[ccp4bb] School on Single molecule biophysics in cell lysates, 13-17 May 2024, IBT, Vestec, Czech Republic
Dear colleagues, We welcome registrations to a specialized course focused on *Single molecule biophysics* Find all the relevant details on this page https://www.mosbri.eu/training/basic-level-schools/bls2/ This basic-level school is aimed at biologists, biophysicists, biochemists, structural biologists, etc., who want to learn a technique enabling high throughput screening for dynamic parameters of biochemical interactions on a single molecule level. The deadline for submission of an application to participate in this course is: *31 March 2024*. *Invited speakers* Carsten Janke, Institut Curie Tim Mitchison, Harvard Medical School *There is no participation fee. There are twenty travel bursaries of a maximum 200 euros to cover travel costs and local accommodation in shared twin hotel rooms. * Apply via the course web page *https://www.mosbri.eu/training/basic-level-schools/bls2/ <https://www.mosbri.eu/training/basic-level-schools/bls2/>* or contact directly the course organizers for more information zdenek.lan...@ibt.cas.cz (Scientific Organizer) magdalena.schneider...@ibt.cas.cz (Course Admin) Jan Dohnalek MoB-IBT centre of MOSBRI -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
[ccp4bb] Reminder: School on Single molecule biophysics in cell lysates, 13-17 May 2024, IBT, Vestec, Czech Republic
Just a reminder - the registration to this course is open till *29 February.* Dear colleagues, The registration to a specialized course - Basic level school of MOSBRI is open. Find all the relevant details on this page https://www.mosbri.eu/training/basic-level-schools/bls2/ This basic-level school is aimed at biologists, biophysicists, biochemists, structural biologists, etc., who want to learn a technique enabling high throughput screening for dynamic parameters of biochemical interactions on a single molecule level. The deadline for submission of an application to participate in this course is: Thursday 29th February 2024. Jan Dohnalek MoB-IBT centre of MOSBRI -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
[ccp4bb] School on Single molecule biophysics in cell lysates, 13-17 May 2024, IBT, Vestec, Czech Republic
Dear colleagues, The registration to a specialized course - Basic level school of MOSBRI is open. Find all the relevant details on this page https://www.mosbri.eu/training/basic-level-schools/bls2/ This basic-level school is aimed at biologists, biophysicists, biochemists, structural biologists, etc., who want to learn a technique enabling high throughput screening for dynamic parameters of biochemical interactions on a single molecule level. The deadline for submission of an application to participate in this course is: Thursday 29th February 2024. Jan Dohnalek MoB-IBT centre of MOSBRI Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] extra Fo-Fc density in two Cysteines
We have seen quite a few of these. Oxidation of S. Mostly in our case a result if reaction with beta-mercaptoethanol.. Jan On Mon, Dec 18, 2023 at 6:14 PM Liliana Margent < lmarg...@gradcenter.cuny.edu> wrote: > Hi there, We’ve been having an issue in trying to clear regions of Fo-Fc > density from a few cysteines during the refinement process. We were > wondering if anyone had seen something similar so they could offer some > insight on the likely chemistry at hand, and a potential refinement > solution. Attached are two images of the observed extra density at two > cysteines, 505 and 518. We have modeled acetylated cysteine, > s-hydroxycysteine, and s-mercaptocysteine but it does not solve the > density. The protein in question is a Protein Tyrosine Phosphatase known as > STEP (PTPN5), with data collected to a resolution of 1.79 Å. The crystals > were grown in bis-tris pH 6.65, 200mM Li2SO4, ~30% PEG3350. Of note, prior > to data collection the crystal was conserved at room temp for long time > where it dried, and was subsequently rehydrated with mother liquor. Thank > you so much. > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
[ccp4bb] Is the PDBe deposition server broken?
I get this when attempting to log into our current deposition session.Error: 500 There was a technical error. Something has gone wrong with our web server when attempting to make this page. Unfortunately, the service you are trying to access is currently unavailable. Please try again later. -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] Dry shipper in limbo
FedEx dry shipper shipment in our experience: just forget about it. A couple of times they damaged the samples, actually the status of the dewar looked like it was tossed around. All our effort to contact them to get explanation, money, apologies went into nowhere = nobody even attempted to talk to us ... Avoid FedEX!!! Jan Dohnalek On Fri, Jul 28, 2023 at 5:16 AM Dr. Kevin M Jude wrote: > My first adventure in international crystallography is off to an > inauspicious start. On Monday, I sent a dry shipper “overnight” from > California to Saskatchewan, but it has been stuck in the Memphis FedEx > facility for a few days. I’ve gotten several conflicting explanations of > the status from FedEx on the phone, but the most likely seems that it has > “pre-cleared” customs and yet has not yet made it to Calgary. It’s not > clear whether anyone actually knows where the shipping case is, since I was > asked to give a physical description of it. Is there anything else I can do > from a few thousand miles away, or do I just have to wait this out? > > > > -- > > Kevin Jude, PhD > > Structural Biology Research Specialist, Garcia Lab > > Howard Hughes Medical Institute > > Stanford University School of Medicine > > Beckman B177, 279 Campus Drive, Stanford CA 94305 > > Phone: (650) 723-6431 > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] Structure prediction - waiting to happen
n. > > Quoting https://scripts.iucr.org/cgi-bin/paper?S0907444998012645 : > > "Data of 0.94 A resolution for the 237-residue protein concanavalin A are > used in unrestrained and restrained full-matrix inversions to provide > standard uncertainties sigma(r) for positions and sigma(l) for bond > lengths. sigma(r) is as small as 0.01 A for atoms with low Debye B values > but increases strongly with B." > > There's a yawning gap between 1.0 - 1.5 Ang. and 0.01 Ang.! Perhaps > AlphaFold structures should be deposited using James Holton's new PDB > format (now that is an April Fool's !). > > One final suggestion for a reference in your grant application: > https://www.biorxiv.org/content/10.1101/2022.03.08.483439v2 . > > Cheers > > -- Ian > > > On Sat, 1 Apr 2023 at 13:06, Subramanian, Ramaswamy > wrote: > >> Dear All, >> >> I am unsure if all other groups will get it - but I am sure this group >> will understand the frustration. >> >> My NIH grant did not get funded. A few genuine comments - they make >> excellent sense. We will fix that. >> >> One major comment is, “Structures can be predicted by alpfafold and other >> software accurately, so the effort put on the grant to get structures by >> X-ray crystallography/cryo-EM is not justified.” >> >> The problem is when a company with billions of $$s develops a method and >> blasts it everywhere - the message is so pervasive… >> >> *Question: I*s there a canned consensus paragraph that one can add with >> references to grants with structural biology (especially if the review >> group is not a structural biology group) to say why the most modern >> structure prediction programs are not a substitute for structural work? >> >> Thanks. >> >> >> Rams >> subra...@purdue.edu >> >> >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] Alexey Vagin
So sad. Alexei was a great scientist and a good friend. I will have only good memories of him. Jan On Mon, Mar 27, 2023 at 5:20 AM Nukri Sanishvili wrote: > Sad news indeed for so many of us, those who knew Alexei personally and > those who benefited professionally from his selfless dedication to > computational crystallography. > A wise man once said something along the lines of anyone successful today > standing on the shoulders of giants of the past. Unfortunately, Alexei has > just become one such giant. > I am so blessed to have known him professionally from my time at IKAN and > to have him as a friend. And I am sure this sentiment is shared by all his > colleagues and anyone who knew him personally. > Writing this with a very heavy heart, on behalf of my wife as well. > Nukri > > > > On Sun, Mar 26, 2023 at 1:29 PM Eugene Krissinel - STFC UKRI < > 6fcecdb9c847-dmarc-requ...@jiscmail.ac.uk> wrote: > >> Dear All, >> >> It is with a great sadness that I share with you that Alexey Vagin passed >> away this Saturday in the Radcliffe Hospital in Oxford after suffering from >> a heart attack with subsequent complications. He was 78 years old. >> >> Alexey made many developments in methods and software for macromolecular >> crystallography, to which he devoted his whole life. He is known for his >> BLANC Suite for structure solution done at the Moscow Institute of >> Crystallography in the 1980s, as well as for his contributions to Refmac >> and Monomer Library. Many thousands of researchers have benefited from his >> work on Molrep and Balbes software for Molecular Replacement. After his >> retirement in 2010, Alexey developed and actively maintained the MorDA >> software for MR, which became a monument to his efforts. >> >> Alexey's work will continue to serve generations of researchers through >> his contributions to CCP4, where we will take the best care of his >> distinguished legacy. >> >> With sympathy to everyone who knew Alexey personally and for whom this is >> very sad news, >> >> Eugene >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] anomalous data usage
We are hitting the same problems also with students (so no rigidified brains I think) ... the concept of "files" seems absolutely natural (also to them) and when they ask about solving more tricky problems in i2 ... we do the obvious, go back to ccp4i. I2 is fine when things are smooth and easy. Jan On Wed, Mar 15, 2023 at 3:52 PM Randy John Read wrote: > Hi Jon, > > My understanding of the philosophy is that new users would prefer to think > about crystallographic data objects, rather than worrying about the arcana > of MTZ files and the many different flavours of columns. There are > tradeoffs — it can indeed be more difficult to find the bits of information > you need, but you should be thinking in terms of the stored objects from > the imports at the beginning of the project, rather than the files that > hold them. > > Personally, I find multicolumn MTZ files easier to think about, but my > brain probably rigidified a decade or two ago! > > Best wishes, > > Randy > > > On 15 Mar 2023, at 13:09, Jon Cooper < > 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > > > > Hello Ian, > > > > if I understand you and Eleanor correctly, this is the philosophy of the > mini-MTZ, i.e. if you are doing anything independent of i2, you have to dig > around a bit to find which output file contains the columns you need. > > > > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com > > > > Sent from Proton Mail mobile > > > > > > > > Original Message > > On 13 Mar 2023, 23:27, Ian Tickle < ianj...@gmail.com> wrote: > > > > > > Eleanor, which program is doing that and more to the point, why? > > > > -- Ian > > > > > > On Mon, 13 Mar 2023 at 20:17, Eleanor Dodson > wrote: > > fIf you are using ccp4I2 for some forgotten reason the final output has > one reflection with I+ and I-, another with Imean, another with Fmean - > aagghh > > > > > > On Mon, 13 Mar 2023 at 19:40, Ian Tickle wrote: > > > > Hi Gottfried > > > > AIMLESS definitely outputs IMEAN (and SIGIMEAN) by default. > > > > Cheers > > > > -- Ian > > > > > > On Mon, 13 Mar 2023 at 18:53, Palm, Gottfried > wrote: > > Dear all, > > I have a few questions handling (non) anomalous data: > > By default aimless seems to produce Iplus and Iminus columns. Can I > force it to (also) create an Imean column? > > What does refmac do, when it gets Iplus and Iminus (and their sigmas) as > input. Does it take only one of them or does it calculate and use Imean? > > Greetings > > Gottfried > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > - > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > The Keith Peters Building > Hills Road E-mail: > rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > > > > > 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/ > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] Problem downloading models maps in from PDBe in Coot
This has been quite variable in (several?) last versions of Coot. I have some three latest versions available and when one does not work I start another one. Sad but true. Jan On Thu, Sep 15, 2022 at 11:39 AM Robbie Joosten wrote: > Not sure if this is a PDBe bug or a Coot bug (or a combination thereof)... > > I'm using the latest WinCoot in CCP4 8.0. When I try to 'Fetch PDB using > Accession Code', I do not get any models so I guess the target URL is > wrong. > When I use Fetch PDB & Map using EDS, I sometimes get a map (1cbs, 3fvl), > sometimes I don't (1ctn, 1lee and many more). All of these maps used to be > available and PDB-REDO versions of all these entries exist. Does anyone > know what is going on? > > Cheers, > Robbie > > > > 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/ > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] PDBx-format utilities
We have our internal PDBCOP program that extracts all the info you need when refining a structure, i.e. extremes of B values, of occupancies, listing of all alternatives, all compounds found in the file and an option to provide the largest differences between two versions of the same structure, i.e. most of the time used to see "what really happened" during the last refinement run. Jan On Thu, Sep 8, 2022 at 9:29 PM Paul Emsley wrote: > A spectre is haunting structural biology - it is the spectre of the PDBx > format. > > We at CCP4 are interested in providing tools that are equivalents of > those that one might have trivially made with utilities such as grep or > sed. > > For example: > > delete the hydrogen atoms > > extract the hydrogen atoms > > extract the SD of MET > > find the atoms with B-factors greater than 100.0 > > > So, what useful tool have you made can that works because it based on > the PDB format - that (of course) doesn't work with PDBx? > > > Thanks, > > Paul. > > > > 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/ > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] Lower b-factors with increasing T
There could be a release of sum stress in the crystal with increasing temperature which could even lead to better ordering I can imagine. But that would need a very close inspection and mainly - are the structures completely isomorphous?? I.e. are there changes at all? If not then I am puzzled. Jan On Thu, Sep 8, 2022 at 3:03 AM Tom Peat wrote: > I think the basic question being asked is why are the B-factors going the > 'wrong' way? > That is, as the temperature increases, one might expect higher B-factors > (at least that is what we are taught) whereas what Matt is seeing is the > opposite- decreasing B-factors as one goes up in temperature (which I also > think is a little strange and I don't have an explanation). > cheers, tom > -- > *From:* CCP4 bulletin board on behalf of Phoebe > A. Rice > *Sent:* Thursday, September 8, 2022 10:48 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Lower b-factors with increasing T > > > I guess the big question is what is the question that you’re trying to > address from those numbers? I’d be nervous about making conclusions about > trends in B factors from just 1 data set per temperature. As you probably > know, the B factors will reflect static differences in atomic position > across asymmetric units as well as thermal motion, and it can be difficult > to control variables such as exactly how fast a crystal freezes or how much > trauma it experiences in its journey from sitting happily in a drop to the > frozen state. > > > > *From: *CCP4 bulletin board on behalf of Matt > McLeod > *Date: *Wednesday, September 7, 2022 at 1:57 PM > *To: *CCP4BB@JISCMAIL.AC.UK > *Subject: *[ccp4bb] Lower b-factors with increasing T > > Hi everyone, > > I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A), > 313K (2.2A) and I am curious as to the details in determining B-factors. > > I have treated these datasets more-or-less identically for comparison's > sake. I used DIALS to index, integrate, and scale the data. I scaled the > data to a ~0.6 CC1/2 cutoff. > > After fully refining the datasets, there is an odd trend with respect to > temperature (from what has been previously published) and I assume that > this is because of "behind-the-scenes" computation rather than a > biophysical observation. The B-factors slightly decrease from 252-293K, > and then significantly drop at 313K. The maps look pretty well identical > across the datasets. > > 253K - 53.8 A^2 > 273K - 48.4 A^2 > 293K - 45.5 A^2 > 313K - 18.6 A^2 > > I compared the wilson intensity plots from DIALS scaling for 273K and 313K > and they are very comparable. > > I am looking for suggestions as to where to look at how these b-factors > are selected or how to validate that these B-factor are or are not > accurate. Also, any relevant literature would be welcomed. From what I > have read, there is a general trend that as T increase, the atoms have more > thermal energy which raises the b-factors and this trend is universal when > comparing datasets from different temperatures. > > Thank you and happy to supply more information if that is helpful, > Matt > > > > 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/ > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] Checking X-ray sequence (no more protein).
If you know at least something about your protein, organism, type of molecule, ..., you could try mass spectrometry peptide mapping to known sequences, this may give you some answers for the ambiguities you might be seeing, if nothing else .. Jan On Fri, Jul 29, 2022 at 12:15 PM Jon Cooper < 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > Hello, I am looking for suggestions of ways to check a 1.7 Angstrom X-ray > sequence for a protein where it is impractical to do experimental > sequencing, protein or DNA. The structure refines to publishable R/R-free > and the main ambiguities seem to be Thr/Val, Asp/Asn and Glu/Gln where > alternative H-bonding networks are possible. Running alpha-fold seems an > interesting option? Any suggestions much appreciated. > > Cheers, Jon.C. > > Sent from ProtonMail mobile > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] Discrepancy in His library used by CCP4 and Molprobity?
Dear all, We also have had problems with FAD, FMN and I think NAD when depositing to the PDB. The ligand checks in PDB were expecting values different for some bonds and angles and our values either corresponded to the CCP4 dictionaries (and/or) to our defined values where there were modifications, always taken from the CSD average values and checked against similar situations found in the CCP4 dictionaries. I.e. we left the "raised flags" in the PDB without much attention as we assumed that for some reasons the geometrical values being used there are not what CCP4 and we are convinced would be the right ones. Now, Jan's question triggered mine .. Anybody else had similar experience with such ligands? Jan Dohnalek On Fri, Jul 29, 2022 at 11:54 AM Jan Stransky wrote: > Hi all, > > while validating X-ray structure using Molprobity (web service), we got > systematic outlier flags on CE1-NE2 distance in histidines. The distance > is 1.36A. > > I have tested it also using high resolution lysozyme structure, I have > laying around. There the distance refines as 1.31A and Molprobity is > happy, but when Bong Angels are called in Coot (Regularize zone button > :-)) the bond length goes to 1.36A and Molprobity is unhappy again. > > So I would like to ask, who is right or where else the problem can be. > > Best regards, > > Jan > > P.S. CCP4 is version 8.0.002 > > > > 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/ > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] displaying residues (as a surface perhaps) for one component of a p-p-i
Dear Fred, CCP4MG has this capability of automated interface display. When opening a structure you can select from many predefined styles of display. My favourite is Interfaces, then "residues", the surface can be displayed when you ask for PISA analysis within CCP4MG and then select a particular interface and display it. I hope it works for you, Jan On Tue, May 31, 2022 at 8:12 AM Fred Vellieux wrote: > Dear bb members, > > I am quite certain that someone must have needed to do this already. I > looked at publications but no details were given concerning how figures > were prepared. > > So here is the problem: > > Given a protein protein interface (with the 3D structure of the complex > available) I am looking for a method allowing me to identify and display > the interface forming residues of one of the protein components. Plus a > surface representation of that part, for the 3D structure. > > Thanks in advance for any tips. > > Regards, > > Fred. Vellieux > > -- > MedChem, 1st F. Medicine, Charles University > BIOCEV, Vestec, Czech Republic > > > > 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/ > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
[ccp4bb] Reminder and Extension - Survey on Data Standards and Databases in Molecular Biophysics
Dear colleagues, I would to remind/invite those who would like to contribute to this effort by filling in the survey below that you can still do so, at the latest *on 16 March 2022.* A big thank you to all those who already filled in this questionnaire and help us shape further efforts in this area. J. Dohnalek *Anonymous survey on Biophysical Data Standards and Accessibility* We would like to know your experience and views on the current status and needs for data standardization and availability of databases for the individual techniques of molecular biophysics. You are invited to contribute to this world-wide survey and have your voice heard! Not all the biophysical data of your projects (spectroscopy, hydrodynamic parameters, microscopy, thermodynamics, etc.) have standard data formats and open access database, respecting the FAIR principles (i.e. making the data Findable, Accessible, Interoperable, and Reusable). Within this HORIZON 2020 MOSBRI project (https://www.mosbri.eu) we want to contribute toward standardizing biophysical data formats and archival. Your anonymous answers will help us identify the priorities for data standardization in non-structural molecular biophysics techniques. Our further steps in the project will be directly influenced by your answers. The survey results will be published. Please, fill in your answers here (~10-15 minutes): *https://forms.biocev.org/index.php/114374?lang=en <https://forms.biocev.org/index.php/114374?lang=en>* We appreciate your answers The survey will close on 4 March 2022 *Feel free to contact us at mosbri-d...@ibt.cas.cz * Jan Dohnálek & Jan Stránský for the team of Standards for data archiving & exploitation MOSBRI -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
[ccp4bb] Survey on Data Standards and Databases in Molecular Biophysics
*Anonymous survey on Biophysical Data Standards and Accessibility* We would like to know your experience and views on the current status and needs for data standardization and availability of databases for the individual techniques of molecular biophysics. You are invited to contribute to this world-wide survey and have your voice heard! Not all the biophysical data of your projects (spectroscopy, hydrodynamic parameters, microscopy, thermodynamics, etc.) have standard data formats and open access database, respecting the FAIR principles (i.e. making the data Findable, Accessible, Interoperable, and Reusable). Within this HORIZON 2020 MOSBRI project (https://www.mosbri.eu) we want to contribute toward standardizing biophysical data formats and archival. Your anonymous answers will help us identify the priorities for data standardization in non-structural molecular biophysics techniques. Our further steps in the project will be directly influenced by your answers. The survey results will be published. Please, fill in your answers here (~10-15 minutes): *https://forms.biocev.org/index.php/114374?lang=en <https://forms.biocev.org/index.php/114374?lang=en>* We appreciate your answers The survey will close on 4 March 2022 *Feel free to contact us at mosbri-d...@ibt.cas.cz * Jan Dohnálek & Jan Stránský for the team of Standards for data archiving & exploitation MOSBRI -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] Validation of structure prediction
R factor). I would > argue that if you don't have an R factor then you should get one, but I am > interested in opinions about alternatives. > > I.E. What if we could train an AI to predict Rfree by looking at the > coordinates? > > -James Holton > MAD Scientist > > On 12/21/2021 9:25 AM, Pavel Afonine wrote: > > Hi Reza, > > If you think about it this way... Validation is making sure that the model > makes sense, data make sense and model-to-data fit make sense, then the > answer to your question is obvious: in your case you do not have > experimental data (at least in a way we used to think of it) and so then of > these three validation items you only have one, which, for example, means > you don’t have to report things like R-factors or completeness in > high-resolution shell. > > Really, the geometry of an alpha helix does not depend on how you > determined it: using X-rays or cryo-EM or something else! So, most (if not > all) model validation tools still apply. > > Pavel > > On Mon, Dec 20, 2021 at 8:10 AM Reza Khayat wrote: > >> Hi, >> >> >> Can anyone suggest how to validate a predicted structure? Something >> similar to wwPDB validation without the need for refinement statistics. I >> realize this is a strange question given that the geometry of the model is >> anticipated to be fine if the structure was predicted by a server that >> minimizes the geometry to improve its statistics. Nonetheless, the journal >> has asked me for such a report. Thanks. >> >> >> Best wishes, >> >> Reza >> >> >> Reza Khayat, PhD >> Associate Professor >> City College of New York >> Department of Chemistry and Biochemistry >> New York, NY 10031 >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
This is good to know indeed. Will improve my teaching now, I also did not know this is now done automatically. Thanks for pointing it out. Jan On Mon, Aug 30, 2021 at 9:44 PM Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > Dear Eleanor, > > Thanks for pointing out that CCP4 FreeRflag selects the test set in the > highest possible symmetry for the crystal class! I didn't know that. > > The following sentences (which are somewhat difficult to understand for > me) in https://www.ccp4.ac.uk/html/freerflag.html appear to document that: > "The FreeR_flag is randomly and uniformly distributed > reflexion-by-reflexion, but, additionally, if the keyword NOSYM is not set, > all reflections that are equivalent by the symmetry of the point group of > the twin lattice (assuming the data is twinned), obtain the same flag. This > includes both the possibility of merohedral and pseudomerohedral twinning. > In the latter case, the obliquity parameter can be set using the keyword > OBL." > > I wonder since which CCP4 version (or date) this is the default behaviour. > > best wishes, > Kay > > On Mon, 30 Aug 2021 18:28:23 +0100, Eleanor Dodson < > eleanor.dod...@york.ac.uk> wrote: > > >Back to FreeR factors - Phenix, and I believe FreeRflag now select FreeRs > >in the highest possible symmetry for the crystal class - eh P6/mmm for a > >trigonal crystal, and expand the set to fill the actual space group. This > >means the Free R assignment is suitable if later the crystal symmetry is > >reassigned. But this was not always done in the past so if you are trying > >to reuse free/work assignments from an old project there are possibilities > >of not getting this. Maybe the best solution is to just generate a new > Free > >R set ? > >Eleanor > > > ... > > > > 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/ > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] off-topic: structural motif / domain comparison
Like PDBeFOLD search? https://www.ebi.ac.uk/msd-srv/ssm/ Jan On Fri, Aug 6, 2021 at 8:43 AM Sam Tang wrote: > Dear all > > Sorry for an off-topic question here. I wonder if anyone may be aware of > any search program which allows one to 'blast' a protein domain just like > we 'blast' a protein sequence? For example I have an epitope in hand and > would like to find out whether this also exists in other proteins. Most > programs I accessed are based on sequence similarity but is there any > program which searches a structure against a database of structures? > > BRs > > Sam > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] Open position - data management in biophysics
Perhaps I should have finished that sentence. I meant "If you do your work well, you will get more work” Yes, ideal: "If you trust me (director/uni/government/grant provider ...whoever gives the funds) give me space, money AND infrastructure, i.e. good admin! including, for 5 or 10 years ..." Fineprint - assuming nobody asks for reports, further applications, silly record tables, appraisal documents, in that period .. Back to real world. Jan On Fri, Jan 22, 2021 at 11:49 AM Pearce, N.M. (Nick) wrote: > "If you do your work well, you will get more ..” Is a nice ideal, but I > don’t think it factors in the real-life factors such as administrative > burden (i.e. wasted time), mental-health effects and frankly, random > chance. Does anyone enjoy applying for grants/jobs? Does it > improve their lives/productivity? Does it improve the science? I suspect > (more accurately, I’m damned sure that) I would have been much more > productive over the last couple of years if I hadn’t been constantly > worried about missing the next hurdle (ironically making it all the more > likely that I _would_ miss the hurdle!). On top of that, I could have > enjoyed such lofty ambitions as “thinking about buying a house and starting > a family” which is difficult when you don’t have career stability over > longer than 1-2 years. > > I would also consider amending the statement to "If you do your work well, > you _might_ get more ..”. > > It seems to me a lot of time and energy could be saved by skipping the > biennial/triennial re-employment ritual/lottery, and if I am lucky enough > to ever make it to the point where I am able to employ people, I hope I > remember how thoroughly miserable the experience of this purgatory has made > me, and make the effort to employ my staff on reasonable contract lengths > (i.e. for as long as possible), and petition to funding bodies to change > their policies. For instance, if the Wellcome Trust now leaves it up to > the project leader to decide such things, as Eleanor has stated, they > should absolutely be applauded for that. > > After all, as Frank said, we do this for the science, and it shouldn’t > need to include personal sacrifice. > > Nick > > On 22 Jan 2021, at 11:18, Pearce, N.M. (Nick) wrote: > > Meant to write “perpetual impending unemployment”. > > Thanks, > Nick > > On 22 Jan 2021, at 11:02, Jan Dohnalek wrote: > > > On Fri, Jan 22, 2021 at 10:54 AM Pearce, N.M. (Nick) > wrote: > >> Academia, one of the only careers where _success_ is rewarded with >> perpetual impending employment every two+ years. >> >> Which translates "If you do your work well, you will get more .." > > Jan > > > > > > >> Nick >> >> On 22 Jan 2021, at 08:25, Eleanor Dodson < >> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> It is a long time since I had any practical concerns with this issue, but >> some funding bodies are more flexible than others. Welcome gives project >> grants then leaves it up to the recipient to hire and plan. And I guess the >> big research institutes like the crick and lmb have similar systems. It is >> obvious that this approach is much more productive than the shorter term >> grants - is there any mileage in someone doing a survey of >> “outcomes”(horrible word) and pointing out that productivity increases with >> more security? >> And as for the national scandal of milking money fir visas from those who >> come here from abroad - already saving us from the cost of their education >> - I don’t know what to say! >> Eleanor >> >> On Fri, 22 Jan 2021 at 07:11, Frank von Delft < >> frank.vonde...@cmd.ox.ac.uk> wrote: >> >>> For me as hiring PI, what's repeatedly dismaying is that it's our >>> funders and universities that set the terms, and only with extreme >>> creativity can one shift the dial, and only on indidual recruitments, >>> certainly not the high politics of the system as a whole. >>> >>> No, I don't know what will break this - it exploits our fundamental >>> weakness, that we go into science because we *want* to do it, and are >>> already investiging all our energy at convincing a system that something >>> else is worth doing (getting our mad science funded at all) -- so things >>> like collective striking or unionising don't really come naturally. >>> >>> I do hope the next wave of scientists (am I that old already?) have some >>> aggressively constructive thoughts, because mine and the one before mine >>> sure don't. >>> >>> >>> Fr
Re: [ccp4bb] Open position - data management in biophysics
s, CV >> and three references with their application. >> >> >> >> >> 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/ >> >> >> >> 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/ >> >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue
We also recently encountered this way of coordinates treatment - did not find it useful but just left it as it was (life has other more exciting adventures waiting ...). I strongly support the solution suggested by Luca, A nice day to all, Jan Dohnalek On Fri, Dec 4, 2020 at 8:48 AM Luca Jovine wrote: > CC: pdb-l > > Dear Zhijie and Robbie, > > I agree with both of you that the new carbohydrate chain assignment > convention that has been recently adopted by PDB introduces confusion, not > just for PDB-REDO but also - and especially - for end users. > > Could we kindly ask PDB to improve consistency by either assigning a > separate chain to all covalently attached carbohydrates (regardless of > whether one or more residues have been traced), or reverting to the old > system (where N-/O-glycans inherited the same chain ID of the protein to > which they are attached)? The current hybrid solution hardly seems > optimal... > > Best regards, > > Luca > > > On 3 Dec 2020, at 20:17, Robbie Joosten > wrote: > > > > Dear Zhijie, > > > > In generally I like the treatment of carbohydrates now as branched > polymers. I didn't realise there was an exception. It makes sense for > unlinked carbohydrate ligands, but not for N- or O-glycosylation sites as > these might change during model building or, in my case, carbohydrate > rebuilding in PDB-REDO powered by Coot. Thanks for pointing this out. > > > > Cheers, > > Robbie > > > >> -Original Message- > >> From: CCP4 bulletin board On Behalf Of Zhijie > Li > >> Sent: Thursday, December 3, 2020 19:52 > >> To: CCP4BB@JISCMAIL.AC.UK > >> Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the > >> PDB -- N-glycans are now separate chains if more than one residue > >> > >> Hi all, > >> > >> I was confused when I saw mysterious new glycan chains emerging during > >> PDB deposition and spent quite some time trying to find out what was > >> wrong with my coordinates. Then it occurred to me that a lot of recent > >> structures also had tens of N-glycan chains. Finally I realized that > this > >> phenomenon is a consequence of this PDB policy announced here in July. > >> > >> > >> For future depositors who might also get puzzled, let's put it in a > short > >> sentence: O- and N-glycans are now separate chains if it they contain > more > >> than one residue; single residues remain with the protein chain. > >> > >> > >> > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdocumentation%2Fcarbohydrate-remediationdata=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684263065%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=mBrkCJECFpZyCih4kOCcCvLT1GzQHxD5GD7bZDI9s1s%3Dreserved=0 > >> > >> "Oligosaccharide molecules are classified as a new entity type, > branched, > >> assigned a unique chain ID (_atom_site.auth_asym_id) and a new mmCIF > >> category introduced to define the type of branching > >> (_pdbx_entity_branch.type) . " > >> > >> > >> > >> > >> > >> I found the differential treatment of single-residue glycans and > multi-residue > >> glycans not only bit lack of aesthetics but also misleading. When a > structure > >> contains both NAG-NAG... and single NAG on N-glycosylation sites, it > might > >> be because of lack of density for building more residues, or because > that > >> some of the glycosylation sites are now indeed single NAGs (endoH etc.) > >> while some others are not cleaved due to accessibility issues. > Leaving NAGs > >> on the protein chain while assigning NAG-NAG... to a new chain, feels > like > >> suggesting something about their true oligomeric state. > >> > >> > >> For example, for cryoEM structures, when one only builds a single NAG > at a > >> site does not necessarily mean that the protein was treated by endoH. In > >> fact all sites are extended to at least tri-Man in most cases. Then why > >> keeping some sites associated with the protein chain while others kicked > >> out? > >> > >> Zhijie > >> > >> > >> > >> > >> > >> From: CCP4 bulletin board on behalf of John > >> Berrisford > >> Sent: Thursday, July 9, 2020 4:39 AM > >> To: CCP4BB@JISCMAIL
Re: [ccp4bb] metal coordination at low resolution - restraints
It is the active site which is very well defined, with high occupancy and tight binding. We also have high resolution structures of these .. However, restraints (for protein-metal contacs) were not necessary to refine these sites. Atoms site where they should be ... Jan On Tue, Sep 8, 2020 at 2:08 PM Oganesyan, Vaheh < vaheh.oganes...@astrazeneca.com> wrote: > Hi Jan, > > > > They hold nice because of high occupancy or because you have very high > resolution and no restraints are necessary at all (even for protein part)? > > > > Thank you > > > > Vaheh > > > > *From:* CCP4 bulletin board * On Behalf Of *Jan > Dohnalek > *Sent:* Tuesday, September 8, 2020 8:01 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] metal coordination at low resolution - restraints > > > > Hi Garib, > > > > > > > > On 8 Sep 2020, at 11:39, Jan Dohnalek wrote: > > > > These are structural. > > > > Are they tetrahedral or octahedral? From the list of neighbours they do > not look like tetrahedral. Some of them do look like octahedral. > > > > They are involved in reaction. > > Two are ~ octahedral (skewed though, two positions filled by catalysis > participant), one is ~tetrahedral, but actually can also accept a fifth > coordinating atom. > > > > But as I said - in all our structures restraining the coordination > geometry is not necessary, they hold nice. > > > > Jan > > > > > > Jan > > > > > > On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov > wrote: > > What are these numbers? > > > > If I understand these numbers correctly: none of your Zn atoms is > structural (4 coordinated tetrahedral). If that is the case then you need > specific links or restraints. If my reading of your numbers is correct then > there could be some chemistry change of the surrounding residues. > > > > If it is not structural Zn then it is likely that coordination is 6. But > without seeing coordinates and maps it is difficult to say what is there. > > > > Regards > > Garib > > > > > > On 8 Sep 2020, at 11:11, Eleanor Dodson wrote: > > > > Hmm - here is my problem - a list of ZN contacts for the two molecules.. > > residue 602 is a phosphate, and there possibly should be a few more waters > .. > > No idea how best to tackle it.. > > E > > > > > > Z 401 ZN A W 21 NA 2.057 X,Y,Z 1.00 > 8.73 > > Z 401 ZN A W 21 OA 2.220 X,Y,Z 1.00 > 8.76 > > Z 401 ZN A H 26 NE2 A 2.000 X,Y,Z 1.00 > 8.39 > > Z 401 ZN A D 139 OD1 A 2.085 X,Y,Z 1.00 > 8.61 > > Z 401 ZN A Z 601 O2 A 1.927 X,Y,Z 0.60 > 10.74 > > Z 401 ZN A O 821 OC 2.006 X,Y,Z 0.40 > 7.51 > > > > Z 402 ZN A H 80 ND1 A 2.033 X,Y,Z 1.00 > 8.94 > > Z 402 ZN A H 135 NE2 A 2.032 X,Y,Z 1.00 > 8.70 > > Z 402 ZN A D 139 OD2 A 2.024 X,Y,Z 1.00 > 8.70 > > Z 402 ZN A Z 601 O2 A 2.131 X,Y,Z 0.60 > 11.05 > > Z 402 ZN A O 821 OC 1.829 X,Y,Z 0.40 > 7.81 > > > > Z 403 ZN A H 145 NE2 A 2.027 X,Y,Z 1.00 > 10.50 > > Z 403 ZN A H 168 NE2 A 2.030 X,Y,Z 1.00 > 10.19 > > Z 403 ZN A D 172 OD2 A 2.062 X,Y,Z 1.00 > 12.66 > > Z 403 ZN A Z 601 O3 A 1.953 X,Y,Z 0.60 > 11.54 > > Z 403 ZN A O 820 OC 2.207 X,Y,Z 0.20 > 9.09 > > Z 403 ZN A O 822 OC 2.059 X,Y,Z 0.40 > 13.79 > > > > Z 401 ZN A Z 402 ZN A 3.349 X,Y,Z 1.00 > 8.73 > > > > > > Z 401 ZN B W 21 NB 2.099 X,Y,Z 1.00 > 9.22 > > Z 401 ZN B W 21 OB 2.184 X,Y,Z 1.00 > 8.91 > > Z 401 ZN B H 26 NE2 B 2.009 X,Y,Z 1.00 > 8.79 > > Z 401 ZN B D 139 OD1 B 2.069 X,Y,Z 1.00 > 8.76 > > Z 401 ZN B Z 601 O3 B 1.981 X,Y,Z 0.70 > 9.31 > > > > Z 402 ZN B H 80 ND1 B 2.032 X,Y,Z 1.00 > 9.49 > > Z 402 ZN B H 135 NE2 B 2.024 X,Y,Z 1.00 > 9.22 > > Z 402 ZN B D 139 OD2 B 2.032 X,Y,Z
Re: [ccp4bb] metal coordination at low resolution - restraints
Hi Garib, > > On 8 Sep 2020, at 11:39, Jan Dohnalek wrote: > > These are structural. > > > Are they tetrahedral or octahedral? From the list of neighbours they do > not look like tetrahedral. Some of them do look like octahedral. > > They are involved in reaction. Two are ~ octahedral (skewed though, two positions filled by catalysis participant), one is ~tetrahedral, but actually can also accept a fifth coordinating atom. But as I said - in all our structures restraining the coordination geometry is not necessary, they hold nice. Jan Jan On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov wrote: > What are these numbers? > > If I understand these numbers correctly: none of your Zn atoms is > structural (4 coordinated tetrahedral). If that is the case then you need > specific links or restraints. If my reading of your numbers is correct then > there could be some chemistry change of the surrounding residues. > > If it is not structural Zn then it is likely that coordination is 6. But > without seeing coordinates and maps it is difficult to say what is there. > > Regards > Garib > > > On 8 Sep 2020, at 11:11, Eleanor Dodson wrote: > > Hmm - here is my problem - a list of ZN contacts for the two molecules.. > residue 602 is a phosphate, and there possibly should be a few more waters > .. > No idea how best to tackle it.. > E > > > Z 401 ZN A W 21 NA 2.057 X,Y,Z 1.00 > 8.73 > Z 401 ZN A W 21 OA 2.220 X,Y,Z 1.00 > 8.76 > Z 401 ZN A H 26 NE2 A 2.000 X,Y,Z 1.00 > 8.39 > Z 401 ZN A D 139 OD1 A 2.085 X,Y,Z 1.00 > 8.61 > Z 401 ZN A Z 601 O2 A 1.927 X,Y,Z 0.60 > 10.74 > Z 401 ZN A O 821 OC 2.006 X,Y,Z 0.40 > 7.51 > > Z 402 ZN A H 80 ND1 A 2.033 X,Y,Z 1.00 > 8.94 > Z 402 ZN A H 135 NE2 A 2.032 X,Y,Z 1.00 > 8.70 > Z 402 ZN A D 139 OD2 A 2.024 X,Y,Z 1.00 > 8.70 > Z 402 ZN A Z 601 O2 A 2.131 X,Y,Z 0.60 > 11.05 > Z 402 ZN A O 821 OC 1.829 X,Y,Z 0.40 > 7.81 > > Z 403 ZN A H 145 NE2 A 2.027 X,Y,Z 1.00 > 10.50 > Z 403 ZN A H 168 NE2 A 2.030 X,Y,Z 1.00 > 10.19 > Z 403 ZN A D 172 OD2 A 2.062 X,Y,Z 1.00 > 12.66 > Z 403 ZN A Z 601 O3 A 1.953 X,Y,Z 0.60 > 11.54 > Z 403 ZN A O 820 OC 2.207 X,Y,Z 0.20 > 9.09 > Z 403 ZN A O 822 OC 2.059 X,Y,Z 0.40 > 13.79 > > Z 401 ZN A Z 402 ZN A 3.349 X,Y,Z 1.00 > 8.73 > > > Z 401 ZN B W 21 NB 2.099 X,Y,Z 1.00 > 9.22 > Z 401 ZN B W 21 OB 2.184 X,Y,Z 1.00 > 8.91 > Z 401 ZN B H 26 NE2 B 2.009 X,Y,Z 1.00 > 8.79 > Z 401 ZN B D 139 OD1 B 2.069 X,Y,Z 1.00 > 8.76 > Z 401 ZN B Z 601 O3 B 1.981 X,Y,Z 0.70 > 9.31 > > Z 402 ZN B H 80 ND1 B 2.032 X,Y,Z 1.00 > 9.49 > Z 402 ZN B H 135 NE2 B 2.024 X,Y,Z 1.00 > 9.22 > Z 402 ZN B D 139 OD2 B 2.032 X,Y,Z 1.00 > 9.70 > Z 402 ZN B Z 601 O3 B 1.973 X,Y,Z 0.70 > 9.58 > > Z 403 ZN B H 145 NE2 B 2.027 X,Y,Z 1.00 > 10.80 > Z 403 ZN B H 168 NE2 B 2.029 X,Y,Z 1.00 > 10.65 > Z 403 ZN B D 172 OD2 B 2.089 X,Y,Z 1.00 > 13.12 > Z 403 ZN B Z 601 O4 B 1.938 X,Y,Z 0.70 > 14.10 > Z 403 ZN B O 825 OC 2.322 X,Y,Z 0.20 > 10.61 > ~ > > > On Tue, 8 Sep 2020 at 10:47, Garib Murshudov > wrote: > >> Hi Robbie and Eleanor >> >> There are links for Zn-His and Zn-Cys. They meant to be used >> automatically, obviously something is not entirely right. >> >> Link names are: >> ZN-CYS >> >> It has a bond between Zn and S as well as an angle: >> ZN-CYS 1 ZN 2 SG 2 CB 109.0003.000 >> >> This also removes H of Cys to make covalent bond between Zn and Cys. >> >> Similar links are available for Zn and His ND1 and Zn - HIS NE2 >> Link names are: >> >> ZN-HISND >> ZN-HISNE >> >> Again these links have angles bet
Re: [ccp4bb] metal coordination at low resolution - restraints
nces are in the dictionaries but the angles involve three >> different residues so these cannot be in the current dictionary. We could >> add the program that generates these restraints to CCP4 though. >> >> Cheers, >> Robbie >> >> -Original Message- >> From: Eleanor Dodson >> Sent: Tuesday, September 8, 2020 11:38 >> To: Robbie Joosten ; Garib N Murshudov >> >> Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls > lmb.cam.ac.uk> >> Subject: Re: [ccp4bb] metal coordination at low resolution - restraints >> >> Robbie - could that be added to the distributed dictionaries? Zn binding >> is >> common and at low resolution distance restraints are not enough.. >> Eleanor >> >> On Tue, 8 Sep 2020 at 10:33, Robbie Joosten > <mailto:robbie_joos...@hotmail.com > > wrote: >> >> >> Hi Anna, >> >> Yes you can do this in Refmac by adding external restraints. If you >> have structural Zinc sites (Zn coordinated by 4 histidines or cysteines) >> you >> can also use PDB-REDO to generate the restraints automatically. The >> restraints are written to the output so you can continue using them in >> Refmac. >> >> HTH, >> Robbie >> >> > -Original Message- >> > From: CCP4 bulletin board > <mailto:CCP4BB@JISCMAIL.AC.UK > > On Behalf Of >> anna >> > anna >> > Sent: Tuesday, September 8, 2020 11:28 >> > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK >> > >> > Subject: [ccp4bb] metal coordination at low resolution - restraints >> > >> > Dear all, >> > >> > quickly: is there a way to restrain metal coordination geometry >> (even angles) >> > in refmac? >> > >> > I am refining a low resolution structure (3.3A) with 2 zinc binding >> sites. >> > I am pretty sure about metal position (strong anomalous signal) >> and what >> > are the residues involved in coordination since I solved the apo- >> structure at >> > good resolution and Zn-binding does not induce huge structural >> variations. >> > However, as you can imagine, electron density is poorly defined >> and Refmac >> > gives a very distorted coordination geometry. >> > I noticed that in phenix it is possible to generate restraints with >> readyset but >> > I'd like to work with refmac. >> > >> > Many thanks for your suggestions. >> > >> > Cheers, >> > Anna >> > >> > >> > >> > >> > To unsubscribe from the CCP4BB list, click the following link: >> > https://www.jiscmail.ac.uk/cgi-bin/WA- >> JISC.exe?SUBED1=CCP4BB=1 >> >> >> >> >> >> 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 >> <http://www.jiscmail.ac.uk/CCP4BB> , a mailing list hosted by >> www.jiscmail.ac.uk <http://www.jiscmail.ac.uk> , terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ >> >> >> >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] dewar horror stories
The trouble is no other company does international LN2 shipments here ... So we stopped shipping dewars completely. Jan On Thu, Jun 25, 2020 at 2:27 PM Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > I had a similar one-sided discussion with FEDEX about their ignoring of > our customs declarations for Switzerland. That was then the last Dewar we > sent by FEDEX. > > > > Best, > > Herman > > > > *Von:* CCP4 bulletin board *Im Auftrag von *Jan > Dohnalek > *Gesendet:* Donnerstag, 25. Juni 2020 08:34 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* [EXTERNAL] Re: [ccp4bb] dewar horror stories > > > > *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk > > > > We have the suspicion (after several heavy FEDEX failures) they just toss > them around ... then the neck easily breaks off. > > That only explains everything we have seen with completely damaged > samples, lost, flying around the dewar etc ... > > When trying to communicate seriously with FEDEX about these issues - they > even did not reply ... > > > > Jan > > > > > > > > On Wed, Jun 24, 2020 at 9:27 PM Patrick Loll wrote: > > Hello community, > > > > We recently had a dry shipping dewar fail catastrophically (while en route > to the beam line, so, major trauma). I sent it to a company that > specializes in repair and refurbishing of cryogenic tanks, and they told me > it has an internal leak, and hence is not reparable. I was expecting that > the valve had failed, so the internal leak diagnosis came as a surprise. > > > > Has anyone else had a similar experience? Any ideas about how an internal > leak might come about? The dewar is (was) a Taylor/Wharton CX100, and it > was traveling in its bespoke shipping case. > > > > Thanks for any insights that might satisfy my curiosity and/or prevent > future mishaps of this sort. > > > > Cheers, > > > > Pat > > > > __ > > > > Patrick J. Loll, PhD > > Professor of Biochemistry & Molecular Biology > > Drexel University College of Medicine > > Room 10-102 New College Building > > 245 N. 15th St. > > Philadelphia, PA 19102-1192 USA > > > > (215) 762-7706 > > pj...@drexel.edu > > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=tHIcVAtKk5YdRxIBzLho11ppNDkaH-avpnFs_37lwH0=PYxKUwCdRR-6mIIlKRTPRWC1bueGjj3go5N923mkOnk=> > > > > -- > > Jan Dohnalek, Ph.D > Institute of Biotechnology > > Academy of Sciences of the Czech Republic > > Biocev > > Prumyslova 595 > > 252 50 Vestec near Prague > > Czech Republic > > Tel. +420 325 873 758 > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=tHIcVAtKk5YdRxIBzLho11ppNDkaH-avpnFs_37lwH0=PYxKUwCdRR-6mIIlKRTPRWC1bueGjj3go5N923mkOnk=> > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
Re: [ccp4bb] dewar horror stories
We have the suspicion (after several heavy FEDEX failures) they just toss them around ... then the neck easily breaks off. That only explains everything we have seen with completely damaged samples, lost, flying around the dewar etc ... When trying to communicate seriously with FEDEX about these issues - they even did not reply ... Jan On Wed, Jun 24, 2020 at 9:27 PM Patrick Loll wrote: > Hello community, > > We recently had a dry shipping dewar fail catastrophically (while en route > to the beam line, so, major trauma). I sent it to a company that > specializes in repair and refurbishing of cryogenic tanks, and they told me > it has an internal leak, and hence is not reparable. I was expecting that > the valve had failed, so the internal leak diagnosis came as a surprise. > > Has anyone else had a similar experience? Any ideas about how an internal > leak might come about? The dewar is (was) a Taylor/Wharton CX100, and it > was traveling in its bespoke shipping case. > > Thanks for any insights that might satisfy my curiosity and/or prevent > future mishaps of this sort. > > Cheers, > > Pat > > __ > > Patrick J. Loll, PhD > Professor of Biochemistry & Molecular Biology > Drexel University College of Medicine > Room 10-102 New College Building > 245 N. 15th St. > Philadelphia, PA 19102-1192 USA > > (215) 762-7706 > pj...@drexel.edu > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 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/
[ccp4bb] Project applications to CMS, IBT Biocev - Covid-19
*The Centre of Molecular Structure* as part of CIISB is committed to the use of its resources in response to the emergency situation of the COVID-19 virus pandemic. CIISB ensures that available technologies support primarily researchers in their efforts to study the virus and projects aiming to the development of an effective vaccine or treatment. In this context, we are offering priority access to groups that need to use *CMS structural biology services for projects directly related to the COVID-19 disease and its treatment*. *Priority access* will ensure a faster review of research proposals relating to COVID-19. To request priority access to CMS services for COVID-19 related research, please submit a research proposal with COVID-19 in the title of the proposal at https://www.ciisb.org/open-access/proposal-submission Successfully accepted proposals will be *free of charge*, and no financial contribution will be requested for the measurement/service. Stay safe The CMS team http://www.ibt.cas.cz/core-facility/CMS/index.html -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Figure of merit in refinement
Dear all, regarding the "remaining strong differences" between measured data and calculated SFs from a a finished (high res structure) I once investigated a bit into this going back to images and looking up some extreme outliers. I found the same - those were clear strong diffraction spots, not ice, not small molecule, genuine protein diffraction. So I had no explanation for those. Some were even "forbidden" intensities, because of screw axes which were correct. structure refined perfectly, no problems at all. I then found some literature about the possibilities of multiple reflections - I guess this is possible but I wonder if you could get easily say a 25 sigma I in this way. And as we often end our beer-discussions - may be all protein space groups are actually true P1, just close enough to satisfy the high symmetry rules .. but this is getting a bit philosophical I know .. Jan Dohnalek On Wed, Oct 16, 2019 at 6:24 PM Randy Read wrote: > James, > > Where we diverge is with your interpretation that big differences lead to > small FOMs. The size of the FOM depends on the product of Fo and Fc, not > their difference. The FOM for a reflection where Fo=1000 and Fc=10 is very > different from the FOM for a reflection with Fo=5000 and Fc=4010, even > though the difference is the same. > > Expanding on this: > > 1. The FOM actually depends more on the E values, i.e. reflections smaller > than average get lower FOM values than ones bigger than average. In the > resolution bin from 5.12 to 5.64Å of 2vb1, the mean observed intensity is > 20687 and the mean calculated intensity is 20022, which means that > Eobs=Sqrt(145.83/20687)=0.084 and Ecalc=Sqrt(7264/20022)=0.602. This > reflection gets a low FOM because the product (0.050) is such a small > number, not because the difference is big. > > 2. You have to consider the role of the model error in the difference, > because for precisely-measured data most of the difference comes from model > error. In this resolution shell, the correlation coefficient between Iobs > and Fcalc^2 is about 0.88, which means that sigmaA is about Sqrt(0.88) = > 0.94. The variance of both the real and imaginary components of Ec (as an > estimate of the phased true E) will be (1-0.94^2)/2 = 0.058, so the > standard deviations of the real and imaginary components of Ec will be > about 0.24. In that context, the difference between Eobs and Ecalc is > nothing like a 2000-sigma outlier. > > Looking at this another way, the reason why the FOM is low for this > reflection is that the conditional probability distribution of Eo given Ec > has significant values on the other side of the origin of the complex > plane. That means that the *phase* of the complex Eo is very uncertain. > The figures in this web page ( > https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html) > should help to explain that idea. > > Best wishes, > > Randy > > On 16 Oct 2019, at 16:02, James Holton wrote: > > > All very true Randy, > > But nevertheless every hkl has an FOM assigned to it, and that is used to > calculate the map. Statistical distribution or not, the trend is that hkls > with big amplitude differences get smaller FOMs, so that means large > model-to-data discrepancies are down-weighted. I wonder sometimes at what > point this becomes a self-fulfilling prophecy? If you look in detail and > the Fo-Fc differences in pretty much any refined structure in the PDB you > will find huge outliers. Some are hundreds of sigmas, and they can go in > either direction. > > Take for example reflection -5,2,2 in the highest-resolution lysozyme > structure in the PDB: 2vb1. Iobs(-5,2,2) was recorded as 145.83 ± 3.62 (at > 5.4 Ang) with Fcalc^2(-5,2,2) = 7264. A 2000-sigma outlier! What are the > odds? On the other hand, Iobs(4,-6,2) = 1611.21 ± 30.67 vs > Fcalc^2(4,-6,2) = 73, which is in the opposite direction. One can always > suppose "experimental errors", but ZD sent me these images and I have > looked at all the spots involved in these hkls. I don't see anything wrong > with any of them. The average multiplicity of this data set was 7.1 and > involved 3 different kappa angles, so I don't think these are "zingers" or > other weird measurement problems. > > I'm not just picking on 2vb1 here. EVERY PDB entry has this problem. Not > sure where it comes from, but the FOM assigned to these huge differences is > always small, so whatever is causing them won't show up in an FOM-weighted > map. > > Is there a way to "change up" the statistical distribution that assigns > FOMs to hkls? Or are we stuck with this systematic error? > > -James Holton > MAD Scientist > > On 10/4/2019 9:31 AM, Randy
Re: [ccp4bb] Can H-clashes be ignored ?
We focus mainly on non-H clashes. Careful inspection of H-clashes can sometimes lead to an improvement of the structure (better conformer). Very often we find the listed H-clashes "unavoidable", i.e. under the given data and converged refinement we cannot do anything anyway. So a very serious H-clash is checked, otherwise mostly not. Jan Dohnalek On Fri, Aug 17, 2018 at 6:27 PM Firdous Tarique wrote: > Hello everyone. > > I have a basic question. When a validation report of a coordinate is > generated we often come across a term known as "Too-Close Contacts". > First of all can somebody please explain me what is the shortest > interatomic distance between the two atoms which is permissible ? > Next, in this list there are Non-H and H columns list, their Interatomic > distance and Clash overlap. I could see two types of clashes in my > validation report. One in which interatomic distance between the two atom > (one is always a modeled H) ranges from 1.7-2.4A, and clash overlap from > 04-1.0. The other in which the interatomic distance between two atom is > greater than 2.2A and the clash overlap is between 0.4-0.6 (always between > two non H-atoms). > > So my question is that out of so many clashes shown in the list which are > one which actually need to be fixed and can't be ignored specially because > one of my ligand is an amino acid which is showing lots of these H clashes > (interatomic distance less than 1.5A). > > Regards > > Kahkashan > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Course on fragment screening using crystallography laboratory equipment
We would like to remind you about our invitation to an Instruct/CIISB course on fragment screening using crystallography laboratory equipment Dates: *April 5-6, 2018* Venue: Centre of Molecular Structure, IBT CAS v.v.i., *BIOCEV, Vestec, Prague-West*, Czech Republic See the website https://www.biocev.eu/event/instruct-ciisb-fragment-screening-course/ or the attached file for details. *Apply before February 9 2018 to frederic.velli...@ibt.cas.cz <frederic.velli...@ibt.cas.cz>.* Jan Dohnalek Institute of Biotechnology, Biocev Centre of Molecular Structure -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 Instruct_course_announcement.pdf Description: Adobe PDF document
Re: [ccp4bb] Glycoprotein expression question
We had experience with a relatively small glycoprotein - when glycosylation
sites were deleted, solubility went drastically down - we could not express
soluble any more. Back to eukaryotic expression system which worked.
So may be you were really lucky.
Jan
On Tue, Apr 11, 2017 at 10:34 PM, Bernhard Rupp <hofkristall...@gmail.com>
wrote:
> Hi Fellows,
>
>
>
> a humble question for our glyco-expressionists:
>
>
>
> I have mutated out the Asns of the N-glycoslation consensus sites for Asp
>
> (Asp simply because the PNGaseF treated protein stays stable so I thought
> that might be a good guess)
>
> and indeed the unglycosilated mutant expresses well and gets secreted as
> planned.
>
>
>
> But rumor has it that glycoproteins that are mutated to non-glyc often are
> not processed correctly and
>
> that we had just dumb luck.
>
>
>
> May I poll the educated opinion of the erudite here?
>
>
>
> Cheers, BR
>
>
>
> --
>
> Bernhard Rupp
>
> Crystallographiae Vindicis Militum Ordo
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429 <(925)%20209-7429>
>
> +43 767 571 0536 <+43%207675%20710536>
>
> --
>
> :(){ :|: & };:
>
> --
>
>
>
--
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic
Tel. +420 325 873 758
Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports
Dear all, I had this experience: going pedantically to the individual points the RSRZ and other validation statistics in the form were reporting - in a vast majority of the cases nothing was wrong at all. So it seems to be somewhat overdoing its job - not that this is bad on its own - but we are losing contrast quite a bit between the really serious issues on ... all the other. Jan Dohnalek On Wed, Nov 30, 2016 at 2:33 AM, dusan turk <dusan.t...@ijs.si> wrote: > Guys, > > I have a two issues to add here: > > 1. RSZS validation does not tolerate chain IDs longer than 1 character, so > it kills one of the very essential reasons why mmCIF format was introduced > (to enable deposition of large structures in a single file). > > 2. I have noticed in validation report of my own structure (4PIA) that the > RSZS does not ALWAYS work right. For example, the "PHE 63" is well resolved > with a hole in the ring, yet the validation declares it as a density > outlier. Besides there are several other residues in this structure that > "sit" well in the density, but are considered outliers, whereas several, > for which side chains the density is missing, are not listed. > > Has anyone else had a similar experience? > > Taken all remarks together they suggest that something needs to be done > with RSZS software or density validation procedure to resolve these issues. > > > > best, > dusan > > > On 30/11/16 01:00, CCP4BB automatic digest system wrote: > >> Date:Mon, 28 Nov 2016 20:35:44 -0800 >> From:Pavel Afonine<pafon...@gmail.com> >> Subject: Re: Calculation of RSRZ Score in PDB Validation Reports >> >> I find Lothar's comments regarding H and RSRZ excellent! I would think of >> it as a pretty much bug report. I hope developers at that end listen. This >> goes very well in line with Phoebe's comment earlier today. >> >> Pavel >> >> On Mon, Nov 28, 2016 at 2:51 PM, Dale Tronrud<de...@daletronrud.com> >> wrote: >> >> On 11/28/2016 12:52 PM,esse...@helix.nih.gov wrote: >>> >>>> I found that one can get RSRZ to go way down by loosening the geometry >>>>> restraints. The result is a crappy structure and I don't recommend >>>>> >>>> doing >>> >>>> that, but it does get all the atoms crammed into some sort of density. >>>>> >>>>Your observation is quite interesting. I can add this: when we were >>>> >>> working >>> >>>> with low to medium resolution structures, deleting the hydrogen atoms >>>> >>> from >>> >>>> the model after refinement moved the very bad RSRZ statistic to about >>>> the >>>> average in the given resolution range! Note, no re-refinement was done >>>> >>> just >>> >>>> a simple deletion of the riding H-atoms. I find this to be odd given the >>>> fact that, say the phenix developers favor the inclusion of H-atoms on >>>> riding positions even in cases of low resolution structures. (I assume >>>> >>> the >>> >>>> refmac5 and BUSTER-TNT developers have also a favorable opinion about >>>> including H-atoms in the final model - and during refinement). >>>> >>>> In my mind, it may be tempting to delete H-atoms to improve this >>>> >>> statistic but >>> >>>> when you use them in refinement they should be included regardless of >>>> the >>>> outcome of the RSRZ analysis. >>>> >>> Of course, if you trick a validation statistic like this you haven't >>> accomplished anything. All you are saying is that one should rank RSRZ >>> scores with and without hydrogen atoms separately. Perhaps you should >>> suggest that to the PDB validation people. >>> >>> Dale Tronrud >>> >>>> RSRZ, in my most humble of opinions, seems like one of those statistics >>>>> >>>> that >>> >>>> is far more useful in theory than reality. Particularly for >>>>> medium-resolution structures, the fit of each entire side chain to the >>>>> >>>> density >>> >>>> is likely to be imperfect because the density is imperfect, especially >>>>> >>>> toward >>> >>>> the tips of those side chains. >>>>> >>>>> Then again, it can be a good flag for bits of the structure worth a >>>>> >>>> second >>>
Re: [ccp4bb] PAD images
interpretable raw data images would be quite useful... Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org http://www.ruppweb.org/ - The man who follows the crowd will get no further than the crowd. The man who walks alone will find himself in places where no one has been before. - -- Jan Dohnalek, Ph.D Institute of Biotechnology Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 +420 226 201 571 Fax: +420 296 809 410
[ccp4bb] Position of a manager of central laboratories
For our new research centre Biocev http://www.biocev.eu/en/ we are looking for a manager of the Centre of molecular structure (includes protein crystallization, diffraction, biophysical methods and mass spec FT-ICR). Start around January 2015 or earlier. There is some preference for a protein crystallographer with some research experience and some facility management experience. The person will be responsible 50% for PR of the facility, attracting users, level of internal and external service, politics of all this, 50% for his/her specialization activity on the facility for the users (i.e. crystallographer would 50% of his time support crystallization and diffraction users or perhaps in some cases solve structures, possibly synchrotron measurements). A formal call will be later this year, this is a preliminary search. Anyone with a serious interest - I am happy to answer your questions via email. Jan Dohnalek Guarantor of CMS, Biocev Coordinator of Central facilities -- Jan Dohnalek, Ph.D Institute of Biotechnology Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 +420 226 201 571 Fax: +420 296 809 410
Re: [ccp4bb] Validity of Ion Sites in PDB
Given the average resolution of protein structures, reliability of ion site identification is almost always in question. Realistically, I think that only a combination of approaches and evaluation of several factors (including other experimental methods) leads to good answers (as I am trying to teach in my lectures). Therefore also an easy and uniformly reliable evaluation of ion sites in the PDB is not possible (too many details to be included in the analysis which are not part of the PDB record). In many cases though it is fairly easy to say wrong ion. Jan Dohnalek IBT Prague On Fri, Mar 7, 2014 at 7:09 AM, Robbie Joosten robbie_joos...@hotmail.comwrote: Dear Jacob, There are a lot of potential problems with ion validation, that make obtaining a reliable answer difficult. If you want to datamine ion validation results, you can use the ready-made WHAT_CHECK files in the PDBREPORT databank for original PDB files or in the PDB_REDO databank for their re-refined or rebuilt counterparts (note that PDB_REDO does not explicitly do anything with ions, yet). WHAT_CHECK uses the bond valence method to check for waters that should be ions and ions that should be other ions or water and mines the crystallisation conditions for hints of what could be there. HTH, Robbie Sent from my Windows Phone -- Van: Keller, Jacob Verzonden: 6-3-2014 20:45 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] Validity of Ion Sites in PDB Dear Crystallographers, I was curious whether there has been a rigorous evaluation of ion binding sites in the structures in the pdb, by PDB-REDO or otherwise. I imagine that there is a considerably broad spectrum of habits and rigor in assigning solute blobs to ion X or water, and in fact it would be difficult in many cases to determine which ion a given blob really is, but there should be at least some fraction of ions/waters which can be shown from the x-ray data and known geometry to be X and not Y. This could be by small anomalous signals (Cl and H2O for example), geometric considerations, or something else. Maybe this does not even matter in most cases, but it might be important in others... All the best, Jacob Keller *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *** -- Jan Dohnalek, Ph.D Institute of Biotechnology Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 +420 226 201 571 Fax: +420 296 809 410
Re: [ccp4bb] Strange diffraction image
Could be an organic crystal - what's the resoution of the lowest order reflections? Jan D. On Fri, Oct 12, 2012 at 8:11 AM, Chang Qing robie0...@gmail.com wrote: Hi, everyone: I just got some strange diffraction images from crystals with triangular pyramid shape. I think this should not be protein diffraction. I never saw so strange images like this. Does anyone know what it is? Is it a kind of salt diffraction? Thank you very much Chang -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 Fax: +420 296 809 410
Re: [ccp4bb] On maps and doubts
Have you got two very similar datasets (isomorphous) inbetween which the mentioned difference should be pronounced? You could try a cross-crystal difference map as well. Jan On Fri, Oct 5, 2012 at 8:40 AM, herman.schreu...@sanofi.com wrote: ** Dear Israel, I wonder why you do not see anything in your Fo-Fc (mFo-DFc?) maps, since the limit for a (n+1) * mFo - n * DFc map, when n approaches inifinity, is the mFo-DFc difference map. There is nothing wrong in going further like with 4mFo-3DFc maps, but you should bear in mind that they are becoming more and more difference map-like and less and less regular maps. What I think is happening is that since you added your ribosomal factor to preformed crystals, you have incomplete occupancy, say the factor bound only to 50% or less of the ribosomes. This means that you have to go down in contour level from the 3 sigma which is the default for difference maps to maybe 1.5 or even 1 sigma. If the factor is bound indeed at lower level you will see relatively nice density, if nothing is there, you will see only noise. To prove a conformational change at a single residue, I would just leave it out and refine. Since the refinement program has no reason to bias either conformation, the result should be unbiased. However, in the case of partial occupancy, the resulting map will be a superposition of both conformations. Also to reduce model bias, you might want to try the Buster program. Best regards, Herman -- *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Israel Sanchez *Sent:* Thursday, October 04, 2012 9:17 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] On maps and doubts Hello everyone, I would like to share my experience with one dataset and request some advice on which is the best way to prove a conformational change seen in a density map. The first issue arose when we were looking for an extra ribosomal factor added to a crystalized ribosome. After careful data collection and refinement (I/sigma last shell 1.2, 3.1A and CC1/2 around 22%) the sigma-A-weighted maps 2mFo-DFc and Fo-Fc does not show any clear difference density that we could interpret as the expected factor. Interestingly, a computed map with coefficients 3mFo-2DFc started to show some features that clearly could be explained as a fragment of the factor. The density improved even more with a B-sharpened map. We have seen this behavior before and I was wondering if someone else is using this kind of maps and may could explain the reason behind this density improvement. Is it a crazy idea to go even higher like 4mFo-3DFc? The second query has to do with which is the best way to prove that a conformational change is present in an specific residue (in this case and RNA base) in your structure. To my knowledge, a classic omit map with simulated annealing would do the job regarding removing the model bias. Actually, I found an interesting alternative in PHENIX called a Kick map, were a series of maps computed from a ramdoinised set of models yields a averaged map ideally free from model bias. Does anyone has a preference for any of those schemes? Are there more alternative to prove a conformational change in a model phased with a molecular replacement solution? Thank you very much in advance. -- Israel Sanchez Fernandez PhD Ramakrishnan-lab MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 Fax: +420 296 809 410
Re: [ccp4bb] Phaser Fatal runtime error.
Data from Crysalis in mtz format are not merged I think - you have to go through the scale and merge step in Scala first ... Jan Dohnalek On Tue, Jun 26, 2012 at 11:21 PM, Steiner, Roberto roberto.stei...@kcl.ac.uk wrote: Don't know where the exact problem is. However, it is definitely possible to use a Crysalis-Scala-Truncate-Phaser pipeline without runtime errors. I have done a few times. I am sure you will be able to get help from Agilent people. If not, feel free to get back to me. Best Roberto On 26 Jun 2012, at 18:34, Stephen Carr wrote: Dear CCP4bb I have collected a data-set using the supernova x-ray generator from Agilent and taken the mtz file generated by the data processing software in crysalis pro forward for structure solution. The data collection was straight forward and the software seemingly processed the data successfully - space-group P2221, overall Rmerge 9%, I/sigmaI 11, redundancy 4.5 etc. Truncate converted the intensities to structure factors with no problems, but when I tried to use the data for molecular replacement with Phaser it produced the following error: FATAL RUNTIME ERROR: Reflections are not a unique set by symmetry I'm not sure how to proceed from here as other programs in the suite do not seem to detect this problem. Also when this error has been mentioned in the past on the bb it was with a data set collected on a Bruker home source and the data processed with Denzo/scalepack, and the suggested solution was to use the Bruker software to process the data. I am currently attempting to reprocess the data with mosflm, but that is likely to be the subject of another post! Any suggestions will be gratefully received. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 Roberto Steiner, PhD Group Leader Randall Division of Cell and Molecular Biophysics King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.stei...@kcl.ac.uk -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 Fax: +420 296 809 410
[ccp4bb] Drawing plt and libXaw lib
Dear all, in Fedora 15 I am having troubles to get the .plt outputs drawn. The complaint is Using CCP4 programs from /protein/ccp4-6.2/ccp4-6.2.0/bin xplot84driver: error while loading shared libraries: libXaw.so.7: cannot open shared object file: No such file or directory libXaw.so.7 is in the system - the 64 bit version though. Anybody knows the way out? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 Fax: +420 296 809 410
Re: [ccp4bb] resolution on PDB web page
We indeed used the US portal for deposition which may be the difference. Nevertheless the recent reported resolution values etc. are projected also to the PDBe portal. Jan On Wed, Apr 25, 2012 at 10:10 AM, Mark J van Raaij mjvanra...@cnb.csic.eswrote: Phoebe, Jan, PDB, is this something particular to the US portal of the PDB, or general? We always use the European portal pdbe and have not had such problems. Mark Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 25 Apr 2012, at 09:41, Jan Dohnalek wrote: There have been other manipulations with user-input values. We could not input solvent content 83% for 3cg8 (the real value!!!) as being out of the allowed range. The resulting value in the PDB is NULL not showing the actually interesting feature of the structure. I also noticed that the reported resolution values are nonsensically advertised with three decimal positions after the point which is not the way we would put it, is it? Either fight it or live with it ... Jan Dohnalek On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Rice pr...@uchicago.edu wrote: I just noticed that the PDB has changed the stated resolution for one of my old structures! It was refined against a very anisotropic data set that extended to 2.2 in the best direction only. When depositing I called the resolution 2.5 as a rough average of resolution in all 3 directions, but now PDB is advertising it as 2.2, which is misleading. I'm afraid I may not have paid enough attention to the fine print on this issue - is the PDB now automatically advertising the resolution of a structure as that of the outermost flyspeck used in refinement, regardless of more cautious assertions by the authors? If so, I object! = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 Fax: +420 296 809 410 -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 Fax: +420 296 809 410
Re: [ccp4bb] Any calculation function in CCP4 to analyze coordinate file?
We have been doing a bit of this using a simple program under Linux - pdbskim. A linux binary available on request. Very simple output though, focused on infromation on occ, Bs alternatives, etc to help make decisions during structure refinement. Jan On Sat, Feb 25, 2012 at 11:59 PM, WENHE ZHONG wenhezhong.xmu@gmail.comwrote: Dear members, Just have a silly question past my mind: is there any program in CCP4 can be used to analyze coordinate file (.pdb format) to have a very general/overall discription about the structure? --such as the total number of protein residues/water/ligand, the total atoms of protein/water/ligand, the average b-factor of protein/water/ligand, the number of residues which have alternative side chians, and so on. Thank you. King regards, Wenhe -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 Fax: +420 296 809 410
Re: [ccp4bb] Postdoctoral position in structure-function studies of enzymes for biotechnologies
Apologies - the limiting date for PhD title is different, as stated here: The applicant has received PhD degree after March 28, 2008. Jan Dohnalek IMC Prague On Sun, Feb 26, 2012 at 9:52 PM, Jan Dohnalek dohnalek...@gmail.com wrote: DEADLINE APPROACHING! Our group has been involved in structural studies of several novel enzymes interesting from the point of view of biotechnologies, such as Laccase from *S. coeliocolor, *beta-galactosidase from Arthrobacter (660 kDa) or recently plant metal-dependent bifunctional nuclease or bacterial organophosphate anhydrolases for removal of toxic warfare agents. To continue studies in this area and apply mostly structure-driven analysis on further targets we are still accepting applications for a postdoc position. The Institute of Macromolecular Chemistry of the Academy of Sciences (IMC) in Prague, Czech Republic searches for highly motivated young researchers for a full time research postdoctoral position in the area of *Structural Analysis of Biomacromolecules.* The position is offered within the Department of Structural Analysis of Biomacromolecules (http://www.imc.cas.cz/en/umch/o_struanal.html) where the central technique is x-ray diffraction analysis of mostly protein structures. *Topic A: Structure and function of enzymes for biotechnologies* *Structure-function studies of enzymes with biotechnological applications. * The work will be focused on defining macromolecular targets, protein production and purification in collaboration with a partner, crystallization, X-ray diffraction, determination and interpretation of structure, design of mutations and complementary biophysical techniques, including measurements of reaction kinetics, inhibition and complex formation. The successful applicant will be also involved in ligand selection/design and studies of complexes of such compounds with the target macromolecules. The applicant has received PhD or equivalent in one of the following fields: biophysics, physics, biochemistry, chemistry, molecular biology or closely related. Required experience and skills: protein crystallography, biochemistry, reaction kinetics, inhibition. Practical experience with protein-ligand interaction studies (ITC, SPR, etc.) and with enzyme modification/optimization is welcome. * * The applicant has received PhD degree after May 28, 2008. *Contract type: * Full time, fixed term, 3 years, starting 1st July 2012, EU funded via the Czech Ministry of Education. You can contact me on this e-mail address or send your full application according to instructions available here: http://www.imc.cas.cz/en/umch/aktuality.htm?id=97 The deadline for full applications is February 29! Jan Dohnalek IMC Prague -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410 -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 Fax: +420 296 809 410
[ccp4bb] Postdoctoral position in structure-function studies of enzymes for biotechnologies
DEADLINE APPROACHING! Our group has been involved in structural studies of several novel enzymes interesting from the point of view of biotechnologies, such as Laccase from *S. coeliocolor, *beta-galactosidase from Arthrobacter (660 kDa) or recently plant metal-dependent bifunctional nuclease or bacterial organophosphate anhydrolases for removal of toxic warfare agents. To continue studies in this area and apply mostly structure-driven analysis on further targets we are still accepting applications for a postdoc position. The Institute of Macromolecular Chemistry of the Academy of Sciences (IMC) in Prague, Czech Republic searches for highly motivated young researchers for a full time research postdoctoral position in the area of *Structural Analysis of Biomacromolecules.* The position is offered within the Department of Structural Analysis of Biomacromolecules (http://www.imc.cas.cz/en/umch/o_struanal.html) where the central technique is x-ray diffraction analysis of mostly protein structures. *Topic A: Structure and function of enzymes for biotechnologies* *Structure-function studies of enzymes with biotechnological applications.* The work will be focused on defining macromolecular targets, protein production and purification in collaboration with a partner, crystallization, X-ray diffraction, determination and interpretation of structure, design of mutations and complementary biophysical techniques, including measurements of reaction kinetics, inhibition and complex formation. The successful applicant will be also involved in ligand selection/design and studies of complexes of such compounds with the target macromolecules. The applicant has received PhD or equivalent in one of the following fields: biophysics, physics, biochemistry, chemistry, molecular biology or closely related. Required experience and skills: protein crystallography, biochemistry, reaction kinetics, inhibition. Practical experience with protein-ligand interaction studies (ITC, SPR, etc.) and with enzyme modification/optimization is welcome. * * The applicant has received PhD degree after May 28, 2008. *Contract type: * Full time, fixed term, 3 years, starting 1st July 2012, EU funded via the Czech Ministry of Education. You can contact me on this e-mail address or send your full application according to instructions available here: http://www.imc.cas.cz/en/umch/aktuality.htm?id=97 The deadline for full applications is February 29! Jan Dohnalek IMC Prague -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
[ccp4bb] Postdoctoral positions in protein crystallography, computational and biophysical techniques
Call for POSTDOC positions The Institute of Macromolecular Chemistry of the Academy of Sciences (IMC) in Prague, Czech Republic searches for highly motivated young researchers for full time research postdoctoral positions in the area of *Structural Analysis of Biomacromolecules.* The positions are offered within the Department of Structural Analysis of Biomacromolecules (http://www.imc.cas.cz/en/umch/o_struanal.html) where the central technique is x-ray diffraction analysis of mostly protein structures. *Topic A: Structure and function of enzymes for biotechnologies* *Structure-function studies of enzymes with biotechnological applications.* The work will be focused on defining macromolecular targets, protein production and purification in collaboration with a partner, crystallization, X-ray diffraction, determination and interpretation of structure, design of mutations and complementary biophysical techniques, including measurements of reaction kinetics, inhibition and complex formation. The successful applicant will be also involved in ligand selection/design and studies of complexes of such compounds with the target macromolecules. The applicant has received PhD or equivalent in one of the following fields: biophysics, physics, biochemistry, chemistry, molecular biology or closely related. Required experience and skills: protein crystallography, biochemistry, reaction kinetics, inhibition. Practical experience with protein-ligand interaction studies (ITC, SPR, etc.) and with enzyme modification/optimization is welcome. * * *Topic B: Interaction between biological a synthetic macromolecules* *Molecular modeling, polymer structure database, mechanistic interpretation of processes (function, inhibition) in macromolecular systems.* · Solves the problems of molecular modeling and molecular dynamics and ensures compatibility between the experimental and theoretical results of structure analysis. · Determines protein structures by diffraction methods. · Introduces a new methodology in study of interactions between biological and synthetic macromolecules. · Maintains templates used in protein structure refinement. · Maintains the „Polymer structure database“ compiling information on the polymer interactions with biological molecules and also on molecular structure of polymers in solid phase. · Maintains the WEB server with „Polymer structure database“. · Interprets the processes in biological systems on the basis of structure and dynamics, and leads works directed to practical applications in a design of safer and more efficient drugs. The applicant has received PhD degree after May 28, 2008. He has sufficient knowledge in the above mentioned subjects. An advantage is knowledge of polymer chemistry, biochemistry, practical experience with diffraction methods, with molecular modeling, and with simulation of molecular dynamics. *Contract type: * Full time, fixed term, 3 years, starting 1st July 2012, EU funded via the Czech Ministry of Education. Please, send your expression of interest via e-mail as soon as possible to myself at dohnalek...@gmail.com. You will receive further details necessary for a full application. -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] image compression
I think that real universal image depositions will not take off without a newish type of compression that will speed up and ease up things. Therefore the compression discussion is highly relevant - I would even suggest to go to mathematicians and software engineers to provide a highly efficient compression format for our type of data - our data sets have some very typical repetitive features so they can be very likely compressed as a whole set without loosing information (differential compression in the series) but this needs experts .. Jan Dohnalek On Tue, Nov 8, 2011 at 8:19 AM, Miguel Ortiz Lombardia miguel.ortiz-lombar...@afmb.univ-mrs.fr wrote: So the purists of speed seem to be more relevant than the purists of images. We complain all the time about how many errors we have out there in our experiments that we seemingly cannot account for. Yet, would we add another source? Sorry if I'm missing something serious here, but I cannot understand this artificial debate. You can do useful remote data collection without having look at *each* image. Miguel Le 08/11/2011 06:27, Frank von Delft a écrit : I'll second that... can't remember anybody on the barricades about corrected CCD images, but they've been just so much more practical. Different kind of problem, I know, but equivalent situation: the people to ask are not the purists, but the ones struggling with the huge volumes of data. I'll take the lossy version any day if it speeds up real-time evaluation of data quality, helps me browse my datasets, and allows me to do remote but intelligent data collection. phx. On 08/11/2011 02:22, Herbert J. Bernstein wrote: Dear James, You are _not_ wasting your time. Even if the lossy compression ends up only being used to stage preliminary images forward on the net while full images slowly work their way forward, having such a compression that preserves the crystallography in the image will be an important contribution to efficient workflows. Personally I suspect that such images will have more important, uses, e.g. facilitating real-time monitoring of experiments using detectors providing full images at data rates that simply cannot be handled without major compression. We are already in that world. The reason that the Dectris images use Andy Hammersley's byte-offset compression, rather than going uncompressed or using CCP4 compression is that in January 2007 we were sitting right on the edge of a nasty CPU-performance/disk bandwidth tradeoff, and the byte-offset compression won the competition. In that round a lossless compression was sufficient, but just barely. In the future, I am certain some amount of lossy compression will be needed to sample the dataflow while the losslessly compressed images work their way through a very back-logged queue to the disk. In the longer term, I can see people working with lossy compressed images for analysis of massive volumes of images to select the 1% to 10% that will be useful in a final analysis, and may need to be used in a lossless mode. If you can reject 90% of the images with a fraction of the effort needed to work with the resulting 10% of good images, you have made a good decision. An then there is the inevitable need to work with images on portable devices with limited storage over cell and WIFI networks. ... I would not worry about upturned noses. I would worry about the engineering needed to manage experiments. Lossy compression can be an important part of that engineering. Regards, Herbert At 4:09 PM -0800 11/7/11, James Holton wrote: So far, all I really have is a proof of concept compression algorithm here: http://bl831.als.lbl.gov/~jamesh/lossy_compression/ Not exactly portable since you need ffmpeg and the x264 libraries set up properly. The latter seems to be constantly changing things and breaking the former, so I'm not sure how future proof my algorithm is. Something that caught my eye recently was fractal compression, particularly since FIASCO has been part of the NetPBM package for about 10 years now. Seems to give comparable compression vs quality as x264 (to my eye), but I'm presently wondering if I'd be wasting my time developing this further? Will the crystallographic world simply turn up its collective nose at lossy images? Even if it means waiting 6 years for Nielsen's Law to make up the difference in network bandwidth? -James Holton MAD Scientist On Mon, Nov 7, 2011 at 10:01 AM, Herbert J. Bernstein y...@bernstein-plus-sons.com wrote: This is a very good question. I would suggest that both versions of the old data are useful. If was is being done is simple validation and regeneration of what was done before, then the lossy compression should be fine in most instances. However, when what is being done hinges
[ccp4bb] Installation of CCP4 under Windows 7
does not seem to create anything runnable - please any experience here? I downloaded the latest Windows package all users - type. Installed under admin (as it would not let me otherwise). Now as a user I cannot start the interface no matter what I try. There is no ccp4.setup file ... Jan -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] should the final model be refined against full datset
Regarding refinement against all reflections: the main goal of our work is to provide the best possible representation of the experimental data in the form of the structure model. Once the structure building and refinement process is finished keeping the Rfree set separate does not make sense any more. Its role finishes once the last set of changes have been done to the model and verified ... J. Dohnalek On Fri, Oct 14, 2011 at 10:23 PM, Craig A. Bingman cbing...@biochem.wisc.edu wrote: Recent experience indicates that the PDB is checking these statistics very closely for new depositions. The checks made by the PDB are intended to prevent accidents and oversights made by honest people from creeping into the database. Getting away with something seems to imply some intention to deceive, and that is much more difficult to detect. On Oct 14, 2011, at 3:09 PM, Robbie Joosten wrote: The deposited R-free sets in the PDB are quite frequently 'unfree' or the wrong set was deposited (checking this is one of the recommendations in the VTF report in Structure). So at the moment you would probably get away with depositing an unfree R-free set ;) -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
[ccp4bb] CCP4MG 2.5.0 troublesome start
Dear all, with the new MG version the program wants to start the previous session giving me an empty window without any buttons no matter how hard I delete or rename previous .CCP4MG files (presumably containing the status files etc...). As a result I cannot start new MG under my login ... Any ideas? Jan -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] Trying to digest PISA results
Wasn't the original question directed to our (growing) feeling that many times PISA says No obvious oligomerization pattern but we already have evidence of dimer formation etc.. This should happen occasionally as the approach implied in the calculations is statistical in a sense. We should not be getting such contradictions on a regular basis. Possible I misunderstood the original point ... Jan On Thu, Sep 1, 2011 at 7:46 AM, Karthik S biokart...@gmail.com wrote: http://www.ebi.ac.uk/msd-srv/prot_int/pi_ilist_css.html so it depends on how many 'stable assemblies' pisa can find i suppose. more interfaces and especially if stable enough will make your fraction go down. i would have been more surprised or worried if that conservative mutation showed radically different CSS scores say one close to zero and the other one or close to it. so the exclamation marks here are really pointless (since both values are close to zero). hence i would ignore the CSS in these two cases. CSS is a statistical measure and does not imply biological meaning. in making me (us) assume the latter through this one singular value leads to all misconceptions. -- Karthik On Wed, Aug 31, 2011 at 7:52 PM, Yuri Pompeu yuri.pom...@ufl.edu wrote: I was playing around with PDBe PISA and came across the following: For pdb entry 1OYA. The most promising interface has an area bury of around 720A^2 and DeltaG of -10.6Kcal/mol. sym_op(y,x,-z+1) and CSS of 0.039! Assembly analysis says it has no strong indications that point to stable quaternary structure. This protein has been extensively studied and determined to be a dimer. Entry 3RND is the same protein with one single conservative mutation deep in the active site. They align with a RMSD of 0.3 A, 99.8% sequence identity. Superposition and inspection of the regions that contact the adjacent monomer shows they are basically identical. The interface here shows Area bury of 760 A^2 and DeltaG = -6.6Kcal/mol. sym_op (-y,-x,-z-1/2) CSS=0.00 ! Assembly analysis basically says no stable oligomers form. This enzyme also is dimer according to gel filtration. Could anyone ellaborate on this please, if they feel like they have the time... Cheers -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] Trying to digest PISA results
I guess both of the mentioned possibilities occur and it is hard to judge which one it is for a particular case. PISA is extremely useful for clear-cut cases to judge them quick. In the borderline ones it remains to be the task of the research teams to prove what sort of oligomerisation state is biologically relevant. I wish we had a method that delivers a reliable answer regarding the real state of any protein studied... Jan On Thu, Sep 1, 2011 at 8:41 AM, Ethan Merritt merr...@u.washington.eduwrote: On Wednesday, 31 August 2011, Jan Dohnalek wrote: Wasn't the original question directed to our (growing) feeling that many times PISA says No obvious oligomerization pattern but we already have evidence of dimer formation etc.. This should happen occasionally as the approach implied in the calculations is statistical in a sense. We should not be getting such contradictions on a regular basis. I think there are at least two possibilities 1) the interface seen in the crystal is a real dimer interface, but the PISA score fails to rate it as significant 2) the protein has crystallized as a monomer even though it [sometimes] exists in solution as a dimer. The interface seen in the crystal is not the real dimer interface and thus the PISA score is correct. I have no idea which, if either, of these might be the case for 1OYA. Ethan Possible I misunderstood the original point ... Jan On Thu, Sep 1, 2011 at 7:46 AM, Karthik S biokart...@gmail.com wrote: http://www.ebi.ac.uk/msd-srv/prot_int/pi_ilist_css.html so it depends on how many 'stable assemblies' pisa can find i suppose. more interfaces and especially if stable enough will make your fraction go down. i would have been more surprised or worried if that conservative mutation showed radically different CSS scores say one close to zero and the other one or close to it. so the exclamation marks here are really pointless (since both values are close to zero). hence i would ignore the CSS in these two cases. CSS is a statistical measure and does not imply biological meaning. in making me (us) assume the latter through this one singular value leads to all misconceptions. -- Karthik On Wed, Aug 31, 2011 at 7:52 PM, Yuri Pompeu yuri.pom...@ufl.edu wrote: I was playing around with PDBe PISA and came across the following: For pdb entry 1OYA. The most promising interface has an area bury of around 720A^2 and DeltaG of -10.6Kcal/mol. sym_op(y,x,-z+1) and CSS of 0.039! Assembly analysis says it has no strong indications that point to stable quaternary structure. This protein has been extensively studied and determined to be a dimer. Entry 3RND is the same protein with one single conservative mutation deep in the active site. They align with a RMSD of 0.3 A, 99.8% sequence identity. Superposition and inspection of the regions that contact the adjacent monomer shows they are basically identical. The interface here shows Area bury of 760 A^2 and DeltaG = -6.6Kcal/mol. sym_op (-y,-x,-z-1/2) CSS=0.00 ! Assembly analysis basically says no stable oligomers form. This enzyme also is dimer according to gel filtration. Could anyone ellaborate on this please, if they feel like they have the time... Cheers -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] Do manufacturers change their crystallogenesis screens?
I have witnessed a change in the Hampton additive screen some years ago - on purpose - the formulation simply did not work OK. So I guess there are changes occasionally. Jan On Wed, Aug 24, 2011 at 5:21 PM, Chris Morris chris.mor...@stfc.ac.ukwrote: HI, I've recently seen two examples where the description of a screen in a local database was different to the current one on the manufacturer's web site. This happened in two different labs, using different software, and with different screen manufacturers. This could potentially lead to an optimisation screen that finds no hits, because the wrong condition is being optimised. Does anyone have experience of this? Am I just looking at a few one-off errors, or is there a general problem here? The ideal solution is for screen manufacturers to give version numbers to their screens. Failing that, a good fix at the laboratory is to download the screen description every time a deep-well plate is received, and second best would be to download it every time a trial plate is set up. If there is a real concern here, we will implement one of these in xtalPiMS. Regards, Chris Chris Morris chris.mor...@stfc.ac.uk Tel: +44 1925 603689 Fax: +44 1925 603825 Mobile: 07921-717915 http://pims.instruct-fp7.eu/ STFC, Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
[ccp4bb] SLOW CCP4 Interface
Dear all, my ccp4 interface 6.1.3 became REALLY slow in response on a new i7 PC with Fedora core 15 2.6.38.8-35.fc15.x86_64 . Any ideas where to go from here? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] SLOW CCP4 Interface
Was a SELinux issue. Jan Dohnalek On Thu, Jul 21, 2011 at 1:44 PM, Jan Dohnalek dohnalek...@gmail.com wrote: Dear all, my ccp4 interface 6.1.3 became REALLY slow in response on a new i7 PC with Fedora core 15 2.6.38.8-35.fc15.x86_64 . Any ideas where to go from here? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410 -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] Follow-up: non-waters among structured solvent atoms
We often fight these questions when various ligands bind to our proteins. Generally, even if we know it's not water but an unidentified ligand which cannot be properly modeled or we are not brave enough to place it in the density we leave majority of the density uninterpreted but DO model a few waters in the closest H-bonding positions to protein. If the ligand was not there water would probably occupy that space anyway and who knows - may be our ligand is present only 50% and the other 50% is water ... Modeling more UNKNOWN atoms might be the future for these cases? Jan D. On Wed, Jun 15, 2011 at 7:01 PM, wtempel wtem...@gmail.com wrote: Thank you everyone for your replies. The Nayal Di Cera (1996) paper may be what I had in mind. I was looking for some estimate of how often water atoms are placed in protein models where they do not belong, and I expected a relatively high percentage. Simply extrapolating from the 0.01% water - sodium misassignments in that paper, the problem does not appear as significant as my intuition told me. Here is what started our lab's discussion: 1. crystal structure of 1000 aa residues with approx. 60% solvent content, a little better than 3A resolution, mean B factor approx 75 A**2. 2. approx. 50 Fo-Fc peaks 4*sigma in very reasonable polar environments, BUT many of them with coinciding with 2Fo-Fc density ONLY when contoured at 1*sigma 3. an anomalous difference Fourier map (calculated with a high resolution limit of 3.5A) shows 3*sigma peaks only for some metal ions that I know are present in the structure. My initial argument, outlined below, rests on these assumptions: A1. a conservative 10% of waters in a typical crystal structure are really something else. I have no evidence for this, just my own experience of the rigor I apply when modelling waters. A2. 0.5-2 waters per aa residue. LevittPark 1993. Structure 1: 223-6 How should we treat/model the Fo-Fc peaks for this specific example? I argue to either ignore them or model them as unknown atoms. They could be noise. But if they are not, they are among the strongest diffracting 10% of the expected number of solvent atoms. I have reasonable doubt that they are all waters. Heck, based on my assumptions, many of them probably ARE NOT water. I welcome your opinions. Wolfram Tempel -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] Criteria For Solvent Components
I do not think we are there yet especially when partial occupancies come into play. Then it is a real mess. We always collect all available evidence (databases, CSD, PDB seraches, anomalous, distances, geometry, fluorescence spectrum at beamline etc.) and then try to make the best guestimate .. Na+ is and will be always uneasy. Jan D. On Tue, Jun 14, 2011 at 11:34 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear Crystallographers, While I acknowledge that assigning solvent/ions/waters to blobs of density is prone to subjectivity, does anyone here know of any attempts to rigorously assign solvent blobs based on their characteristics, e.g., nearby residue types, height of peak, etc? I wrote previously to the BB about distinguishing Na from water, and got the message that it is far from simple to distinguish the two, but what about others? I guess the question driving this email is to what degree can one trust solvent assignments in the pdb? Does it have to be a case-by-case evaluation? Does anyone know of a good publication addressing this dilemma? Jacob -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] Problems in refinement
In the last months we have seen different versions of Refmac give different maps when displayed in Coot, i.e. one version giving nicer agreement and no difference peaks in some difficult areas and another version resulting in sharp differences where it was hard to build the protein. We did not investigate much further as most of the time use of two or three versions gave us a good picture of what's going on ..probably a feature which would disappear with newer versions anyway. What's the version of Refmac you use, Petr? Jan Dohnalek On Thu, May 26, 2011 at 12:11 PM, Petr Kolenko kole...@imc.cas.cz wrote: Dear colleagues, I have two problems in two structure refinements using REFMAC5. 1) 1.8A resolution, zinc in the active site. Refinement using work reflections - ADP for Zinc was about 14. Final refinement including all reflections increase ADP to 20 or even higher values - followed by very high positive difference density in position of the zinc. I have tried also PHENIX, the same thing. I changed ADP manually to 14 and only calculated maps (no refinement) look good. May I deposit the structure using manually fixed ADP according to the best agreement to the observed and difference electron density? By the way, it is clear that this is zinc. 2) 1.9A resolution, about 600AA, all of them OK in electron density. But, somehow, about ten atoms give very strong positive electron density suggesting they are not taken into account in refinement. On the other hand, ADPs are reasonable and seem to be refined. All of these atoms are fully occupied. I tried to omit whole residues and build them again, but the maxima appeared again. Using of PHENIX resulted in no difference electron density for these atoms. I have also tried to take PHENIX output to REFMAC, but the maxima are there again. It is always one or two atoms from the same residues - sometimes Calpha, sometimes Cbeta, sometimes C, sometimes NH1, but still on the same five residues. Does anyone have any idea how to solve this problem? Many thanks for any response. Petr -- Petr Kolenko petr.kole...@biochemtech.uni-halle.de http://kolda.webz.cz -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
[ccp4bb] UNESCO/IUPAC course 2011/12
Call for new participants of a graduate student course at the Institute of Macromolecular Chemistry in Prague, Czech Republic. Within this annual training program for graduate students UNESCO/IUPAC Postgraduate Course in Polymer Science a project focused on biochemistry-structural biology of chitinolytic enzymes is open: Unraveling the details of chitinolytic complex from human symbiotic bacterium influencing immunity. Interested potential candidates, please, follow this link to find out more: http://www.imc.cas.cz/unesco/projects.html#dohnalek General information on the course and participants status, etc. can be found at: http://www.imc.cas.cz/unesco/index.html as well as instructions regarding conditions and applications. Jan Dohnalek IMC Prague -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
[ccp4bb] Older cryocooling system
Would anybody offer an older crystal cooling system to go? -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] Clarification and another question . . .
In the end it comes to the question what added value above the current approaches you could offer. If you increase the success rate of crystallizability and good diffraction data from a given protein by a factor of two or more it becomes interesting - I am afraid this is not the case for microg grown crystals ... Jan On Sun, May 9, 2010 at 8:26 PM, Jack Reynolds jdr7...@yahoo.com wrote: --- On Sun, 5/9/10, Klaus Fütterer k.futte...@bham.ac.uk wrote: Dear Jack, I believe your venture would enter a mature market, and, if you were to offer growing growing crystals in microgravity, a market characterised by very high costs and (presumably) very low margins. I wouldn't offer crystal growth, I would offer access to the data from x-ray diffraction of space-grown crystals. Is the data from significantly improved crystals not a valuable commodity? If the pharmaceutical industry (and other researchers, for that matter) could grow crystals in space, and extract critical data from the x-ray diffraction of these space-grown crystals (in space); AND if costs could be reduced by 30-50%; AND if the end-product is the data, not the crystals . . . do you still think (profit) margins would be nominal? Is your assessment of very low margins based on assumed very high costs? Jack -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] Micro-g Crystal Growth and the literature
by very high costs and (presumably) very low margins. I wouldn't offer crystal growth, I would offer access to the data from x-ray diffraction of space-grown crystals. Is the data from significantly improved crystals not a valuable commodity? If the pharmaceutical industry (and other researchers, for that matter) could grow crystals in space, and extract critical data from the x-ray diffraction of these space-grown crystals (in space); AND if costs could be reduced by 30-50%; AND if the end-product is the data, not the crystals . . . do you still think (profit) margins would be nominal? Is your assessment of very low margins based on assumed very high costs? Jack -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] Distinguishing Between Na+ and H2O
This may be true for many structures but in general I am not a friend of massive changes made to already deposited structures - it more likely produces more errors than better structures. 2.4 Angstrom hydorgen bonds for water are probably not entirely impossible and on the other hand some close distances can result just from bad structure refinement or relatively low resolution of the data (there are even examples of non-refined structures in the PDB) and in those cases making this kind of changes would be a complete disaster... Jan On Wed, Feb 17, 2010 at 6:32 PM, Jacob Keller j-kell...@md.northwestern.edu wrote: Dear Crystallographers, Having looked into the structure I mentioned using the atomic contacts feature of the whatif server, it seems that both the 1.0 Ang structure I previously mentioned, as well as another, lower-resolution related structure, have a significant number of waters which are 2.6 Ang from polar atoms, with many in the 2.4 Ang regime (suggesting Na+). Both structures were solved in the presence of Na+. It seems impossible for water to bind at this distance, so would it not be best for the PDB to add some distance cutoff to its validation process? Should the PDB retrospectively review all structures for waters binding at these distances, cross-checking, of course, for sodium in the protein stock and/or crystallization condition? I am not sure about the profundity of the consequences of such a natrification, but truth is truth, however mundane, no? Regards, Jacob Keller ps I am curious about how many structures would be affected by this. *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, February 16, 2010 5:00 AM Subject: Re: [ccp4bb] Distinguishing Between Na+ and H2O A few years ago we thought that the bond valence method might provide an answer to this problem and wrote a paper on the subject (Acta Cryst. 2003 D59 32-37). Subsequent experience has convinced me that although this method works well for identifying ions such as Mg2+ and Ca2+ with good resolution data, it is not reliable in other cases such as Na+, and for this reason I never distributed the version of SHELXPRO that includes the bond valence test (I would not like my programs to get a bad name). In fact we currently have a protein crystallized from a high NaCl concentration that is giving us a lot of problems distinguishing between Na+ and water molecules. Since we were able to find some chlorides in the anomalous map we know that cations must also be present, but the anomalous data are too weak to help much with Na+ because of its lower f. There are however some tentative indicators for Na+. The bond valence sum (the sum of the 'bond orders' to the surrounding atoms estimated from the distances) tends to be higher than for Cl- or H2O. Tetrahedral coordination is more likely to be water or Cl-, Na+ prefers 5 or 6 neighbors. And of course two cations (or two anions) that are close to each other should not have an occupancy sum greater than unity. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Tue, 16 Feb 2010, Eleanor Dodson wrote: Yes - we are puzzling over the same phenomena. Look at this web site set up by Marjorie Harding http://tanna.bch.ed.ac.uk/ It lists the likely coordination patterns. We certainly have ideal Na bonding in our structure - but unfortunately we wanted to find Ca which has a very similar pattern!! Grrr Eleanor Jacob Keller wrote: Dear Crystallographers, I am looking at a 1.0 Angstrom structure which contains many waters, but I am wondering whether some of them might really be sodium ions. Is there any straightforward way to distinguish between these two, and if so, what is the software which implements this? Although the electron density difference between sodium and water should be very small, perhaps the binding geometry would provide a clearer distinction? Has anybody encountered this question before? Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy
[ccp4bb] Example of a good crystallization facility design?
Dear all, could anyone recommend a lab in Europe with a crystallization lab designed with a good, clever working environment for temperature/(humidity) control with sufficient air conditioning backup, etc? Especially if it includes lower and higher temperature environments (~10 or 30 deg). I do not mean robotic setups by this .. Jan Dohnalek, IMC Prague -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] Distinguishing Between Na+ and H2O
After having seen many Na+ ions very likely correctly built and refined and many potential Na+ sites with a very clear indication that the bond valence sum is already on the border of being water and being an ion I would say that Na+ binding in proteins happens quite often and probably escapes unobserved by which I mean that we do not notice because it simply is not so clear in so many cases. If one assumes the very likely alternative of Na+/water alternative occupancy it muddles the distances sufficiently for us not to be able to say a clear YES or NO. I sometimes wish we had a sodium detector for such structures .. Jan On Tue, Feb 16, 2010 at 12:00 PM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: A few years ago we thought that the bond valence method might provide an answer to this problem and wrote a paper on the subject (Acta Cryst. 2003 D59 32-37). Subsequent experience has convinced me that although this method works well for identifying ions such as Mg2+ and Ca2+ with good resolution data, it is not reliable in other cases such as Na+, and for this reason I never distributed the version of SHELXPRO that includes the bond valence test (I would not like my programs to get a bad name). In fact we currently have a protein crystallized from a high NaCl concentration that is giving us a lot of problems distinguishing between Na+ and water molecules. Since we were able to find some chlorides in the anomalous map we know that cations must also be present, but the anomalous data are too weak to help much with Na+ because of its lower f. There are however some tentative indicators for Na+. The bond valence sum (the sum of the 'bond orders' to the surrounding atoms estimated from the distances) tends to be higher than for Cl- or H2O. Tetrahedral coordination is more likely to be water or Cl-, Na+ prefers 5 or 6 neighbors. And of course two cations (or two anions) that are close to each other should not have an occupancy sum greater than unity. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Tue, 16 Feb 2010, Eleanor Dodson wrote: Yes - we are puzzling over the same phenomena. Look at this web site set up by Marjorie Harding http://tanna.bch.ed.ac.uk/ It lists the likely coordination patterns. We certainly have ideal Na bonding in our structure - but unfortunately we wanted to find Ca which has a very similar pattern!! Grrr Eleanor Jacob Keller wrote: Dear Crystallographers, I am looking at a 1.0 Angstrom structure which contains many waters, but I am wondering whether some of them might really be sodium ions. Is there any straightforward way to distinguish between these two, and if so, what is the software which implements this? Although the electron density difference between sodium and water should be very small, perhaps the binding geometry would provide a clearer distinction? Has anybody encountered this question before? Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
[ccp4bb] Refmac and links between ligands
Dear all I understand that when I use the Refmac keyword make link no Refmac should not apply found links. It keeps finding links between ligands (Na+ and ligand OH) and (I think) refines them as it issues a warning (not INFO), does not say (not be used) for these and the output .pdb file contains the LINK records newly created for these atoms. The actual distances look pretty much as if they were restrained ... Is there a way to make Refmac ignore these links? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] Refmac and links between ligands
Problem solved. One must also switch to the make sugar NO keyword. Otherwise Refmac tries to use the discovered sugar and ion as if it was sugar-peptide bond. Jan Dohnalek On Mon, Feb 1, 2010 at 2:52 PM, Jan Dohnalek dohnalek...@gmail.com wrote: Dear all I understand that when I use the Refmac keyword make link no Refmac should not apply found links. It keeps finding links between ligands (Na+ and ligand OH) and (I think) refines them as it issues a warning (not INFO), does not say (not be used) for these and the output .pdb file contains the LINK records newly created for these atoms. The actual distances look pretty much as if they were restrained ... Is there a way to make Refmac ignore these links? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410 -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] SHELXL eating REFMAC5 waters - whom to trust?
Dear Wulf, I have had a similar experience recently when water treatment in SHELXL became a nightmare - as you say they started shifting away even if those were clear water sites. I have not found a final solution to this but I was not worried by those where density disappeared - those were the weak ones anyway so I attributed this behaviour to the different refinement algorithm and treatment of bulk solvent etc. I still believe that this is related to the max. likelihood vs. conjugated gradients and FFT vs. full summation Fourier and bulk solvent treatment in those programs. My way was to leave this water fiddling to the very last cycle and not let them go away too much. Those that went completely wrong were deleted. I wish I had a more satisfying answer. Jan On Thu, Nov 12, 2009 at 8:53 AM, Wulf Blankenfeldt wulf.blankenfe...@mpi-dortmund.mpg.de wrote: Dear all, I am blessed/tormented with a 0.8 A data set for a small protein. I first refined it using COOT/REFMAC5 until I deemed it done, which meant manually adding quite a few water molecules that were weak and a little more distant to the protein. R is 10.2%, R-free is 10.8%. I realize that referees will probably ask for a SHELXL refinement, so I spent the last few days learning about FVAR and SUMP instructions and the like and finally got it running in a way I thought should be correct. Using my final REFMAC5 model, I get R=10.8% and R-free=11.1% - I can certainly live with this, but: When I now look at the electron density, a large number of my tenderly curated water molecules have lost their 2FO-FC electron density (50 out of 200; I usually use a 1 sigma cutoff), or they have shifted to lie beside a density blob. It may have to do with the fact that I assigned 0.5 occupancy to some of them and now they have been BUMPed away, others may simply be too weak to stay in place. I wonder what to do now. Do I have to rebuild the water structure again and refine everything in SHELXL exclusively? Or are there any flags I could use to keep the old waters intact (risking higher R-factors)? Any help is highly appreciated! Thank you in advance, Wulf -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
[ccp4bb] Special position refinement
Dear all, we have seen again with the 5.5.0102 version that water O or Fe ion are not held on the crystallographic axis automatically. What should we do except using possibly the restrain keyword? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
[ccp4bb] Discussion workshop on Eukaryotic Expression - last call
This is the second and the last announcement of the Discussion Workshop on Eukaryotic Expression to be held in Prague, Czech Republic on 26th October 2009. There are still a few places available. Deadline for registration is on 19th October 2009. The final program is attached. The event is organized and funded by the project TeachSG of the European Commission and in connection with the project SPINE2-Complexes. The purpose of the workshop is to facilitate an overview of methods and approaches in eukaryotic protein expression (not only) for structural studies in a condensed way together with a few application talks mainly by younger scientists (see the attached preliminary program). We hope that the workshop program together with your visit of the city of Prague will be an efficient use of time. The one day event is open to participants from academia and industry. There is no fee for participation in the workshop. As the lecture hall capacity is limited and we need to make preparations for refreshments each participant must recieve an e-mail confirmation from one of the organizers before arrival. Those intending to participate should reply to this e-mail message stating their full name and affiliation. (Please, send your emails to dohnalek...@gmail.com). For all participants a light buffet lunch and refreshments will be provided. We cannot cover your travel or accommodation expenses. We can provide a limited assistance with finding your hotel accommodation in Prague. Jan Dohnalek, Institute of Macromolecular Chemistry, Prague, Tel: +420 296809390 Ondrej Vanek, Institute of Microbiology, Prague Workshop organizers DiscussionWorkshoponEukaryoticExpression_Prague26Oct2009.pdf Description: Adobe PDF document
[ccp4bb] Discussion workshop on Eukaryotic expression
A Discussion workshop on Eukaryotic expression will be held in Prague, Czech Republic, on 26th October 2009. The event is organized and funded by the project TeachSG of the European Commission and in connection with the project SPINE2-Complexes. The purpose of the workshop is to facilitate an overview of methods and approaches in eukaryotic protein expression (not only) for structural studies in a condensed way together with a few application talks mainly by younger scientists (see the attached preliminary program). We hope that the workshop program together with your visit of the city of Prague will be an efficient use of time. The one day event is open to participants from academia and industry. There is no fee for participation in the workshop. As the lecture hall capacity is limited and we need to make preparations for refreshments each participant must recieve an e-mail confirmation from one of the organizers before arrival. Those intending to participate should reply to this e-mail message stating their full name and affiliation. For all participants a light buffet lunch and refreshments will be provided. We cannot cover your travel or accommodation expenses. We can provide a limited assistance with finding your hotel accommodation in Prague. Jan Dohnalek, Institute of Macromolecular Chemistry, Prague, Tel: +420 296809390 Ondrej Vanek, Institute of Microbiology, Prague Workshop organizers DiscussionWorkshoponEukaryoticExpression_Prague26Oct2009_preliminary.pdf Description: Adobe PDF document
[ccp4bb] refmac twin operator problems
Dear all, I assume that the current versions (from 5.5.0072) take the input line twin operator parameters. However we are getting the Problem get_symm_from_text message whatever we do. What is the correct format here? We do for example twin operator h,-k,-l thanks Jan -- == Mr. Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Laboratory of Structural Analysis of Molecules Heyrovskeho nam. 2 16206 Prague 6 Tel: +420 296809390 Fax: +420 296809410 http://protein.awardspace.com/ ==
[ccp4bb] TeachSG workshop Expertise in Macromolecular Structure Refinement in Prague April 3-4
This is a reminder - the application deadline is approaching - 24th February. Jan Dohnalek A two-day workshop focused on both the basics and the current development in macromolecular single crystal structure refinement techniques will be held in Prague on April 3-4 2009. The workshop is organized within the TeachSG project of the EC (tightly connected with the project Spine2-Complexes) to support dissemination of knowledge in the field of structural biology. Several highly qualified speakers and tutors confirmed their contributions to the workshop (see the attached preliminary program). There will be a limited number of places so hurry up if you want to be here in April. The workshop is aimed at young researchers, students, PhD students, young post-docs (exceptions can be made if reasonably justified). We expect a wide spectrum of students from beginners in refinement to experienced users seeking proficiency in the field. To apply for participation, please, send an e-mail to myself (Jan Dohnalek, cc: dusk...@imc.cas.cz) containing a motivation letter (within the e-mail message is OK), a letter of support from your supervisor or head of group, and a short professional CV (one page). It should be clear from your documents why participation in such workshop is necessary for your career. The deadline for applications is: Tuesday 24th February 2009. The selected participants will be notified by e-mail within several days after the deadline date. The organizers provide and cover the costs of conference materials, refreshments during the course including lunches and a workshop dinner on the 3rd. Workshop participants are asked to make their own travel arrangements and accommodation bookings. We are ready to give you advice on travel if necessary. You can contact Jan Dohnalek or Jarmila Duskova (duskova at imc.cas.cz) for more details. Looking forward to see you in Prague, Jan Dohnalek IMC Prague -- == Mr. Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Laboratory of Structural Analysis of Molecules Heyrovskeho nam. 2 16206 Prague 6 Tel: +420 296809390 Fax: +420 296809410 http://protein.awardspace.com/ == TeachSG_workshop_Refinement_PragueApril.xls Description: application/msexcel
[ccp4bb] TeachSG workshop Expertise in Macromolecular Structure Refinement in Prague April 3-4
A two-day workshop focused on both the basics and the current development in macromolecular single crystal structure refinement techniques will be held in Prague on April 3-4 2009. The workshop is organized within the TeachSG project of the EC (tightly connected with the project Spine2-Complexes) to support dissemination of knowledge in the field of structural biology. Several highly qualified speakers and tutors confirmed their contributions to the workshop (see the attached preliminary program). There will be a limited number of places so hurry up if you want to be here in April. The workshop is aimed at young researchers, students, PhD students, young post-docs (exceptions can be made if reasonably justified). We expect a wide spectrum of students from beginners in refinement to experienced users seeking proficiency in the field. To apply for participation, please, send an e-mail to myself (Jan Dohnalek, cc: dusk...@imc.cas.cz) containing a motivation letter (within the e-mail message is OK), a letter of support from your supervisor or head of group, and a short professional CV (one page). It should be clear from your documents why participation in such workshop is necessary for your career. The deadline for applications is: Tuesday 24th February 2009. The selected participants will be notified by e-mail within several days after the deadline date. The organizers provide and cover the costs of conference materials, refreshments during the course including lunches and a workshop dinner on the 3rd. Workshop participants are asked to make their own travel arrangements and accommodation bookings. We are ready to give you advice on travel if necessary. You can contact Jan Dohnalek or Jarmila Duskova (duskova at imc.cas.cz) for more details. Looking forward to see you in Prague, Jan Dohnalek IMC Prague -- == Mr. Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Laboratory of Structural Analysis of Molecules Heyrovskeho nam. 2 16206 Prague 6 Tel: +420 296809390 Fax: +420 296809410 http://protein.awardspace.com/ == TeachSG_workshop_Refinement_PragueApril.xls Description: application/msexcel
Re: [ccp4bb] [SPAM:#] [ccp4bb] O/T: can a protein which dimerizes in solution crystallize as a monomer?
I would strongly argue against protein crystals (in most cases) being solid state. Most of the surface of a molecule is actually solvated and protein crystals as they are miss some of the typical properties of solid state. Although in some cases oligomerization occuring upon protein crystallization indicates fairly strong interactions between molecules, still the crystals are actually half liquid. This is the main reason why many ligand exchange and activity studies could be performed even in protein crystals. Quite often (I think) protein crystallographers would actually like their crystals to really behave like solids (stability, localization of disordered regions, etc.) no need for cryoprotection and it is hard to make them ... Jan Dohnalek IMC Prague Jayashankar wrote: Here we are dealing with two different state of chemistry, solid state and solution state, If one of the minima in solid state resembles the biological state minimum, then there is a possiblw way to clearly define the biology and its significant interaction of that particular 'mer' of a protein, other wise we end up with pure physical interaction. But my question is have we answered Wouldn't the high concentration in the crystallization drop further favor dimerization? this part ... S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Thu, Dec 11, 2008 at 5:53 PM, Phoebe Rice pr...@uchicago.edu mailto:pr...@uchicago.edu wrote: Mass action is on the crystal's side. Two recent examples of proteins that are dimers by standard solution assays, but form weak/transient/co-factor-dependent tetramers to function, and those tetramers are seen in the crystal. (There is good solution data to back up the relevance of the tetramer in both cases). Yuan P, Gupta K, Van Duyne GD. Tetrameric structure of a serine integrase catalytic domain. Structure. 2008 Aug 6;16(8):1275-86. Mouw KW, Rowland SJ, Gajjar MM, Boocock MR, Stark WM, Rice PA. Architecture of a serine recombinase-DNA regulatory complex. Mol Cell. 2008 Apr 25;30(2):145-55. Phoebe == Original message Date: Thu, 11 Dec 2008 10:09:33 -0600 From: Santarsiero, Bernard D. b...@uic.edu mailto:b...@uic.edu Subject: [SPAM:#] [ccp4bb] O/T: can a protein which dimerizes in solution crystallize as a monomer? To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK In parallel with the discussion around this off-CCP4-topic, are they any good examples of the opposite case, where the protein is a monomer in solution (as evident from light scattering, MW determination through centrifugation, EPR, etc.) but crystallizes as a dimer or higher multimer? Bernie Santarsiero Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 RNA is really nifty DNA is over fifty We have put them both in one book Please do take a really good look http://www.rsc.org/shop/books/2008/9780854042722.asp -- == Mr. Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Laboratory of Structural Analysis of Molecules Heyrovskeho nam. 2 16206 Prague 6 Tel: +420 296809390 Fax: +420 296809410 http://protein.awardspace.com/ ==
[ccp4bb] Topp fails: TOP: Open failed: File: /people/...../myfile.pdb
Hi all, Using the 6.0.2 distribution of CCP4, the top program keeps failing because it just can't see the pdb files. The files can be accessed by the text viewer of CCP4. (the button VIEW) I have tried to put them in other directories to make the path string shorter, etc. None of those helped. I have tried moving to various Linux versions (64bit,32bit, var. levels of Fedora or RHEL) Any ideas? Jan Dohnalek -- == Mr. Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Laboratory of Structural Analysis of Molecules Heyrovskeho nam. 2 16206 Prague 6 Tel: +420 296809205 Fax: +420 296809410 http://protein.awardspace.com/ ==
Re: [ccp4bb] How to obtain an oca file?
We miss the MSD target service a lot. Is there a real reason why it's gone? Jan Dohnalek Eleanor Dodson wrote: Thwe MSD target service has gone, and that was the way I created oca files comparing sequences? Is there another web site which will give back the same format? Eleanor -- == Mr. Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Laboratory of Structural Analysis of Molecules Heyrovskeho nam. 2 16206 Prague 6 Tel: +420 296809205 Fax: +420 296809410 ==
[ccp4bb] Douglas Instruments Oryx crystallisation robots
We are thinking about getting the Oryx8 robot (Douglas Instruments) for crystallisation experiments. Is anyone out there with any kind of experience with these? Jan Dohnalek IMC Prague
[ccp4bb] TeachSG Workshop on ligand searching and docking in Prague
There are still places available at the TeachSG Workshop: Biological macromolecules and their ligands Techniques in X-ray structure analysis and Docking This workshop will be held from 10th -11th Jun 2007 in Prague. The workshop is designed to give protein crystallographers good background on proper geometry definitions for ligands in protein-ligand complexes, to help crystallographers use properly the up-to-date tools for ligand searching in electron density maps, automated or semi-automated ligand building and refinement and give them a chance to try out and be able to apply the current computational techniques of docking, when experimental data on complexes are missing. The lectures and tutorials should focus on smaller ligands but a lot of this knowledge will be applicable in the cases of macromolecular ligands as well. The workshop is also meant for computational biologists to provide them with basic knowledge and some skills in experimental determination of complexes between molecules of biological relevance. Workshop program is available from the SPINE2 web site: http://www.spine2.eu/documents/program_TeachSG.doc. The workshop is organised within the TeachSG project and there is no fee connected with participation. It is mainly designed for students and young post-docs but still each application will be considered individually. If you have someone who would benefit from attending, please could you ask them to send a short CV, a short expression of interest explaining the reason for participation, and a letter of support from their group or laboratory head. The applications should be send by e-mail to Sarit Goren [EMAIL PROTECTED])or to Jan Dohnalek ([EMAIL PROTECTED]) as soon as possible. The participants have to fund their travel and accommodation expenses. 12 Successful applicants will receive an invitation letter in several days after the deadline. There is information on venue, travel and recommended accommodation and the program available on the SPINE2 web page (meetings) http://www.spine2.eu/meetings/ Jan Dohnalek Institute of Macromolecular Chemistry Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Sarit Goren SPINE2-Complexes Training Manager Division of Structural Biology Henry Wellcome Building for Genomic Medicine Roosevelt Drive, Oxford, OX3 7BN, UK
