
> and beam position reference.
> 
> Cheers,
> 
> Tom
> 
> 
> On 16/7/20, 9:26 pm, "CCP4 bulletin board on behalf of Harry Powell - 
> CCP4BB"  193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
>Hi
> 
>Does anyone bother collecting a powder image (e.g. Si powder) these days 
> so they actually have a reference that can be used to check both the 
> wavelength and the beam centre? Or is this considered just something that old 
> folk do?
> 
>Harry
> 
>> On 16 Jul 2020, at 12:19, Gerard DVD Kleywegt  wrote:
>> 
>> There was a case a few years ago (not too many though) where a 1.6 Å 
>> structure had been solved using an incorrect value for the wavelength (~5% 
>> too low, leading to a cell that was slightly too small for its contents to 
>> be comfortable). It was later corrected so we could compare their validation 
>> statistics. Some interesting observations:
>> 
>> - the geometry had been very tightly restrained so that didn't give a clue
>> about the cell error (WhatCheck only suggested a very small change)
>> 
>> - somewhat surprisingly (I thought) the Ramachandran plot did not improve in
>> the correct model (0.3% outliers in the wwPDB validation report), and the
>> sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)
>> 
>> - the map looked surprisingly good for the incorrect cell
>> 
>> - however, RSR-Z told clearly that the map was not good enough for the 
>> claimed
>> resolution - the model had 24% outliers! (3% in the corrected model which
>> still only put it at the ~50th percentile)
>> 
>> - another good indicator was the clashscore (went from 44 to 7)
>> 
>> - the original model did not include an Rfree, but the R-value (>0.3 at 1.6Å
>> resolution) ought to have provided a clue to the crystallographers and
>> reviewers one would think
>> 
>> It would be interesting to see what would happen if the wavelength would be 
>> set 5% too high.
>> 
>> --Gerard
>> 
>> 
>> 
>> On Thu, 16 Jul 2020, Clemens Vonrhein wrote:
>> 
>>> Hi Robbie,
>>> 
>>> On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote:
>>>> At the same time if you have a a more relaxed approach to restraints
>>>> than you might find systematic deviations in bond lengths. A test
>>>> for that has been in WHAT_CHECK for decades and it actually works
>>>> surprisingly well to detect cell dimension problems.
>>> 
>>> Indeed.
>>> 
>>>> That said, the problem is uncommon now.
>>> 
>>> Not so sure about that: we all rely on an accurate value of the
>>> energy/wavelength from the instrument/beamline - and if that is off
>>> (for whatever reasons) it will result in incorrect cell dimensions and
>>> a systematic deviation from the various restraints.
>>> 
>>> This would even affect the best experiment done on the best crystal
>>> ... so fairly easy to spot at the refinement stage, especially if such
>>> an energy/wavelength offset is constant over a long period of time on
>>> a given instrument. To spot this at the data collection stage one
>>> would hope that at some point a crystal with very pronounced ice-rings
>>> will be looked at properly (and the fact these are not where we expect
>>> them to should cause some head-scratching).
>>> 
>>> Cheers
>>> 
>>> Clemens
>>> 
>>> 
>>> 
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>> 
>>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>>> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
>>> https://www.jiscmail.ac.uk/policyandsecurity/
>>> 
>> 
>> 
>> Best wishes,
>> 
>> --Gerard
>> 
>> 

Re: [ccp4bb] Quote source inquiry

[Harry Powell - CCP4BB]

Hi Gerard

Indeed. Calibration used to be part of the experiment, but it’s often forgotten 
these days (or it’s assumed that someone else has done it to an adequate 
standard - fortunately, this assumption is usually valid enough).

Harry 

> On 16 Jul 2020, at 12:37, Gerard Bricogne  wrote:
> 
> Dear Harry,
> 
> I think that sharp ice rings (or, better, a powder pattern from silicon
> powder) are only part of the solution to the calibration of beam energy, as
> there is an interaction with the detector distance. If I recall what I saw
> in my now distant days at LURE, a precise energy calibration would be done
> using an absorption edge. I can remember Richard Kahn using a Cu metal foil
> to lock precisely onto an energy close to the Ytterbium edge he wanted to
> use in a MAD experiment. When the beam energy is precisely established by
> this diffraction-free method, then a Si powder allows a precise calibration
> of detector distance (and location of beam centre). 
> 
> 
> With best wishes,
> 
>  Gerard.
> 
> --
> On Thu, Jul 16, 2020 at 12:25:55PM +0100, Harry Powell - CCP4BB wrote:
>> Hi
>> 
>> Does anyone bother collecting a powder image (e.g. Si powder) these days so 
>> they actually have a reference that can be used to check both the wavelength 
>> and the beam centre? Or is this considered just something that old folk do?
>> 
>> Harry
>> 
>>> On 16 Jul 2020, at 12:19, Gerard DVD Kleywegt  wrote:
>>> 
>>> There was a case a few years ago (not too many though) where a 1.6 Å 
>>> structure had been solved using an incorrect value for the wavelength (~5% 
>>> too low, leading to a cell that was slightly too small for its contents to 
>>> be comfortable). It was later corrected so we could compare their 
>>> validation statistics. Some interesting observations:
>>> 
>>> - the geometry had been very tightly restrained so that didn't give a clue
>>> about the cell error (WhatCheck only suggested a very small change)
>>> 
>>> - somewhat surprisingly (I thought) the Ramachandran plot did not improve in
>>> the correct model (0.3% outliers in the wwPDB validation report), and the
>>> sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)
>>> 
>>> - the map looked surprisingly good for the incorrect cell
>>> 
>>> - however, RSR-Z told clearly that the map was not good enough for the 
>>> claimed
>>> resolution - the model had 24% outliers! (3% in the corrected model which
>>> still only put it at the ~50th percentile)
>>> 
>>> - another good indicator was the clashscore (went from 44 to 7)
>>> 
>>> - the original model did not include an Rfree, but the R-value (>0.3 at 1.6Å
>>> resolution) ought to have provided a clue to the crystallographers and
>>> reviewers one would think
>>> 
>>> It would be interesting to see what would happen if the wavelength would be 
>>> set 5% too high.
>>> 
>>> --Gerard
>>> 
>>> 
>>> 
>>> On Thu, 16 Jul 2020, Clemens Vonrhein wrote:
>>> 
>>>> Hi Robbie,
>>>> 
>>>> On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote:
>>>>> At the same time if you have a a more relaxed approach to restraints
>>>>> than you might find systematic deviations in bond lengths. A test
>>>>> for that has been in WHAT_CHECK for decades and it actually works
>>>>> surprisingly well to detect cell dimension problems.
>>>> 
>>>> Indeed.
>>>> 
>>>>> That said, the problem is uncommon now.
>>>> 
>>>> Not so sure about that: we all rely on an accurate value of the
>>>> energy/wavelength from the instrument/beamline - and if that is off
>>>> (for whatever reasons) it will result in incorrect cell dimensions and
>>>> a systematic deviation from the various restraints.
>>>> 
>>>> This would even affect the best experiment done on the best crystal
>>>> ... so fairly easy to spot at the refinement stage, especially if such
>>>> an energy/wavelength offset is constant over a long period of time on
>>>> a given instrument. To spot this at the data collection stage one
>>>> would hope that at some point a crystal with very pronounced ice-rings
>>>> will be looked at properly (and the fact these are not where we expect
>>>> them to should cause some head-scratching).
>>>> 
>>>> Cheers
>>>> 
>>>> Cle

Re: [ccp4bb] Quote source inquiry

[Harry Powell - CCP4BB]

Hi

Does anyone bother collecting a powder image (e.g. Si powder) these days so 
they actually have a reference that can be used to check both the wavelength 
and the beam centre? Or is this considered just something that old folk do?

Harry

> On 16 Jul 2020, at 12:19, Gerard DVD Kleywegt  wrote:
> 
> There was a case a few years ago (not too many though) where a 1.6 Å 
> structure had been solved using an incorrect value for the wavelength (~5% 
> too low, leading to a cell that was slightly too small for its contents to be 
> comfortable). It was later corrected so we could compare their validation 
> statistics. Some interesting observations:
> 
> - the geometry had been very tightly restrained so that didn't give a clue
>  about the cell error (WhatCheck only suggested a very small change)
> 
> - somewhat surprisingly (I thought) the Ramachandran plot did not improve in
>  the correct model (0.3% outliers in the wwPDB validation report), and the
>  sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)
> 
> - the map looked surprisingly good for the incorrect cell
> 
> - however, RSR-Z told clearly that the map was not good enough for the claimed
>  resolution - the model had 24% outliers! (3% in the corrected model which
>  still only put it at the ~50th percentile)
> 
> - another good indicator was the clashscore (went from 44 to 7)
> 
> - the original model did not include an Rfree, but the R-value (>0.3 at 1.6Å
>  resolution) ought to have provided a clue to the crystallographers and
>  reviewers one would think
> 
> It would be interesting to see what would happen if the wavelength would be 
> set 5% too high.
> 
> --Gerard
> 
> 
> 
> On Thu, 16 Jul 2020, Clemens Vonrhein wrote:
> 
>> Hi Robbie,
>> 
>> On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote:
>>> At the same time if you have a a more relaxed approach to restraints
>>> than you might find systematic deviations in bond lengths. A test
>>> for that has been in WHAT_CHECK for decades and it actually works
>>> surprisingly well to detect cell dimension problems.
>> 
>> Indeed.
>> 
>>> That said, the problem is uncommon now.
>> 
>> Not so sure about that: we all rely on an accurate value of the
>> energy/wavelength from the instrument/beamline - and if that is off
>> (for whatever reasons) it will result in incorrect cell dimensions and
>> a systematic deviation from the various restraints.
>> 
>> This would even affect the best experiment done on the best crystal
>> ... so fairly easy to spot at the refinement stage, especially if such
>> an energy/wavelength offset is constant over a long period of time on
>> a given instrument. To spot this at the data collection stage one
>> would hope that at some point a crystal with very pronounced ice-rings
>> will be looked at properly (and the fact these are not where we expect
>> them to should cause some head-scratching).
>> 
>> Cheers
>> 
>> Clemens
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
>> https://www.jiscmail.ac.uk/policyandsecurity/
>> 
> 
> 
> Best wishes,
> 
> --Gerard
> 
> **
>   Gerard J. Kleywegt
> 
>  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
> **
>   The opinions in this message are fictional.  Any similarity
>   to actual opinions, living or dead, is purely coincidental.
> **
>   Little known gastromathematical curiosity: let "z" be the
>   radius and "a" the thickness of a pizza. Then the volume
>of that pizza is equal to pi*z*z*a !
> **
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Harry Powell - CCP4BB]

Dear all

I’ve been persuaded that MPR is a useful name (and see that there are 
shortcomings with both “multiplicity” and “redundancy") and I agree with much 
of what’s been said most recently in this thread.

BTW, just because the Physics definition of a measurement/quantity/whatever is 
given on wikipedia (or elsewhere, for that matter), it doesn’t mean that’s what 
we (crystallographers, structural biologists, etc) should use without question. 
If you check 

https://en.wikipedia.org/wiki/Reflection_(physics)

you will find no mention of diffraction maxima corresponding to reflections 
except a link to a page on diffraction. Or maybe we should slavishly follow the 
Physicists and use another term…

H

> On 2 Jul 2020, at 10:41, Schreuder, Herman /DE  
> wrote:
> 
> Dear all,
>  
> While following the development of this thread, I am truly amazed how people 
> cling to names for the number of measurements per reflection whose meaning:
>   • Depends on the cultural/engineering/scientific context
>   • Can only be understood by experts
>   • Where the experts, as witnessed by the discussions in this thread, do 
> not agree on which name to use.
>  
> What is wrong with the name “measurements per reflection”? The definition for 
> measurement is the same as is used to calculate the multiplicity/redundancy.
> The only disadvantage I see is that it can be understood by non-experts as 
> well, which reminds me of medical doctors, who invent complicated Latin names 
> for common ailments to prevent patients to understand where they are talking 
> about. 
>  
> Another 2 cents/pennies from my side,
> Herman
>  
>  
>  
> Von: CCP4 bulletin board  Im Auftrag von James Holton
> Gesendet: Mittwoch, 1. Juli 2020 20:52
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?
>  
> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
> 
>  
> 
> 
> Sorry to take this thread on a detour/diversion: What I was attempting to 
> point out below, perhaps unclearly, is that the different interpretations of 
> the word "redundant" are a cultural difference.  As a student of multiple 
> English languages perhaps I can explain:
> 
> Few US English speakers know that in UK/European/Australian English the word 
> "redundant" has a strong negative connotation. I, for one, was surprised to 
> learn that the phrase "made redundant" is used in the UK to describe loss of 
> employment.  That is, a layoff, firing or perhaps a furlough. So, I think it 
> important to spell out for my fellow US English speakers that the emotional 
> ties to this negative connotation can be strong ones.
> 
> Conversely, many UK English speakers do not know that in US English the word 
> "redundant" has a strong positive connotation.  We never use the phrase "made 
> redundant" to describe a lost job.  Most Americans I think would be confused 
> by such a turn of phrase. If a US English speaker was told their jobs was 
> "made redundant" they would most likely think that a new hire was onboarded 
> to back them up.  This would imply that their job was so important that the 
> company wanted at least two people doing it, just in case you got hit by a 
> bus. This strong positive connotation also has emotional roots.
> 
> Personally, I prefer the positive connotation. Perhaps that is my cultural 
> bias, or perhaps I just generally believe that positivity is better than 
> negativity. Maybe I'm just a "nice" guy. The meaning of the word "nice" has 
> changed enormously over the last few hundred years, and I don't think we're 
> going to change that any more than we are going to change the meaning of 
> "redundant" in these two major forms of English.
> 
> However, just because a word has slightly different meanings in two slightly 
> different languages does not mean we should abandon it.  Are we going to stop 
> eating "chips" just because we are not sure if our fried potato will come as 
> sliced wedges or thin crispy wafers? If you are unhappy with your meal, is it 
> the fault of the culture you are visiting? or the customer for forgetting 
> where they are? Context is everything. 
> 
> So, for those unfamiliar with one or more of the major English-speaking 
> cultures, here are a few other important differences to be aware of: 
> "Football" may not be the game you think it is. 
> If you are offered a "biscuit" in the US, do not expect it to be sweet. 
> If you want to leave a building you should take the "lift" to the "ground 
> floor", but if you take an "elevator" get off on the "1st floor". 
> A "dummy" is a pacifier for a baby in the UK/Australia, but in the US it only 
> means an unintelligent person, or a plastic replica of one. 
> "please" and "thank you" are considered baseline politeness in some English 
> cultures, but their excessive use in others, such as the US, can be seen as 
> rude.
> A "tap" in the US dispenses beer, water comes out of a "faucet".
> A "flat" in the US 

Re: [ccp4bb] Macports and Fink - failed building open source pymol on MacOS Catalina

[Harry Powell - CCP4BB]

Why not just use QTMG rather than Pymol? This is, after all, the _CCP4_ 
bulletin board…

H

> On 14 Jun 2020, at 23:56, Javier Gonzalez  wrote:
> 
> Thank you so much Vijaykumar and Kevin, it worked smoothly!
> Best wishes,
> Javier
> 
> On Sun, Jun 14, 2020 at 5:04 PM Kevin Jin  wrote:
> My OS Version: Catalina 10.15.5;
> 
> brew install brewsci/bio/pymol
> 
> To verify, I just installed Pymol using brew 2 minutes ago. It works.
> 
> On Sat, Jun 13, 2020 at 4:45 PM Javier Gonzalez  wrote:
> Hello,
> I'm attempting to build pymol on a laptop running MacOS Catalina 10.15.5,
> Processor 2.8GHz Quad-Core Intel i7, Graphics Intel Iris Pro 1536 MB
> I downloaded the latest version of Xcode 11.1
> 
> I tried from Fink (fink install pymol-py27) and Macports (sudo port install 
> pymol), as indicated here: https://pymolwiki.org/index.php/MAC_Install
> 
> Both scripts run to download all dependencies but at the end fail with 
> different messages (see below). Any ideas? Is it doable or am I just 
> following outdated instructions?
> Thanks in advance!
> Javier
> 
> Fink: fails at compiling term-readkey-pm5184-2.37-1
> -
> -
> Failed: phase compiling: term-readkey-pm5184-2.37-1 failed
> 
> Before reporting any errors, please run "fink selfupdate" and try again.
> Also try using "fink configure" to set your maximum build jobs to 1 and
> attempt to build the package again.
> If you continue to have issues, please check to see if the FAQ on Fink's 
> website solves the problem.  If not, ask on one (not both, please) of
> these mailing lists:
> 
> The Fink Users List 
> The Fink Beginners List ,
> 
> with a carbon copy to the maintainer:
> 
> Christian Schaffner 
> 
> Note that this is preferable to emailing just the maintainer directly,
> since most fink package maintainers do not have access to all possible
> hardware and software configurations.
> 
> Please try to include the complete error message in your report.  This
> generally consists of a compiler line starting with e.g. "gcc" or "g++"
> followed by the actual error output from the compiler.
> 
> Also include the following system information:
> Package manager version: 0.45.1
> Distribution version: selfupdate-rsync Fri Jun 12 21:49:17 2020, 10.15, x86_64
> Trees: local/main stable/main
> Xcode.app: 11.5
> Xcode command-line tools: 11.5.0.0.1.1588476445
> Max. Fink build jobs:  8
> -
> -
> Macports: apparently there is an issue with py38-pyqt5
> --->  Computing dependencies for pymol
> The following dependencies will be installed:  py38-pyqt5
> Continue? [Y/n]: 
> --->  Fetching archive for py38-pyqt5
> --->  Attempting to fetch py38-pyqt5-5.14.2_0.darwin_19.x86_64.tbz2 from 
> https://packages.macports.org/py38-pyqt5
> --->  Attempting to fetch py38-pyqt5-5.14.2_0.darwin_19.x86_64.tbz2 from 
> http://aus.us.packages.macports.org/macports/packages/py38-pyqt5
> --->  Attempting to fetch py38-pyqt5-5.14.2_0.darwin_19.x86_64.tbz2 from 
> https://ywg.ca.packages.macports.org/mirror/macports/packages/py38-pyqt5
> --->  Building py38-pyqt5
> Error: Failed to build py38-pyqt5: command execution failed
> Error: See 
> /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_python_py-pyqt5/py38-pyqt5/main.log
>  for details.
> Error: Follow https://guide.macports.org/#project.tickets to report a bug.
> Error: Processing of port pymol failed
> -
> -
> -- 
> Dr. Javier M. González
> Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET)
> Universidad Nacional de Santiago del Estero (UNSE)
> RN9, Km 1125. Villa El Zanjón. (G4206XCP)
> Santiago del Estero. Argentina
> Tel: +54-(0385)-4238352
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> -- 
> Kevin Jin
>  
> Sharing knowledge each other is always very joyful..
>  
> Website: http://www.jinkai.org/
>  
> 
> 
> -- 
> Dr. Javier M. González
> Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET)
> Universidad Nacional de Santiago del Estero (UNSE)
> RN9, Km 1125. Villa El Zanjón. (G4206XCP)
> Santiago del Estero. Argentina
> Tel: +54-(0385)-4238352
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 

Re: [ccp4bb] Any advice on specs for a new Mac Laptop to run CCP4 and other Xtal Software?

[Harry Powell - CCP4BB]

Hi

I’d make the decision based largely on where I was going to use it, and how 
much I was going to have to carry it (and if I ever wanted to use it in coach 
class). If it was going to be my machine for “on the road”, I’d go for the 13” 
one, but if it was going to sit on my desk most of the time (and do what a 
traditional desktop does), I’d go for the larger one. 

I “traded down” to a 13” after many years using 15”+ laptops a few years ago 
and have never regretted it, even when I have to put my reading glasses on to 
read what’s on the screen.

However, if you _really_ need 64GB RAM, you don’t have much of a choice.

Just my two ha’porth

Harry

> On 8 Jun 2020, at 17:07, Diana Tomchick  
> wrote:
> 
> Make sure the 13” display is large enough to display all the GUIs for program 
> suites that you are interested in.
> 
> For example, in the past, the 13” Mac laptops couldn’t display the HKL2000 
> GUI. Requirements are found here:
> 
> https://hkl-xray.com/hardware-operating-systems
> 
> Diana
> 
> **
> Diana R. Tomchick
> Professor
> Departments of Biophysics and Biochemistry
> UT Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Rm. ND10.214A
> Dallas, TX 75390-8816
> diana.tomch...@utsouthwestern.edu
> (214) 645-6383 (phone)
> (214) 645-6353 (fax)
> 
> On Jun 8, 2020, at 10:56 AM, Scott Pegan  wrote:
> 
> 
> EXTERNAL MAIL
> 
> 
> Finally looking to replace my 2014 Mac Pro lap (duo core; 16 gb RAM. I would 
> welcome any input or being put in the direction of some related to the 
> following:
> 
> 13" versus 16"
> 
> I know the 16" has a better and standalone GPU.  Is there anyone using a 13" 
> that finds that it works well? If so, what were the specs
> 
> Memory for the 16"
> 
> Torn between 16 gb and 32 gb RAM for the next computer.  Apple asks a premium 
> for the 32 gb, but some say that now with the SSD's it's not as big of a 
> deal. Any thoughts?
> 
> GPU
> 
> For the 15", apple has two 4 gb and an 8 gb. Does anyone have any experience 
> on these for running CCP4 and other Xtal software on these?
> 
> Thanks for your help in advance, looking to get something that is a Mac, 
> robust to last a while spec wise.  However, not looking to buy something that 
> is the equivalent of a small car in price and overkill.
> 
> Scott
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> CAUTION: This email originated from outside UTSW. Please be cautious of links 
> or attachments, and validate the sender's email address before replying.
> 
> 
> 
> 
> UT Southwestern 
> 
> Medical Center
> 
> The future of medicine, today.
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 



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Re: [ccp4bb] Question about small molecule crystallography

[Harry Powell - CCP4BB]

Hi 

Just to echo what has been said before, and expand a little.

(*) 5mm NMR tubes are wonderful for growing small molecule crystals in the way 
Artem describes - partly because they have _extremely_ smooth interior surfaces 
with few nucleation points - so you tend to get fewer, bigger crystals. You 
could also leave the NMR tube sealed, and having run your spectrum at room 
temperature, just “bung it in the ‘fridge or freezer” for a couple of weeks. 
I’ve grown 1st-class crystals by just forgetting the (sealed) nmr tube on my 
bench for a week or so...

(*) PX beamlines are possibly not the best for small molecules because you 
really want to get the high resolution data - say ~0.7Å; a lab-based 
diffractometer in a Chemistry department will do this routinely. If you can 
only grow “tiny" crystals (say << 0.1mm), then you may benefit from a 
synchrotron, but even then a good, modern set-up in a Chem lab would possibly 
still do the job.

(*) I'm being a little picky here, but you don’t use SHELXL to solve structures 
- it’s for refinement. You want one of the structure solution programs like 
SHELXD, SHELXS or SHELXT. If you’re a masochist you could try to get hold of an 
old copy of SHELX-76 and pick your own triplets to solve or try to find the 
heavy atoms “by hand” from thelist of peaks in a Patterson map, and also use 
the same program to refine - but I really, really, wouldn’t recommend it unless 
you don’t have better things to do and don’t mind arguing with referees about 
why you used a program that hasn’t really been developed since Jimmy Carter was 
POTUS!

There are other solutions to solving and refining small molecule structures - 
some I’ve used are Crystals (from the Oxford lab), SIR (in various flavours, 
from Bari), OLEX (from Durham) and Crysalis-Pro (from Rigaku). All work, each 
is slightly different, all are acceptable to all of the major journals.

HTH

Harry

> On 1 Jun 2020, at 23:31, Peat, Tom (Manufacturing, Parkville) 
>  wrote:
> 
> Hello Jiyuan, 
> 
> One small point to note- as Artem says, small molecule crystals are often 
> generated out of solvents and these same solvents often melt the standard 
> protein crystallisation plates, so be careful what you put into a plastic 
> plate. 
> 
> As Artem mentioned, synchrotrons are generally overkill for small molecule 
> structures (although there are exceptions). In this case, I would like to 
> plug for the Australian Synchrotron which has a dedicated small molecule 
> crystallographer and a beamline set up for small molecule crystallography (we 
> do some protein crystallography there too!). So there is help available for 
> those that do want to use synchrotrons for small molecule structures. 
> 
> cheers, tom 
> 
> Tom Peat
> Proteins Group
> Biomedical Program, CSIRO
> 343 Royal Parade
> Parkville, VIC, 3052
> +613 9662 7304
> +614 57 539 419
> tom.p...@csiro.au
> 
> From: CCP4 bulletin board  on behalf of Artem 
> Evdokimov 
> Sent: Tuesday, June 2, 2020 8:07 AM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] Question about small molecule crystallography
>  
> Hi
> 
> A small organic molecule is typically crystallized from organic solvents (or 
> water, if soluble) by means of at least three main techniques:
> 
> 1. slow evaporation of solvent leading to supersaturation and eventual 
> crystallization
> 2. supersaturation at higher temperature followed by gradual drop in 
> temperature causing crystallization
> 3. counter-diffusion of an incompatible solvent to drop solubility of the 
> substance and cause crystallization
> 
> Many times, just leaving an NMR tube with a tiny hole in the plastic cap for 
> a week or so will cause crystals to form.
> 
> Schnobviously, some substances will not crystallize easily - some form oils, 
> amorphous precipitates, etc. and others will form liquid hydrated forms or 
> just plain decompose. If you have any specific questions please don't 
> hesitate to contact me in person. I've spent half of my PhD crystallizing 
> weird small molecules for fun and profit.
> 
> As to how to solve structures of small molecules - any synchrotron is a 
> massive overkill. Just get in touch with a University X-ray lab, many of 
> which still have functional small molecule instruments. SHELX is the software 
> of choice - of course! (I still have the blue/white polka dot SHELX cup, it's 
> one of my more treasured curios).
> 
> Artem
> - Cosmic Cats approve of this message
> 
> 
> On Mon, Jun 1, 2020 at 6:01 PM Jiyuan Ke  wrote:
> Hi Everyone,
> 
> I want to crystallize a small organic molecule. I have very limited 
> experience in small molecule crystallography. I found that the Crystal Screen 
> HT from the Hampton research is good for both small molecule and 
> macromolecule crystallization. Plan to set up a sitting drop screen just like 
> setting up protein crystallization. I don’t know if this is the proper way to 
> do it. Is the MRC sitting drop 2-well plate (HR3-083) used for protein 
> 

Re: [ccp4bb] PDB file header lines...

[Harry Powell - CCP4BB]

Hi Robbie

Many thanks. I should tell the owners of the prediction server that they’re 
writing non-compliant files, in that case.

So “BIDEN” is not compliant but “TRUMP” is? He’d like that…

H

> On 29 May 2020, at 16:02, Robbie Joosten  wrote:
> 
> Hi Harry,
> 
> You need this: 
> http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL
> 
> Essentially you have to make sure a MODEL has a number and a closing tag. It 
> is read as a real PDB record so you have to make sure it is correct BIDEN is 
> not PDB compliant and will be either ignored or a parser will throw an error.
> 
> Cheers,
> Robbie
> 
>> -Original Message-
>> From: CCP4 bulletin board  On Behalf Of Harry
>> Powell - CCP4BB
>> Sent: Friday, May 29, 2020 16:57
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] PDB file header lines...
>> 
>> Hi
>> 
>> Is there something about “MODEL ” lines (i.e. five characters followed by a
>> space) in PDB files that is completely beyond the pale?
>> 
>> I’ve got some PDB files from a protein structure prediction server based in
>> the US that Coot fails to read and that cause QTMG to crash on my Mac. I’ve
>> tracked this down to “MODEL” lines in the file headers.
>> 
>> I’ve tested this most in QTMG, so the following may not be true for Coot. If 
>> I
>> change this line so that it has “M ”, “MO ”, “MOD ”, MODE ”, “MODEL1 ”,
>> “MODEL22 ”, “MODEL678 ” or even “MODEL^&* ” instead of “MODEL ” then
>> all looks hunky-dory.
>> 
>> I thought - “aha - there’s something about 5 characters” - so I tried 
>> replacing
>> “MODEL ” with “TRUMP ” and “BIDEN ” and the files read okay, so it does
>> look very specific.
>> 
>> I’m sure there’s a simple answer to this (is there a “FM” I could read?), 
>> but I
>> haven’t found one yet. Can anyone on the BB help out?
>> 
>> Harry
>> 
>> ###
>> #
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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>> at
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[ccp4bb] PDB file header lines...

[Harry Powell - CCP4BB]

Hi

Is there something about “MODEL ” lines (i.e. five characters followed by a 
space) in PDB files that is completely beyond the pale? 

I’ve got some PDB files from a protein structure prediction server based in the 
US that Coot fails to read and that cause QTMG to crash on my Mac. I’ve tracked 
this down to “MODEL” lines in the file headers. 

I’ve tested this most in QTMG, so the following may not be true for Coot. If I 
change this line so that it has “M ”, “MO ”, “MOD ”, MODE ”, “MODEL1 ”, 
“MODEL22 ”, “MODEL678 ” or even “MODEL^&* ” instead of “MODEL ” then all looks 
hunky-dory.

I thought - “aha - there’s something about 5 characters” - so I tried replacing 
“MODEL ” with “TRUMP ” and “BIDEN ” and the files read okay, so it does look 
very specific.

I’m sure there’s a simple answer to this (is there a “FM” I could read?), but I 
haven’t found one yet. Can anyone on the BB help out?

Harry



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Re: [ccp4bb] Strange Pseudosymmetry Effects

[Harry Powell - CCP4BB]

Hi Tim

You could send out an SOS to some of the other authors in the same issue, who 
might have kept a copy - several are “regular" posters on this forum, e.g.  

Sacha Urzhumtsev
Gerard Kleywegt
Eleanor Dodson

There’s a good chance they’ll be stuck at home at the moment with plenty of 
time to search through old boxes…

Harry

> On 28 May 2020, at 21:04, Tim Gruene  wrote:
> Dear Eddie, dear all
> 
> According to ftp://ftp.ccp4.ac.uk/ccp4/newsletter/jun_95/, this article
> appeare in Newsletter June 95. It is mentioned in the table of contents,
> "Correction on perfection: primary extinction correction in protein
> crystallography" by Polykarpov and Sawyer.
> Unfortunately, the article itself is not there
> 
> Extinction is not the same as the dynamic effects that James mentioned,
> but this seems the closest match.
> 
> Would anyone have a copy they can share with me?
> 
> Thanks a lot!
> 
> Best,
> 
> Tim 



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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)

[Harry Powell - CCP4BB]

Hi folks

I can’t help feeling that if there are data extending to 0.97Å and there are 
multiple conformations/multiple components occupying the same region of (real) 
space/non-unity occupancies, the problem is crying out for SHELXL…

Harry

> On 27 Apr 2020, at 07:53, Schreuder, Herman /DE  
> wrote:
> 
> Dear Abhishek,
> 
> I did not follow the links given by Paul. However the way I proceeded in 
> these cases was to first generate an alternative conformation for the problem 
> residues, save the file and then do the mutation and save the mutated file. 
> Then, using an editor, I would cut the alternative conformation from the 
> original residue and paste in the alternate conformation (e.g. conformation 
> B) from mutated residue.
> 
> It is not very elegant, but it works (if coot and refmac cooperate).
> 
> Best, Herman
> 
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board  Im Auftrag von Abhishek Anan
> Gesendet: Sonntag, 26. April 2020 21:42
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTERNAL] Re: [ccp4bb] modelling MET (methionine) and SME 
> (met-sulfoxide)
> 
> EXTERNAL : Real sender is  owner-ccp...@jiscmail.ac.uk   
> 
> 
> 
> Dear all,
> 
> Thanks for the suggestions. It is synthetic peptide so the residue identity 
> is unambiguous.
> 
> I am not clear on how to model both MET and SME in coot, do a real space 
> refinement and then save the file for refinement in phenix. I tried alternate 
> conformation and then mutating one of them but that didn't work as both 
> conformations were mutated. What I also just noticed is that the refinement 
> of structure with just SME results in positive densities around all side 
> chain carbons even with the SME.cif loaded into phenix. What could be wrong 
> here?
> 
> best wishes,
> Abhishek
> 
> 
> 
> 
> 
> On 4/26/20, Paul Emsley  wrote:
>> 
>> On 26/04/2020 16:21, Abhishek Anan wrote:
>>> Dear all,
>>> 
>>> I have a peptide crystal structure at 0.97 Å that contains two 
>>> surface exposed Methionine. The CE atoms of both MET have a 
>>> suspiciously high b-factor >40 and a positive density. In addition, 
>>> the sulfur atom SD has a large negative density (b-factor ~23).
>>> 
>>> I initially suspected that the MET may have oxidized to MET-sulfoxide 
>>> and tried to model only the MET-sulfoxide. This again resulted in 
>>> negative density.
>>> 
>>> I think that the peptides might be partly oxidized which brings me to 
>>> my question. Is there a way to model both MET and MET-sulfoxide into 
>>> the density much like alternate conformation with options to refine 
>>> their respective occupancies.
>> 
>> 
>> Yes. This is called micro-heterogeneity
>> 
>> And is documented here:
>> 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.wwpdb.org_doc
>> umentation_procedure=DwIFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5
>> qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=CYQUM_mrfiCDADJ1
>> onMNLQYYLwXD23pcMOTm7KnoNkM=A_ke05wSRD1nm9vQxFwLPCzpmUAWRTVlaVkVSTRw
>> z8M=
>> 
>> That should "just work" if you then give the model to refmac.
>> 
>> FWIW, Coot is, AFAIR, not 100% happy with such models.
>> 
>> Paul.
>> 
>> 
>> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
> 
> 
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[ccp4bb] postponement of IUCr XXV to 2021

[Harry Powell - CCP4BB]

Hi folks

I don’t know if this has been announced anywhere else yet, but this year’s IUCr 
meeting in Prague has been postponed to 2021 - see

https://iucr2020.org/news/

I doubt this will be a surprise to anyone.

Keep well

Harry


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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Harry Powell - CCP4BB]

Hi

> While those text files would be heavy, they'd be still lighter than raw 
> images and the whole useless white space they carry with them between 
> reflections.

At the risk of extending this thread into a different direction, the "white 
space (the images) carry with them between reflections” is only useless because 
we (the developers of integration software and structural biologists who use 
X-ray diffraction) choose to throw it away. The same as the can that surrounds 
my beans in tomato sauce...

There are plenty of people out there who have proposed using the non-Bragg 
scattering (aka “diffuse scattering”, inter alia) to give extra structural 
information.

My two ha’porth…

Harry

> On 19 Mar 2020, at 08:47, Julien Cappèle  
> wrote:
> 
> Hi everyone,
> 
> There are some very interesting ideas. 
> 
> Though I agree with you Clement that raw images are amazing to work with as 
> you can use any software you are confortable with, we cannot forget that 
> depositing several TB of data for each lab would be bad for ecological 
> reason. And because detectors are always improving (thank you all!), size of 
> data will increase exponentially. 
> 
> Correct me if I'm wrong, as I am not that familiar with the way that 
> integration of raw images works:
> 
> Could it be possible for a new/already existing software to store reflections 
> (area, intensity from center to border, position x/y on the image, and 
> information of the image) in a lightweight and text only file ? Possibly a 
> new format to be used for integration ?
> 
> While those text files would be heavy, they'd be still lighter than raw 
> images and the whole useless white space they carry with them between 
> reflections.
> 
> If not possible, could we imagine to eliminate all the unused space on these 
> ? Like a super raw image diet-plan for the incoming summer !
> 
> Best regards,
> 
> Julien CAPPELE
> Université de Lorraine, Nancy, France
> PhD student - 2nd Year
> 
> 
> 
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[ccp4bb] iMosflm/Mosflm and Eiger 2 images

[Harry Powell - CCP4BB]

Hi folks

I’ve noticed that the Mosflm help line has recently received several messages 
regarding problems processing Eiger 2 images with iMosflm (e.g. those collected 
on IMCA-CAT) 

Invariably, the users have been trying to use iMosflm/Mosflm 7.2.* series - 
also inevitably, this will not work!

Support for Eiger 2 detectors was added in version 7.3.0;  there were some 
unanticipated (by us…) physical changes to the detector from the original Eiger 
which meant that the 7.2.* code would not run correctly for the newer design. 
This is fixed in 7.3.0.

Unfortunately, as far as I know, 7.3.0 is not yet included in the CCP4 updates, 
so if you want to use iMosflm for processing Eiger 2 images (it works for both 
HDF5 and CBF) you will need to download and install a standalone copy of 
version 7.3.0 - available here:

https://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver730/introduction.html 


As an aside, there are some subtle changes to the installed package in the CCP4 
distro which mean that you can’t just swap in the new version. 

Harry Powell





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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD)

[Harry Powell - CCP4BB]

Hi

Something else I should have mentioned - in iMosflm you can sum your images for 
viewing only if you have them as  HDF5 or Pilatus CBF (as well as summing them 
for processing if you have HDF5).

Harry

> On 12 Feb 2020, at 10:18, Schreuder, Herman /DE  
> wrote:
> 
> Hi Daniele,
>  
> I agree with Wim that the first thing you should check is your space group 
> and especially whether a ncs symmetry element has been mistakenly identified 
> as being crystallographic. Since your Patterson peak is along w (c-axis), you 
> have to change the space group for processing such, that there are no 
> rotation axes or other symmetry elements perpendicular to the c-axis any 
> more. If you have a low-symmetry space group, you could also process in P1 to 
> be absolutely on the safe side. Than you should run MR in this lower symmetry 
> space group.
>  
> Concerning lattice translocation defects, almost every case is unique and I 
> am not aware of any software able to handle this. Here you will have to work 
> out the maths for your particular case yourself and apply the correction with 
> e.g. sftools. I am a little puzzled by your 7Å vector in your (native?) 
> Patterson maps. I guess, if you translate your protein by 7Å it will strongly 
> overlap with itself and I guess the same will be true for your ghost map. You 
> should also have a look at your diffraction images, perhaps after summing 
> them to 1° slices so become human-interpretable. In many cases, LTD is 
> associated with a mix of sharp and fuzzy diffraction spots. Seeing those 
> would be a strong indicator that you have the problem, but there are cases of 
> LTD where all the spots are sharp. You may also want to check for statistical 
> disorder.
>  
> Good luck!
> Herman
>  
> Von: CCP4 bulletin board  > Im Auftrag von Wim Burmeister
> Gesendet: Mittwoch, 12. Februar 2020 08:57
> An: CCP4BB@JISCMAIL.AC.UK 
> Betreff: [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD)
>  
> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk 
> 
>  
> 
> Hello,
> 
> do you have some details about the space group ? Did the integration not miss 
> any sports ? I would rather think of an ncs close to crystallographic 
> symmetry, or maybe some twinning problem.
> 
> I guess these are Pilatus data, can you combine the frames into 1 degree 
> oscillations and try Mosflm processing to see how the patterns integrate ?
> 
> Greetings
> 
> Wim
> 
> Le 11/02/2020 à 22:31, Daniele de Sanctis a écrit :
> Hi all,
>  
> I'm currently dealing with what I think it is a case of LTD (off-origin 
> Patterson peak, with vector along w of ~ 7A and electron density map showing 
> a "ghost" map shifted by 7 A). I saw there are quite a few cases reported in 
> literature  (for example Hare et al, 2006), but what I could not find is how 
> I can demodulate the data. Is there any software that can be used for this?
>  
> Thank you
>  
> Daniele
> 
> -- 
> ἀρετή
> ---
> Daniele de Sanctis, PhD
> 
> Structural Biology Group
> ESRF, Grenoble, France
> Tel 33 (0)4 76 88 2869
>  
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> 
> -- 
> Wim Burmeister
> Professeur
> Institut de Biologie Structurale (IBS) CIBB
> 71 avenue des Martyrs / CS 20192
> 38044 Grenoble Cedex 9, FRANCE
> E-mail: wim.burmeis...@ibs.fr 
> Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
> website 
> 
> map 
> 
> 
> Changement climatique : «Les autres combats n’ont aucun sens si celui-là est 
> perdu» (Aurélien Barrau)   
>  
> 
>  
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> 

Re: [ccp4bb] Lattice-translocation defect (LTD)

[Harry Powell - CCP4BB]

Hi

Apropos Mosflm - if you have HDF5 files from ESRF (or Diamond, probably 
elsewhere) you can sum the images internally to whatever rotation range per 
pseudo image you want (so if you have, say, 0.05º physical images you could 
process 0.1, 0.15, 0.20º, etc), provided you have installed Mosflm 7.3.* (not 
yet distributed as part of CCP4, as far as I can work out [apologies to CCP4 
core group if they’ve done this and I haven’t noticed], although it’s been 
available for quite some time…). 

I wouldn’t recommend summing to 1.0º unless the mosaicity is really quite large 
- iMosflm itself will suggest an appropriate value, and in my limited 
experience of processing reasonable quality datasets (during testing) the 
optimum often turns out to be ~0.2 - 0.5º (based on metrics like CC-1/2, Rmeas, 
I/sig(I) etc).

Just my two ha’porth

Harry

> On 12 Feb 2020, at 07:57, Wim Burmeister  wrote:
> 
> Hello,
> 
> do you have some details about the space group ? Did the integration not miss 
> any sports ? I would rather think of an ncs close to crystallographic 
> symmetry, or maybe some twinning problem. 
> I guess these are Pilatus data, can you combine the frames into 1 degree 
> oscillations and try Mosflm processing to see how the patterns integrate ?
> 
> Greetings
> 
> Wim
> Le 11/02/2020 à 22:31, Daniele de Sanctis a écrit :
>> Hi all,
>> 
>> I'm currently dealing with what I think it is a case of LTD (off-origin 
>> Patterson peak, with vector along w of ~ 7A and electron density map showing 
>> a "ghost" map shifted by 7 A). I saw there are quite a few cases reported in 
>> literature  (for example Hare et al, 2006), but what I could not find is how 
>> I can demodulate the data. Is there any software that can be used for this?
>> 
>> Thank you
>> 
>> Daniele
>> 
>> -- 
>> ἀρετή
>> ---
>> Daniele de Sanctis, PhD
>> 
>> Structural Biology Group
>> ESRF, Grenoble, France
>> Tel 33 (0)4 76 88 2869
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
>> -- 
> Wim Burmeister
> Professeur
> Institut de Biologie Structurale (IBS) CIBB
> 71 avenue des Martyrs / CS 20192
> 38044 Grenoble Cedex 9, FRANCE
> E-mail: wim.burmeis...@ibs.fr 
> Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
> website 
> 
> map 
> 
> 
> Changement climatique : «Les autres combats n’ont aucun sens si celui-là est 
> perdu» (Aurélien Barrau) 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> 



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