Re: [ccp4bb] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy
Dear Marin, The reason why you did not find a recent discussion or review about resolution metrics in X-ray crystallography is that this approach is nowadays obsolete. Having a metric (e.g. I/sigma, Rmerge, Rpim, CC1/2, CC*) can be useful and may give you a good estimate. It is also a fast way to make the decision. However, this is not an optimal estimate (now). Instead of insisting on a certain value of your metric, you should be validating trends in several metrics during the stepwise increase of your resolution - paired refinement. Further reading: Original Paired Refinement paper - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457925/ Program PAIREF for CCP4 users - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7340264/ Program PAIREF for PHENIX users - https://pubmed.ncbi.nlm.nih.gov/34196613/ There is more literature related to this issue. Unfortunately, I cannot comment on metrics for Cryo-EM. Best regards, Petr Od: CCP4 bulletin board za uživatele Marin van Heel Odesláno: pondělí 7. října 2024 18:24 Komu: CCP4BB@JISCMAIL.AC.UK Předmět: [ccp4bb] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy E-maily z adresy marin.vanh...@gmail.com nedostáváte často. Přečtěte si, proč je to důležité<https://aka.ms/LearnAboutSenderIdentification> Dear All, Sayan Bhakta and I have recently posted the preprint of a review on resolution and linearity which will appear in a book to be launched on the 16th of October 2024. ( https://doi.org/10.1201/9781003326106 ). It is the first Cryo-EM review that I have been involved in for 25 years. In our preparation, I was quite amazed about what other authors wrote (or did not write) in their many reviews on these matters. For example, I missed any serious discussion about resolution metrics in X-ray crystallography, which technique is fundamentally non-linear. Linearity is a prerequisite for defining the resolution of any instrument. The iterative refinements applied in X-ray crystallography (and sometimes Cryo-EM) makes that all Phase-residuals and R-factors or fixed threshold values cannot be used to compare the results of independently conducted experiments. What is an obvious consequence of the lack of universality of such metrics like phase-residuals and R-factors, is that they cannot be used outside of the immediate context in which they were defined, like X-ray crystallography or structural biology. In contrast, the Fourier-Ring-Correlation (FRC); Fourier-Shell-Correlation (FSC) and their recent successors: the Fourier-Ring-Information (FRI) and the Fourier-Shell-Information (FSI), plus their integrated versions, are universal metrics that are applicable to all fields of science where 2D and 3D data are dealt with! https://doi.org/10.31219/osf.io/5empt Have fun reading it! Marin To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] I'm hiring!
Greetings, For the first time in forever, I am looking to replace my sole employee, who is retiring. The successful applicant will work one-on one with me, as well as the hundreds of users who come to my beamline. I suppose the position could sound like a lot of user support, which may not sound exciting, but finding the right answers to my users questions is what made me into a MAD Scientist on this BB. https://sjobs.brassring.com/TGnewUI/Search/home/HomeWithPreLoad?PageType=JobDetails&partnerid=6495&siteid=5861&Areq=79597BR#jobDetails=3558174_5861 -James Holton MAD Scientist To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy
Dear Marius Schmidt In my (our) *original FRC/FSC papers* (1982; 1986 ; 2000; 2004; 2017; 2020; 2024) the linearity of these correlation functions/metrics have been extensively discussed. Historically, EM started at a low resolution "blobology" level whereas X-ray crystallography (XRC) at that time, already had reached atomic resolution. This led to the belief that the *XRC resolution metrics* ( like phase residuals and R-factors) were also appropriate as *resolution metrics for EM*. However, in XRC the measurables are *diffraction patterns* for which *amplitudes *corresponding *phases *had to be derived *iteratively*. In EM and in imagining in general, the measurables are the images themselves, that contain both the *amplitude information *and the *phase information*. To revert to the then already established *XRC resolution metrics* like phase residuals or R-factors, implied *discarding *the most important part of the available information (see the Why-O-Why ). ( https://www.linkedin.com/posts/marin-van-heel-5845b422b_whyowhyarchive-activity-7149738255154946048-Oc93/?utm_source=share&utm_medium=member_desktop ). That problem was realized soon and the mentioned *FRC and FSC metrics* were thus suggested which exploit all the available information. Thus, the *XRC atomic resolution* *technique *of the 1980s came with a *low-quality resolution metric* whereas the *Cryo-EM low-resolution blobology *approach of the 1980s came with a *high-quality resolution metric*. Thus, in summary, *all resolution criteria in XRC* are *ad-hoc non-linear metrics* that have no general validity outside of *XRC*. Looking at only the amplitudes of a diffraction pattern is like finding the highest resolution spot in a diffraction pattern, where, even if the spot is clearly visible, that does not mean one would be able to find its phase. We need a more comprehensive metric that has a wide range of applicability. In other words, where a CC1-2 metric cannot be applied to assess the 3D brain scan of a brain-tumor patient, the FRC / FSC, and the newest FRI / FSI metrics can be applied in all cases where 2D and 3D data are dealt with! Hope this helps, Marin van Heel On Mon, Oct 7, 2024 at 3:04 PM Marius Schmidt wrote: > I think this is taken care of: > The CC1/2 and the CC1/2* are appropriate metrics for the resolution limit. > They are all spit out by newer data processing software. > The CC1/2 is directly comparable to the FSC. Many people use CC1/2 = 1/e as > the resolution limit. > In many cases of data the CC1/2 = 1/e is equivalent to I/sigI of 1, which > is used sometimes as a metric for the resolution limit (some use I/sigI = > 2), > and in more cases the CC1/2 corresponds to Rmerge in the range of 40%. > For serial crystallography, the R-split goes through the roof at CC1/2 = > 1/e, > so the CC1/2 is the better metric. > > Best > Marius > > > > > > Marius Schmidt, Dr. rer. Nat. (habil.) > Professor > University of Wisconsin-Milwaukee > Kenwood Interdisciplinary Research Complex > Physics Department, Room 3087 > 3135 North Maryland Avenue > Milwaukee, Wi 53211 > phone (office): 1-414-229-4338 > phone (lab): 414-229-3946 > email: smar...@uwm.edu > https://uwm.edu/physics/people/schmidt-marius/ > https://sites.uwm.edu/smarius/ > https://www.bioxfel.org/ > Nature News and Views: https://www.nature.com/articles/d41586-023-00504-4 > > ------ > *From:* CCP4 bulletin board on behalf of Marin > van Heel > *Sent:* Monday, October 7, 2024 11:24 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Review: Linearity and Resolution in X-Ray > Crystallography and Electron Microscopy > > > Dear All, > > Sayan Bhakta and I have recently posted the preprint of a review on > resolution and linearity which will appear in a book to be launched on the > 16th of October 2024. > ( https://doi.org/10.1201/9781003326106 ). > It is the first Cryo-EM review that I have been involved in for 25 years. > In our preparation, I was quite amazed about what other authors wrote (or > did not write) in their many reviews on these matters. > For example, I missed any serious discussion about resolution metrics in > X-ray crystallography, which technique is fundamentally non-linear. > Linearity is a prerequisite for defining the resolution of any instrument. > The iterative refinements applied in X-ray crystallography (and sometimes > Cryo-EM) makes that all Phase-residuals and R-factors or fixed threshold > values cannot be used to compare the results of independently conducted > experiments. What is an obvious consequence of the lack of universality of > such metrics like phase-residuals and R-factors, is that they cannot be > used outside of the immediate context in which they were defined, like > X-ray crystallography or st
Re: [ccp4bb] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy
I think this is taken care of: The CC1/2 and the CC1/2* are appropriate metrics for the resolution limit. They are all spit out by newer data processing software. The CC1/2 is directly comparable to the FSC. Many people use CC1/2 = 1/e as the resolution limit. In many cases of data the CC1/2 = 1/e is equivalent to I/sigI of 1, which is used sometimes as a metric for the resolution limit (some use I/sigI = 2), and in more cases the CC1/2 corresponds to Rmerge in the range of 40%. For serial crystallography, the R-split goes through the roof at CC1/2 = 1/e, so the CC1/2 is the better metric. Best Marius Marius Schmidt, Dr. rer. Nat. (habil.) Professor University of Wisconsin-Milwaukee Kenwood Interdisciplinary Research Complex Physics Department, Room 3087 3135 North Maryland Avenue Milwaukee, Wi 53211 phone (office): 1-414-229-4338 phone (lab): 414-229-3946 email: smar...@uwm.edu https://uwm.edu/physics/people/schmidt-marius/ https://sites.uwm.edu/smarius/ https://www.bioxfel.org/ Nature News and Views: https://www.nature.com/articles/d41586-023-00504-4 From: CCP4 bulletin board on behalf of Marin van Heel Sent: Monday, October 7, 2024 11:24 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy Dear All, Sayan Bhakta and I have recently posted the preprint of a review on resolution and linearity which will appear in a book to be launched on the 16th of October 2024. ( https://doi.org/10.1201/9781003326106 ). It is the first Cryo-EM review that I have been involved in for 25 years. In our preparation, I was quite amazed about what other authors wrote (or did not write) in their many reviews on these matters. For example, I missed any serious discussion about resolution metrics in X-ray crystallography, which technique is fundamentally non-linear. Linearity is a prerequisite for defining the resolution of any instrument. The iterative refinements applied in X-ray crystallography (and sometimes Cryo-EM) makes that all Phase-residuals and R-factors or fixed threshold values cannot be used to compare the results of independently conducted experiments. What is an obvious consequence of the lack of universality of such metrics like phase-residuals and R-factors, is that they cannot be used outside of the immediate context in which they were defined, like X-ray crystallography or structural biology. In contrast, the Fourier-Ring-Correlation (FRC); Fourier-Shell-Correlation (FSC) and their recent successors: the Fourier-Ring-Information (FRI) and the Fourier-Shell-Information (FSI), plus their integrated versions, are universal metrics that are applicable to all fields of science where 2D and 3D data are dealt with! https://doi.org/10.31219/osf.io/5empt Have fun reading it! Marin To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy
Dear All, Sayan Bhakta and I have recently posted the preprint of a review on resolution and linearity which will appear in a book to be launched on the 16th of October 2024. ( https://doi.org/10.1201/9781003326106 ). It is the first Cryo-EM review that I have been involved in for 25 years. In our preparation, I was quite amazed about what other authors wrote (or did not write) in their many reviews on these matters. For example, I missed any serious discussion about resolution metrics in X-ray crystallography, which technique is fundamentally non-linear. Linearity is a prerequisite for defining the resolution of any instrument. The iterative refinements applied in X-ray crystallography (and sometimes Cryo-EM) makes that all Phase-residuals and R-factors or fixed threshold values cannot be used to compare the results of independently conducted experiments. What is an obvious consequence of the lack of universality of such metrics like phase-residuals and R-factors, is that they cannot be used outside of the immediate context in which they were defined, like X-ray crystallography or structural biology. In contrast, the Fourier-Ring-Correlation (FRC); Fourier-Shell-Correlation (FSC) and their recent successors: the Fourier-Ring-Information (FRI) and the Fourier-Shell-Information (FSI), plus their integrated versions, are universal metrics that are applicable to all fields of science where 2D and 3D data are dealt with! https://doi.org/10.31219/osf.io/5empt Have fun reading it! Marin To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] re- HSSP Database
Thank you all for your valuable suggestions. On Mon, Oct 7, 2024 at 2:13 PM Robbie Joosten wrote: > I agree with Randy about the secondary structure things. The main use of > HSSP in my hand is having ready-made multiple sequence alignments that > allow you to quickly check the distribution of residues at a specific > position: this glycine is 100% conserved in 1337 sequences, I guess it is > rather important. > > Anyway, HSSP is indeed offline but I have the last version of the databank > for anyone who wants it (mail me off-list). A problem with HSSP was that > it was rather maintenance-heavy for the number of users. If it becomes > obvious that there is strong demand for it, may reappear. > > Cheers, > Robbie > > > -Original Message- > > From: CCP4 bulletin board On Behalf Of Randy > > John Read > > Sent: Monday, October 7, 2024 10:26 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] re- HSSP Database > > > > Maybe someone else will have a different opinion, but I suspect that the > very > > best method to predict secondary structure at the moment is to predict > the > > tertiary structure using AlphaFold or another machine-learning structure > > prediction method, and then observe the secondary structure in the > predicted > > structure. These machine-learning methods have clearly learned how to > > generalise from homology to known structures, evolutionary covariance, > and > > probably other aspects of protein structure. > > > > Best wishes, > > > > Randy Read > > > > > On 7 Oct 2024, at 08:24, Bhavita Kattula wrote: > > > > > > Hello everyone, > > > I'm trying to access the Homology-derived Secondary Structure of > Proteins > > (HSSP) database for protein structure-sequence alignments, but I am > > encountering issues. The database does not seem to be functioning as > expected, > > and I'm unable to retrieve the necessary data. > > > Could anyone confirm whether this is a temporary issue or if there are > > ongoing maintenance or updates taking place? Additionally, I would > greatly > > appreciate recommendations for alternative databases that provide similar > > functionalities, particularly for accessing protein structure-sequence > alignments > > and related data. > > > > > > Best wishes, > > > -- > > > Bhavita Kattula > > > Graduate student > > > C/o Dr. Anthony Addlagatta > > > Chief Scientist > > > Structural Biology Lab > > > CSIR-Indian Institute of Chemical Technology, > > > Tarnaka, Hyderabad-57. > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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&A=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/ > -- *Bhavita Kattula* *Graduate student* C/o Dr. Anthony Addlagatta Chief Scientist Structural Biology Lab CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad-57. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Bursaries available for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models
Standard Student Bursaries As in year’s past, CCP4 has made funding available for students, to help with the costs of attending Study Weekend, in the form of a bursary. All students are eligible for a standard bursary which covers the registration fee plus one night’s accommodation in halls. Bursaries will be given out to all students registering during the early bird registration period – 26th September to 11th November 2024. Students obtaining a standard bursary will only need to pay for any additional night’s accommodation. Students wishing to stay in the hotel rather than Rutland halls, will have 1 nights accommodation subsidised at the halls rate and will therefore pay a reduced rate for this night. Additional nights accommodation will need to be paid at the standard cost. Please also note that should you obtain a bursary and cancel after the latest cancellation date of 6 December 2024 you WILL be liable to pay. This is because we have had a number of students obtaining bursaries and then cancelling last minute. Places can be transferred to other people at no charge. Travel bursaries Limited funds will also be made available to help pay travel costs for students and young post-docs from non-UK laboratories. Please send a separate letter, signed by your supervisor and stating the expected cost of travel in pounds sterling, to justify applications for travel support. Supervisors are asked to nominate only one candidate from their Laboratory. Delegates are expected to travel by the most economic means possible. Candidates from less favoured regions will be given preference. Applications should be e-mailed to ccp...@stfc.ac.uk<mailto:ccp...@stfc.ac.uk> : Lauren Giles CCP4 Study Weekend Travel Bursary Applications for travel bursaries need to be in by Thursday 31st October 2024. Regards Karen McIntyre CCP4 Project Administrator CCP4 ED&I Champion UKRI-STFC Rutherford Appleton Laboratory Harwell Campus Didcot OX11 0QX Phone: +44 (0) 1235 44 5790 [cid:image001.png@01DB18A2.7581EFE0] STFC is part of UK Research and Innovation, a public body funded by the UK government. For more information visit www.ukri.org<http://www.ukri.org/> [A grey circle with red text Description automatically generated] Affiliatated Member of the Institute for Continuous Improvement in the Public Sector ***Please note I only work part-time – hours are Monday to Thursday 08:30 to 13:30 and Friday 10:30 to 15:30** To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] re- HSSP Database
I agree with Randy about the secondary structure things. The main use of HSSP in my hand is having ready-made multiple sequence alignments that allow you to quickly check the distribution of residues at a specific position: this glycine is 100% conserved in 1337 sequences, I guess it is rather important. Anyway, HSSP is indeed offline but I have the last version of the databank for anyone who wants it (mail me off-list). A problem with HSSP was that it was rather maintenance-heavy for the number of users. If it becomes obvious that there is strong demand for it, may reappear. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Randy > John Read > Sent: Monday, October 7, 2024 10:26 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] re- HSSP Database > > Maybe someone else will have a different opinion, but I suspect that the very > best method to predict secondary structure at the moment is to predict the > tertiary structure using AlphaFold or another machine-learning structure > prediction method, and then observe the secondary structure in the predicted > structure. These machine-learning methods have clearly learned how to > generalise from homology to known structures, evolutionary covariance, and > probably other aspects of protein structure. > > Best wishes, > > Randy Read > > > On 7 Oct 2024, at 08:24, Bhavita Kattula wrote: > > > > Hello everyone, > > I'm trying to access the Homology-derived Secondary Structure of Proteins > (HSSP) database for protein structure-sequence alignments, but I am > encountering issues. The database does not seem to be functioning as expected, > and I'm unable to retrieve the necessary data. > > Could anyone confirm whether this is a temporary issue or if there are > ongoing maintenance or updates taking place? Additionally, I would greatly > appreciate recommendations for alternative databases that provide similar > functionalities, particularly for accessing protein structure-sequence > alignments > and related data. > > > > Best wishes, > > -- > > Bhavita Kattula > > Graduate student > > C/o Dr. Anthony Addlagatta > > Chief Scientist > > Structural Biology Lab > > CSIR-Indian Institute of Chemical Technology, > > Tarnaka, Hyderabad-57. > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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&A=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] re- HSSP Database
Maybe someone else will have a different opinion, but I suspect that the very best method to predict secondary structure at the moment is to predict the tertiary structure using AlphaFold or another machine-learning structure prediction method, and then observe the secondary structure in the predicted structure. These machine-learning methods have clearly learned how to generalise from homology to known structures, evolutionary covariance, and probably other aspects of protein structure. Best wishes, Randy Read > On 7 Oct 2024, at 08:24, Bhavita Kattula wrote: > > Hello everyone, > I'm trying to access the Homology-derived Secondary Structure of Proteins > (HSSP) database for protein structure-sequence alignments, but I am > encountering issues. The database does not seem to be functioning as > expected, and I'm unable to retrieve the necessary data. > Could anyone confirm whether this is a temporary issue or if there are > ongoing maintenance or updates taking place? Additionally, I would greatly > appreciate recommendations for alternative databases that provide similar > functionalities, particularly for accessing protein structure-sequence > alignments and related data. > > Best wishes, > -- > Bhavita Kattula > Graduate student > C/o Dr. Anthony Addlagatta > Chief Scientist > Structural Biology Lab > CSIR-Indian Institute of Chemical Technology, > Tarnaka, Hyderabad-57. > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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] re- HSSP Database
Hello everyone, I'm trying to access the Homology-derived Secondary Structure of Proteins (HSSP) database for protein structure-sequence alignments, but I am encountering issues. The database does not seem to be functioning as expected, and I'm unable to retrieve the necessary data. Could anyone confirm whether this is a temporary issue or if there are ongoing maintenance or updates taking place? Additionally, I would greatly appreciate recommendations for alternative databases that provide similar functionalities, particularly for accessing protein structure-sequence alignments and related data. Best wishes, -- *Bhavita Kattula* *Graduate student* C/o Dr. Anthony Addlagatta Chief Scientist Structural Biology Lab CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad-57. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] AlphaFold3
Hi Jon, I use AF3 quite often to look at domain boundaries by sequence but not necessarily by their spatial arrangement. This is because protein-protein interactions at least in all cases I’ve tried were not predicted correctly. I have number of Fab-Antigen complexes solved using x-ray crystallography but have not deposited in the PDB for various reasons. Using those molecules as an input to predict interaction interfaces were all plain wrong. Up until last week I did not have even one case where I’d call AF3 wrong for predicting a fold of a protein (a globular one)because all predictions were not only correct but also agree with topological features published within UniProt. Please, take a look at FATP2 (https://www.uniprot.org/uniprotkb/O14975/entry#structure) and you probably will agree that it is wrongly predicted structure. It is predicted with high confidence (dark blue) which is even more surprising. So my message in short would be: trust to some degree but don’t get surprised if it is wrong for cases without analogues in the PDB. Vaheh From: CCP4 bulletin board On Behalf Of Jon Cooper Sent: Saturday, October 5, 2024 9:48 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AlphaFold3 Just wondering if anyone has any comments on, or concrete experiences with, alphafold3. I might try to cobble something together for Crystallography News (he says, having missed the main Nature paper, ahem). My googling has only given me hype and gripe so far ;-0 ;-0 Best wishes, Jon Cooper. jon.b.coo...@protonmail.com<mailto:jon.b.coo...@protonmail.com> Sent from Proton Mail Android To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/<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&A=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 of data reprocessing with XDS
gt;total 447346 3255032613 99.8% 12.7%14.4% >> 4473339.3013.2%99.9*-50.621 14848 >> >> >> >> >> >>Reprocessing the dataset with the new version I ended up with the >> following statistics though I kept the parameters essentially the same： >> >> >> >> RESOLUTIONNUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR >> COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano >> >> LIMITOBSERVED UNIQUE POSSIBLEOF DATA observed expected >> Corr >> >> >> >>5.80 169321220 1240 98.4% 7.2% 8.5% >> 16930 28.65 7.5%99.9* -390.502459 >> >>4.12 298882207 2209 99.9% 9.9% 9.3% >> 29888 25.4610.3%99.7*00.707945 >> >>3.37 348172796 2836 98.6% 14.9%11.7% >> 34817 17.6315.5%99.7*15* 0.9471244 >> >>2.92 425523268 3347 97.6% 24.5%23.5% >> 42552 10.0425.5%99.6* -120.5831481 >> >>2.61 541203811 3816 99.9% 56.8%69.2% >> 541206.1458.9%98.2* -140.5431750 >> >>2.38 609224173 4221 98.9%358.4%464.1% >> 609222.93371.4%93.7* -180.4211897 >> >>2.21 520763861 4566 84.6%-99.9%-99.9% >> 520760.00-99.9%66.9* -370.3061566 >> >>2.06 408233045 4911 62.0%-99.9% -99.9% >> 408230.00-99.9%33.3* -390.1961047 >> >>1.95 347642526 5227 48.3%-99.9%-99.9% >> 347640.00-99.9%14.7* -480.072585 >> >>total 366894 2690732373 83.1% 28.2%29.1% >> 3668927.57 29.2%99.8* -160.493 10974 >> >> >> >>I tried to tweak several parameters, especially for background >> subtraction, but it didn't really help. It would be great if you could give >> me some suggestions. Thank you in advance! >> >> >> >>Best, >> >>Yimin >> >> >> >> >> >>-- >> >>Yimin Hu >> >>(Pronouns: she/her) >> >>PhD Student >> >>Department of Protein Evolution >> >>Max Planck Institute for Biology, Tübingen >> >> >> >> >> >> >> >>To unsubscribe from the CCP4BB list, click the following link: >> >>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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&A=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&A=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&A=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&A=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] 3D classification of a small membrane protein.
Dear all I have a question about the 3D classification of a membrane protein using Relion 3.1, where I aim to remove some junk particles. The protein is relatively small (180 kDa), and its structure has already been resolved by cryoEM. It has minimal features outside the micelle ring and is primarily composed of an alpha-helical bundle. Instead of generating a 3D initial model, I’m considering using the solved structure to create a reference map for the subsequent 3D classification and refinement steps. Therefore would it be more appropriate to use its PDB model (molmap) or the deposited EM map to create the reference map? The EM map includes the micelle ring, which the reference map from the model obviously will not have. Could this difference affect the classification or refinement steps, particularly when the protein is small and the map is low-pass filtered to 60 Å (default)? Also can I modify the resolution limit of the low-pass filter to improve classification? Additionally, the molecule has C2 symmetry. Would it be better to use a C2 symmetric map for classification, or should I opt for a C1 asymmetric map? In 2D classification, I set 'Ignore CTF until first peak' to 'Yes' and limited the E-step resolution to 10 Å. Should I apply the same settings for 3D classification, especially regarding the 'Ignore CTF until first peak' option, or would it be better to set this to 'No'? Lastly, when I set 'Ignore CTF until first peak' to 'Yes' during 2D classification, it resulted in better class distribution compared to 'No,' where all particles plus junk tended to cluster in one class. What could explain this behavior? Is it something specific to small membrane proteins with fewer features? Your advice would be greatly appreciated. Best Firdous #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 of data reprocessing with XDS
9.3% > 29888 25.4610.3%99.7*00.707945 > >>3.37 348172796 2836 98.6% 14.9%11.7% > 34817 17.6315.5%99.7*15* 0.9471244 > >>2.92 425523268 3347 97.6% 24.5%23.5% > 42552 10.0425.5%99.6* -120.5831481 > >>2.61 541203811 3816 99.9% 56.8%69.2% > 541206.1458.9%98.2* -140.5431750 > >>2.38 609224173 4221 98.9%358.4%464.1% > 609222.93371.4%93.7* -180.4211897 > >>2.21 520763861 4566 84.6%-99.9%-99.9% > 520760.00-99.9%66.9* -370.3061566 > >>2.06 408233045 4911 62.0%-99.9%-99.9% > 408230.00-99.9%33.3* -390.1961047 > >>1.95 347642526 5227 48.3%-99.9%-99.9% > 347640.00-99.9%14.7* -480.072585 > >>total 366894 2690732373 83.1% 28.2%29.1% > 3668927.5729.2%99.8* -160.493 10974 > >> > >>I tried to tweak several parameters, especially for background > subtraction, but it didn't really help. It would be great if you could give > me some suggestions. Thank you in advance! > >> > >>Best, > >>Yimin > >> > >> > >>-- > >>Yimin Hu > >>(Pronouns: she/her) > >>PhD Student > >>Department of Protein Evolution > >>Max Planck Institute for Biology, Tübingen > >> > >> > >> > >>To unsubscribe from the CCP4BB list, click the following link: > >>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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&A=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&A=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&A=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] AlphaFold3
Hello, I would like to take this opportunity to announce the release of our new web-tool, FoldScript (https://foldscript.ibcp.fr/), which complements our web-tool ESPript. FoldScript allows to analyze and to filter with experimental results (ie residues known to be involved in intermolecular interfaces) the list of AI-models generated by Alphafold3 (currently 5 models versus 25 with Alphafold-Multimers). We created this web-service because we observed that the top-ranked model supplied by AF3 is not necessarily the most “relevant” one, and we wanted to quickly compare models supplied by AF3, Alphafold-multimer, EMSfold, Rosettafold... As has been related by others, we observe that AI-predicted hetero-oligomeric structures have to be taken with caution. Best patrice Le 2024-10-05 15:48, Jon Cooper a écrit : L'adresse mail de l'expéditeur est extérieure : owner-ccp...@jiscmail.ac.uk En cas de doute : ne répondez pas, ne cliquez pas et signalez le message au Support Informatique Just wondering if anyone has any comments on, or concrete experiences with, alphafold3. I might try to cobble something together for Crystallography News (he says, having missed the main Nature paper, ahem). My googling has only given me hype and gripe so far ;-0 ;-0 Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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 of data reprocessing with XDS
* -18 0.421 1897 >> 2.21 52076 3861 4566 84.6% -99.9% -99.9% 52076 >> 0.00 -99.9% 66.9* -37 0.306 1566 >> 2.06 40823 3045 4911 62.0% -99.9% -99.9% 40823 >> 0.00 -99.9% 33.3* -39 0.196 1047 >> 1.95 34764 2526 5227 48.3% -99.9% -99.9% 34764 >> 0.00 -99.9% 14.7* -48 0.072 585 >> total 366894 26907 32373 83.1% 28.2% 29.1% 366892 >> 7.57 29.2% 99.8* -16 0.493 10974 >> >>I tried to tweak several parameters, especially for background subtraction, >>but it didn't really help. It would be great if you could give me some >>suggestions. Thank you in advance! >> >>Best, >>Yimin >> >> >>-- >>Yimin Hu >>(Pronouns: she/her) >>PhD Student >>Department of Protein Evolution >>Max Planck Institute for Biology, Tübingen >> >>######## >> >>To unsubscribe from the CCP4BB list, click the following link: >>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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&A=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&A=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] AlphaFold3
Dear Jon I did the same for a dimer of a structure we just solved but only now writing the paper. AF3 predicted the monomer to an RMS of about 0.3 and dimer to about 0.5 Angstroms Structure not yet in the PDB, but soon Joel Sent from my iPhone On Oct 5, 2024, at 17:35, Jurgen Bosch <dacafb9366f7-dmarc-requ...@jiscmail.ac.uk> wrote: Caution: External Sender. Do not click on links or open attachments unless you recognize the sender. I used it for PPI prediction of a mAb and our target protein and it was surprisingly accurate compared to our crystal structure. Binding of the mAb was <0.5 rmsd I was stunned. Jürgen P.S. paper should be accepted soon, but you’ll find a current version on BioRxiv if you are interested. AF3 is not part of the paper though. But that’s what I used for benchmarking since the coordinates have not been released yet __ Jürgen Bosch, PhD, MBA Center for Global Health & Diseases Case Western Reserve University https://www.linkedin.com/in/jubosch/ CEO & Co-Founder at InterRayBio, LLC On Oct 5, 2024, at 08:48, Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk>> wrote: Just wondering if anyone has any comments on, or concrete experiences with, alphafold3. I might try to cobble something together for Crystallography News (he says, having missed the main Nature paper, ahem). My googling has only given me hype and gripe so far ;-0 ;-0 Best wishes, Jon Cooper. jon.b.coo...@protonmail.com<mailto:jon.b.coo...@protonmail.com> Sent from Proton Mail Android ######## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=1 ######## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] AlphaFold3
I used it for PPI prediction of a mAb and our target protein and it was surprisingly accurate compared to our crystal structure. Binding of the mAb was <0.5 rmsd I was stunned. Jürgen P.S. paper should be accepted soon, but you’ll find a current version on BioRxiv if you are interested. AF3 is not part of the paper though. But that’s what I used for benchmarking since the coordinates have not been released yet __ Jürgen Bosch, PhD, MBA Center for Global Health & Diseases Case Western Reserve University https://www.linkedin.com/in/jubosch/ CEO & Co-Founder at InterRayBio, LLC On Oct 5, 2024, at 08:48, Jon Cooper < 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: Just wondering if anyone has any comments on, or concrete experiences with, alphafold3. I might try to cobble something together for Crystallography News (he says, having missed the main Nature paper, ahem). My googling has only given me hype and gripe so far ;-0 ;-0 Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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] AlphaFold3
Just wondering if anyone has any comments on, or concrete experiences with, alphafold3. I might try to cobble something together for Crystallography News (he says, having missed the main Nature paper, ahem). My googling has only given me hype and gripe so far ;-0 ;-0 Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 of data reprocessing with XDS
Dear Kay, do have any more information or would you mind explaining a bit more what changes in the XDS code led to these significantly different statistics in the different XDS versions? Thanks,John On Wednesday, October 2, 2024 at 02:35:25 PM CDT, Kay Diederichs wrote: Dear Yimin, similar shortcomings were observed with other datasets with XDS VERSION Jun 30, 2024 that was posted on July 23 at https://xds.mr.mpg.de/html_doc/downloading.html . I am sorry for that! The testing of that version had not uncovered this problem. Corrected binaries were posted today at that site, and my (admittedly limited) testing shows them to be as good as, or better than the old (2023) version. Please install and use these binaries. That previous version was made available for comparison purposes as XDS_old.tar.gz, with expiration date 31 Mar 2025, for Linux; download link is at https://xds.mr.mpg.de/ . Hope this helps, Kay On Wed, 2 Oct 2024 16:30:55 +0200, Yimin Hu wrote: >Dear colleagues， > >I ran into a problem when I reprocessed a dataset after switching to XDS >VERSION Jun 30, 2024. > >Processing the dataset with the old XDS I ended up with these statistics: > >RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR >COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano > LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected > Corr > 5.78 16747 1239 1253 98.9% 7.4% 8.5% 16745 >29.13 7.6% 99.9* 2 0.740 465 > 4.10 29921 2220 2226 99.7% 8.9% 8.7% 29921 >28.12 9.2% 99.8* 9 0.897 951 > 3.35 40065 2848 2849 100.0% 10.1% 9.3% >40065 23.84 10.4% 99.8* 3 0.841 1264 > 2.91 44213 3390 3390 100.0% 13.5% 13.0% 44213 > 14.61 14.1% 99.8* -10 0.717 1537 > 2.60 54235 3827 3827 100.0% 24.6% 28.4% 54235 > 9.08 25.5% 99.5* -15 0.611 1758 > 2.38 62062 4270 4270 100.0% 42.5% 57.6% 62062 > 5.40 44.1% 98.8* -10 0.565 1973 > 2.20 62076 4589 4589 100.0% 76.3% 111.3% >62076 3.06 79.2% 97.0* -7 0.549 2138 > 2.06 67437 4941 4941 100.0% 116.7% 176.7% 67437 > 2.03 121.3% 89.2* -8 0.541 2311 > 1.94 70590 5226 5268 99.2% 232.1% 363.5% 70579 > 0.93 241.2% 64.3* -4 0.511 2451 > total 447346 32550 32613 99.8% 12.7% 14.4% 447333 > 9.30 13.2% 99.9* -5 0.621 14848 > > >Reprocessing the dataset with the new version I ended up with the following >statistics though I kept the parameters essentially the same： > > RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR > COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano > LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected > Corr > > 5.80 16932 1220 1240 98.4% 7.2% 8.5% 16930 >28.65 7.5% 99.9* -39 0.502 459 > 4.12 29888 2207 2209 99.9% 9.9% 9.3% 29888 >25.46 10.3% 99.7* 0 0.707 945 > 3.37 34817 2796 2836 98.6% 14.9% 11.7% 34817 >17.63 15.5% 99.7* 15* 0.947 1244 > 2.92 42552 3268 3347 97.6% 24.5% 23.5% 42552 >10.04 25.5% 99.6* -12 0.583 1481 > 2.61 54120 3811 3816 99.9% 56.8% 69.2% 54120 > 6.14 58.9% 98.2* -14 0.543 1750 > 2.38 60922 4173 4221 98.9% 358.4% 464.1% 60922 > 2.93 371.4% 93.7* -18 0.421 1897 > 2.21 52076 3861 4566 84.6% -99.9% -99.9% 52076 > 0.00 -99.9% 66.9* -37 0.306 1566 > 2.06 40823 3045 4911 62.0% -99.9% -99.9% 40823 > 0.00 -99.9% 33.3* -39 0.196 1047 > 1.95 34764 2526 5227 48.3% -99.9% -99.9% 34764 > 0.00 -99.9% 14.7* -48 0.072 585 > total 366894 26907 32373 83.1% 28.2% 29.1% 366892 > 7.57 29.2% 99.8* -16 0.493 10974 > >I tried to tweak several parameters, especially for background subtraction, >but it didn't really help. It would be great if you could give me some >suggestions. Thank you in advance! > >Best, >Yimin > > >-- >Yimin Hu >(Pronouns: she/her) >PhD Student >Department of Protein Evolution >Max Planck Institute for Biology, Tübingen >
Re: [ccp4bb] Co-Crystallization with drug molecule
ed, Oct 2, 2024 at 2:51 PM amit gaur wrote: > >>> > >>>Hi everyone, > >>> > >>>I am trying to crystallize a protein with a drug molecule. The > >>>protein concentration is 15.5 mg/ml, the drug stock concentration > >>>is 10 mM, and the drug is dissolved in DMSO. I am adding the drug > >>>to a final concentration of 1 mM in 100 ul of protein, and the > >>>DMSO volume is 10 ul for Co-crystallization. I want to know how > >>>much DMSO is permissible during co-crystallization with the drug > >>>and if DMSO can poison crystal formation. I have not been > >>>successful in getting crystals with inhibitors till now, but I > >>>obtained crystals of protein without DMSO, and those diffracted to > >>>2.5A. > >>> > >>>Thanks, > >>> > >>>*Dr. Amit Gaur,* > >>>*Research Scientist* > >>>*Center for Biotechnology and **Interdisciplinary Studies,* > >>>*Rensselaer Polytechnic Institute,* > >>>*1623 15th Street, Troy, NY, 12180* > >>> > >>>* > >>>* > >>> > >>> > >>> -------- > >>> > >>>To unsubscribe from the CCP4BB list, click the following link: > >>>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > >>><https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > >>> > >>> > >>> > >>> > >>>To unsubscribe from the CCP4BB list, click the following link: > >>>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > >>><https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > >>> > >> > >> > >>To unsubscribe from the CCP4BB list, click the following link: > >>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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] Co-Crystallization with drug molecule
:)
Gerard,
"soaking"!
Thanks for the reference!
cheers
guenter
Dear Guenter,
The first description of the idea behind this technique that I am aware
of is that published almost 10 years ago by a French group under the name of
"'dry' co-crystallisation" in the following paper:
http://dx.doi.org/10.1107/S1399004715010342
Best wishes,
Gerard
--
On Fri, Oct 04, 2024 at 05:40:12PM +0200, Guenter Fritz wrote:
Hi Amit,
like Artem wrote below, even despite poor solubility, soaks with
dried compounds work well (also in our hands).
We adapted it from the work of T. Barthel, J. Wollenhaupt and
Manfred Weiss. Also colleagues from industry report good results.
We add compound dissolved in DMSO to the crystallization well, let
DMSO evaporate overnight (37° incubator), then put mother liquor on
top of the dried compound and then the crystals. If all compound
would dissolve again, final concentration would be 10-50 mM. Soak
time from 1-2 h to overnight.
This worked for poorly soluble compounds where we did not succeed
with soaking in the presence of DMSO.
Hope that helps!
Best,
Guenter
Dear Amit
As David already pointed out, all proteins are different and it's
hard to say in advance what amount of DMSO may work (or not).
An additional concern is that DMSO can also interfere with ligand
binding (cases from my personal past history), especially if these
inhibitors/ligands are on the weaker side.
Solutions:
Despite its very high boiling point (189C) DMSO can in fact be
evaporated from a small sample of your inhibitor, resulting in
more or less solid inhibitor sample that can be re-dissolved in
the same DMSO (but higher concentration), some other solvent, or
perhaps directly in the protein solution. The latter is sometimes
the only way to do this - I used to set up drops of DMSO
solutions, then evaporate the DMSO in high vacuum (heating helps)
with a cryofinger, then set up protein drops on top. This of
course requires access to a lyophilizer or something similar.
If you have a vial of your solution you can freeze-dry DMSO with
water, by first diluting the sample then freeze-drying it. Also
water can sometimes crash the substance out (if not water, then
perhaps Ether or another solvent where your inhibitor does not
dissolve) which makes it easier to redissolve (but there will be a
loss of course).
Find a friendly chemist nearby and ask then to put your sample in
a speedvac on 'high BP' setting
Notably, if you're "blessed" with an inhibitor that has the
general solubility of a Sony Walkman, once you get rid of the
DMSO, you may find out that the damned thing does not want to
dissolve in anything else, including your protein solution. This
happens a lot during early discovery phases when compounds are not
very active (micromolar) and also poorly soluble (also
micromolar). This is by far the most frequent cause for failing to
co-crystallize (or soak) a ligand of interest. Very frustrating.
Some success can be achieved using high DMSO or DMF (DMA also can
be good) in your crystallization, or by phase transfer catalysts
like Cyclodextrin(s) or appropriately formulated micelles. All of
which can also mess up crystallization, needless to say.
Best of luck in your endeavors!
Artem
- Cosmic Cats approve of this message
On Wed, Oct 2, 2024 at 2:51 PM amit gaur wrote:
Hi everyone,
I am trying to crystallize a protein with a drug molecule. The
protein concentration is 15.5 mg/ml, the drug stock concentration
is 10 mM, and the drug is dissolved in DMSO. I am adding the drug
to a final concentration of 1 mM in 100 ul of protein, and the
DMSO volume is 10 ul for Co-crystallization. I want to know how
much DMSO is permissible during co-crystallization with the drug
and if DMSO can poison crystal formation. I have not been
successful in getting crystals with inhibitors till now, but I
obtained crystals of protein without DMSO, and those diffracted to
2.5A.
Thanks,
*Dr. Amit Gaur,*
*Research Scientist*
*Center for Biotechnology and **Interdisciplinary Studies,*
*Rensselaer Polytechnic Institute,*
*1623 15th Street, Troy, NY, 12180*
*
*
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Re: [ccp4bb] Problem of data reprocessing with XDS
Dear Yimin and CCP4BB readers, The autoPROC Wiki page mentioned in Clemens's message (below) is being regularly updated with the results emerging from extending that comparison to the improved BUILT=20241002 of the 20240630 version of XDS announced in Kay's message. With best wishes, Gerard. -- On Wed, Oct 02, 2024 at 05:17:56PM +0100, Clemens Vonrhein wrote: > Dear Yimin, > > without wanting to preempt additional feedback that the XDS developers > might be able to provide (concerning the changes within that July 2024 > XDS version that seem to trigger the differences you see), may we > suggest that you have a look at > > > https://www.globalphasing.com/autoproc/wiki/index.cgi?ComparisonProcessing202409 > > Here we have collected a large amount of information and detailed > comparisons regarding the new 2024 XDS version (that we also shared > and discussed in detail with the XDS developers over the last weeks) > ... and just in the last few hours we discovered that (1) a binary for > the previous 2023 version with an extended lifetime is now available > at [1], and that (2) a new/modified 2024 version has been published > with some hints about changes. > > We are testing this very latest version (20241002) as we speak and we > will update the comparison page mentioned above accordingly. So > ... stay tuned ;-) > > Cheers > > Clemens > > [1] https://xds.mr.mpg.de/ > > On Wed, Oct 02, 2024 at 04:30:55PM +0200, Yimin Hu wrote: > > Dear colleagues， > > > > I ran into a problem when I reprocessed a dataset after switching to XDS > > VERSION Jun 30, 2024. > > > > Processing the dataset with the old XDS I ended up with these statistics: > > > > RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR > > COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano > >LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected > > Corr > > 5.78 167471239 1253 98.9% 7.4% 8.5% > > 16745 29.13 7.6%99.9* 20.740 465 > > 4.10 299212220 2226 99.7% 8.9% 8.7% > > 29921 28.12 9.2%99.8* 90.897 951 > > 3.35 400652848 2849 100.0% 10.1% 9.3% > > 40065 23.84 10.4%99.8* 30.8411264 > > 2.91 442133390 3390 100.0% 13.5% 13.0% > > 44213 14.61 14.1%99.8* -100.7171537 > > 2.60 542353827 3827 100.0% 24.6% 28.4% > > 542359.08 25.5%99.5* -150.6111758 > > 2.38 620624270 4270 100.0% 42.5% 57.6% > > 620625.40 44.1%98.8* -100.5651973 > > 2.20 620764589 4589 100.0% 76.3%111.3% > > 620763.06 79.2%97.0*-70.5492138 > > 2.06 674374941 4941 100.0% 116.7%176.7% > > 674372.03121.3%89.2*-80.5412311 > > 1.94 705905226 5268 99.2% 232.1%363.5% > > 705790.93241.2%64.3*-40.5112451 > > total 447346 32550 32613 99.8% 12.7% 14.4% > > 4473339.30 13.2%99.9*-50.621 14848 > > > > > > Reprocessing the dataset with the new version I ended up with the following > > statistics though I kept the parameters essentially the same： > > > > RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR > > COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano > >LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected > > Corr > > > > 5.80 169321220 1240 98.4% 7.2% 8.5% > > 16930 28.65 7.5%99.9* -390.502 459 > > 4.12 298882207 2209 99.9% 9.9% 9.3% > > 29888 25.46 10.3%99.7* 00.707 945 > > 3.37 348172796 2836 98.6% 14.9% 11.7% > > 34817 17.63 15.5%99.7*15* 0.9471244 > > 2.92 425523268 3347 97.6% 24.5% 23.5% > > 42552 10.04 25.5%99.6* -120.5831481 > > 2.61 541203811 3816 99.9% 56.8% 69.2% > > 541206.14 58.9%98.2* -140.5431750 > > 2.38 609224173 4221 98.9% 358.4%
Re: [ccp4bb] Co-Crystallization with drug molecule
Dear Guenter, The first description of the idea behind this technique that I am aware of is that published almost 10 years ago by a French group under the name of "'dry' co-crystallisation" in the following paper: http://dx.doi.org/10.1107/S1399004715010342 Best wishes, Gerard -- On Fri, Oct 04, 2024 at 05:40:12PM +0200, Guenter Fritz wrote: > Hi Amit, > like Artem wrote below, even despite poor solubility, soaks with > dried compounds work well (also in our hands). > We adapted it from the work of T. Barthel, J. Wollenhaupt and > Manfred Weiss. Also colleagues from industry report good results. > We add compound dissolved in DMSO to the crystallization well, let > DMSO evaporate overnight (37° incubator), then put mother liquor on > top of the dried compound and then the crystals. If all compound > would dissolve again, final concentration would be 10-50 mM. Soak > time from 1-2 h to overnight. > This worked for poorly soluble compounds where we did not succeed > with soaking in the presence of DMSO. > Hope that helps! > Best, > Guenter > > >Dear Amit > > > >As David already pointed out, all proteins are different and it's > >hard to say in advance what amount of DMSO may work (or not). > > > >An additional concern is that DMSO can also interfere with ligand > >binding (cases from my personal past history), especially if these > >inhibitors/ligands are on the weaker side. > > > >Solutions: > > > >Despite its very high boiling point (189C) DMSO can in fact be > >evaporated from a small sample of your inhibitor, resulting in > >more or less solid inhibitor sample that can be re-dissolved in > >the same DMSO (but higher concentration), some other solvent, or > >perhaps directly in the protein solution. The latter is sometimes > >the only way to do this - I used to set up drops of DMSO > >solutions, then evaporate the DMSO in high vacuum (heating helps) > >with a cryofinger, then set up protein drops on top. This of > >course requires access to a lyophilizer or something similar. > > > >If you have a vial of your solution you can freeze-dry DMSO with > >water, by first diluting the sample then freeze-drying it. Also > >water can sometimes crash the substance out (if not water, then > >perhaps Ether or another solvent where your inhibitor does not > >dissolve) which makes it easier to redissolve (but there will be a > >loss of course). > > > >Find a friendly chemist nearby and ask then to put your sample in > >a speedvac on 'high BP' setting > > > >Notably, if you're "blessed" with an inhibitor that has the > >general solubility of a Sony Walkman, once you get rid of the > >DMSO, you may find out that the damned thing does not want to > >dissolve in anything else, including your protein solution. This > >happens a lot during early discovery phases when compounds are not > >very active (micromolar) and also poorly soluble (also > >micromolar). This is by far the most frequent cause for failing to > >co-crystallize (or soak) a ligand of interest. Very frustrating. > >Some success can be achieved using high DMSO or DMF (DMA also can > >be good) in your crystallization, or by phase transfer catalysts > >like Cyclodextrin(s) or appropriately formulated micelles. All of > >which can also mess up crystallization, needless to say. > > > >Best of luck in your endeavors! > > > >Artem > > > >- Cosmic Cats approve of this message > > > > > >On Wed, Oct 2, 2024 at 2:51 PM amit gaur wrote: > > > >Hi everyone, > > > >I am trying to crystallize a protein with a drug molecule. The > >protein concentration is 15.5 mg/ml, the drug stock concentration > >is 10 mM, and the drug is dissolved in DMSO. I am adding the drug > >to a final concentration of 1 mM in 100 ul of protein, and the > >DMSO volume is 10 ul for Co-crystallization. I want to know how > >much DMSO is permissible during co-crystallization with the drug > >and if DMSO can poison crystal formation. I have not been > >successful in getting crystals with inhibitors till now, but I > >obtained crystals of protein without DMSO, and those diffracted to > >2.5A. > > > >Thanks, > > > >*Dr. Amit Gaur,* > >*Research Scientist* > >*Center for Biotechnology and **Interdisciplinary Studies,* > >*Rensselaer Polytechnic Institute,* > >*1623 15th Street, Troy, NY, 12180* > > > >* > >* > > > >-----
Re: [ccp4bb] Co-Crystallization with drug molecule
Hi Amit, like Artem wrote below, even despite poor solubility, soaks with dried compounds work well (also in our hands). We adapted it from the work of T. Barthel, J. Wollenhaupt and Manfred Weiss. Also colleagues from industry report good results. We add compound dissolved in DMSO to the crystallization well, let DMSO evaporate overnight (37° incubator), then put mother liquor on top of the dried compound and then the crystals. If all compound would dissolve again, final concentration would be 10-50 mM. Soak time from 1-2 h to overnight. This worked for poorly soluble compounds where we did not succeed with soaking in the presence of DMSO. Hope that helps! Best, Guenter Dear Amit As David already pointed out, all proteins are different and it's hard to say in advance what amount of DMSO may work (or not). An additional concern is that DMSO can also interfere with ligand binding (cases from my personal past history), especially if these inhibitors/ligands are on the weaker side. Solutions: Despite its very high boiling point (189C) DMSO can in fact be evaporated from a small sample of your inhibitor, resulting in more or less solid inhibitor sample that can be re-dissolved in the same DMSO (but higher concentration), some other solvent, or perhaps directly in the protein solution. The latter is sometimes the only way to do this - I used to set up drops of DMSO solutions, then evaporate the DMSO in high vacuum (heating helps) with a cryofinger, then set up protein drops on top. This of course requires access to a lyophilizer or something similar. If you have a vial of your solution you can freeze-dry DMSO with water, by first diluting the sample then freeze-drying it. Also water can sometimes crash the substance out (if not water, then perhaps Ether or another solvent where your inhibitor does not dissolve) which makes it easier to redissolve (but there will be a loss of course). Find a friendly chemist nearby and ask then to put your sample in a speedvac on 'high BP' setting Notably, if you're "blessed" with an inhibitor that has the general solubility of a Sony Walkman, once you get rid of the DMSO, you may find out that the damned thing does not want to dissolve in anything else, including your protein solution. This happens a lot during early discovery phases when compounds are not very active (micromolar) and also poorly soluble (also micromolar). This is by far the most frequent cause for failing to co-crystallize (or soak) a ligand of interest. Very frustrating. Some success can be achieved using high DMSO or DMF (DMA also can be good) in your crystallization, or by phase transfer catalysts like Cyclodextrin(s) or appropriately formulated micelles. All of which can also mess up crystallization, needless to say. Best of luck in your endeavors! Artem - Cosmic Cats approve of this message On Wed, Oct 2, 2024 at 2:51 PM amit gaur wrote: Hi everyone, I am trying to crystallize a protein with a drug molecule. The protein concentration is 15.5 mg/ml, the drug stock concentration is 10 mM, and the drug is dissolved in DMSO. I am adding the drug to a final concentration of 1 mM in 100 ul of protein, and the DMSO volume is 10 ul for Co-crystallization. I want to know how much DMSO is permissible during co-crystallization with the drug and if DMSO can poison crystal formation. I have not been successful in getting crystals with inhibitors till now, but I obtained crystals of protein without DMSO, and those diffracted to 2.5A. Thanks, *Dr. Amit Gaur,* *Research Scientist* *Center for Biotechnology and **Interdisciplinary Studies,* *Rensselaer Polytechnic Institute,* *1623 15th Street, Troy, NY, 12180* * * To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> ---- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Co-Crystallization with drug molecule
Hi Amit, the questions and suggestions by Eta are important ones and I would like to extend them a little bit. For your apo crystals, instead of adding DMSO in one go, transfer the crystal to a drop with 5% DMSO and wait, if it survives, transfer to 10%, to 20% and finally to 30%. Then, do not only test the apo form in the presence of xx % DMSO (whatever the crystals tolerated), determine the structure model and 1) try to locate DMSO molecules in the ED map (are these in the binding site?) 2) is the expected drug binding site accessible for the drug or do crystal contacts prevent the binding? As for as the drug itself is concerned, a concentration of 19-fold the Kd would theoretically give a 95% occupancy. Good luck, J. __ Dr. math. et dis. nat. Jeroen R. Mesters University of Lübeck https://orcid.org/-0001-8532-6699 Am 03.10.2024 um 15:42 schrieb Eta A Isiorho : Hi Dr. Gaur, A few questions: 1. Do you know the kinetics (binding constants, etc) of the drug and the protein? 2. Do you know how soluble the drug is in DMSO (is 10 mM the most concentrated?) 3. Is the drug soluble in a mixture of DMSO and water (70% DMSO)? 4. Have you tried crystal soaking experiments? DMSO can poison crystal formation and it can also enhance it as an additive as well as a cryoprotectant. You’ll have to determine how much DMSO you can add and still obtain diffractable crystals under 2.5 Å. My suggestions would be: * Take an apo crystal and transfer it to a drop with the amount of DMSO you plan on adding in your mother liquor and observe (does it wiggle, did it dissolve, does it still diffract?) * Grow your apo crystal in the presence of DMSO and shoot it (did the crystal grow, diffract, etc) * Get the most concentrated sample of your compound and do * Co-crystallization experiments * Soaking experiments * If DMSO is donking up your experiment, try a different solvent, or a lower concentration of DMSO in water. Best, eta *** Eta A. Isiorho, Ph.D. Research Assistant Professor Macromolecular Crystallization Facility Manager CUNY Advanced Science Research Center 85 Saint Nicholas Terrace, 3.352B/3.134 New York, NY 10031 eisio...@gc.cuny.edu<mailto:eisio...@gc.cuny.edu> From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of amit gaur mailto:cdriamitg...@gmail.com>> Date: Wednesday, October 2, 2024 at 2:51 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: [ccp4bb] Co-Crystallization with drug molecule Hi everyone, I am trying to crystallize a protein with a drug molecule. The protein concentration is 15.5 mg/ml, the drug stock concentration is 10 mM, and the drug is dissolved in DMSO. I am adding the drug to a final concentration of 1 mM in 100 ul of protein, and the DMSO volume is 10 ul for Co-crystallization. I want to know how much DMSO is permissible during co-crystallization with the drug and if DMSO can poison crystal formation. I have not been successful in getting crystals with inhibitors till now, but I obtained crystals of protein without DMSO, and those diffracted to 2.5A. Thanks, Dr. Amit Gaur, Research Scientist Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 1623 15th Street, Troy, NY, 12180 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Co-Crystallization with drug molecule
Dear Amit, If you will decide to try soakings, you could also try to dehydrate the drop to increase ligand concentration, as well as avoiding to wash the crystals in cryo-protection solutions, as described here (https://journals.iucr.org/j/issues/2022/02/00/ap5042/index.html). Good luck! D On 03/10/2024 14:42, Eta A Isiorho wrote: CAUTION: This email originated from outside of the LMB: *.-owner-ccp...@jiscmail.ac.uk-.* Do not click links or open attachments unless you recognize the sender and know the content is safe. If you think this is a phishing email, please forward it to phish...@mrc-lmb.cam.ac.uk -- Hi Dr. Gaur, A few questions: 1. Do you know the kinetics (binding constants, etc) of the drug and the protein? 2. Do you know how soluble the drug is in DMSO (is 10 mM the most concentrated?) 3. Is the drug soluble in a mixture of DMSO and water (70% DMSO)? 4. Have you tried crystal soaking experiments? DMSO can poison crystal formation and it can also enhance it as an additive as well as a cryoprotectant. You’ll have to determine how much DMSO you can add and still obtain diffractable crystals under 2.5 Å. My suggestions would be: * Take an apo crystal and transfer it to a drop with the amount of DMSO you plan on adding in your mother liquor and observe (does it wiggle, did it dissolve, does it still diffract?) * Grow your apo crystal in the presence of DMSO and shoot it (did the crystal grow, diffract, etc) * Get the most concentrated sample of your compound and do o Co-crystallization experiments o Soaking experiments * If DMSO is donking up your experiment, try a different solvent, or a lower concentration of DMSO in water. Best, eta *** Eta A. Isiorho, Ph.D. Research Assistant Professor Macromolecular Crystallization Facility Manager CUNY Advanced Science Research Center 85 Saint Nicholas Terrace, 3.352B/3.134 New York, NY 10031 eisio...@gc.cuny.edu *From: *CCP4 bulletin board on behalf of amit gaur *Date: *Wednesday, October 2, 2024 at 2:51 PM *To: *CCP4BB@JISCMAIL.AC.UK *Subject: *[ccp4bb] Co-Crystallization with drug molecule Hi everyone, I am trying to crystallize a protein with a drug molecule. The protein concentration is 15.5 mg/ml, the drug stock concentration is 10 mM, and the drug is dissolved in DMSO. I am adding the drug to a final concentration of 1 mM in 100 ul of protein, and the DMSO volume is 10 ul for Co-crystallization. I want to know how much DMSO is permissible during co-crystallization with the drug and if DMSO can poison crystal formation. I have not been successful in getting crystals with inhibitors till now, but I obtained crystals of protein without DMSO, and those diffracted to 2.5A. Thanks, *Dr. Amit Gaur,* *Research Scientist* *Center for Biotechnology and **Interdisciplinary Studies,* *Rensselaer Polytechnic Institute,* *1623 15th Street, Troy, NY, 12180* To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Structure Meets Function 35 - ISIDORe
Dear All Register now for the 35th edition of the Instruct-ERIC Structure Meets Function webinar series, taking place 11:00 CET on 15 October 2024. This month's webinar will feature two speakers who have accessed Instruct-ERIC services through ISIDORe. The ISIDORe project aims<https://isidore-project.eu/> to provide funded access to research infrastructure for infectious disease research. Find out more about the webinar and register here.<https://instruct-eric.org/events/instruct-eric-webinar-series-structure-meets-function-35/> Acha Nelson Lekeayi - University of Buea Title: In-silico design and serological characterization of a novel multiepitope antigen as a potential candidate for human monkeypox sero-surveillance in the South West Region of Cameroon George Vavougios - University of Cyprus Title: COVALENT: A COVID-19 Clinical, Research, and Phenotyping Network [https://instruct-eric.org/upload/NQKU6Y35rLASGAlo3MPG0JCc2D5Kufeh.jpg]<https://instruct-eric.org/events/instruct-eric-webinar-series-structure-meets-function-35/> Kind regards Instruct-ERIC To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Three Year Postdoctoral Fellowship
Dear CCP4 members, My group is expanding at the University of Kent, and we have a three-year postdoc position available in my laboratory. We seek an enthusiastic individual interested in structural biology, especially single-particle cryo-electron microscopy and X-ray crystallography techniques. The post is for three years, and the selected candidate will investigate the structures and functions of multi-protein complexes. The proposed work will combine biochemistry, biophysics, and structural biology techniques, especially single-particle cryo-electron microscopy (cryo-EM) and X-ray crystallography. Although experience in cryo-EM is highly desirable, training will be provided to the selected candidate. The role will also involve working closely with our national and international collaborators. We are equipped with a 120keV electron microscope for single-particle work and have access to eBIC, Diamond and the University of Leicester for high-end cryo-data collection. The School of Biosciences at Kent also has numerous other facilities, such as NMR, mass Spectrometry and single-molecule imaging, to complement our structural work. Applicants about to receive PhD in a relevant subject area are strongly encouraged to apply for this post. This is an excellent opportunity to strengthen skills in assembling multi-protein complexes and structural biology. For more information or informal enquiries, you can contact me at m@kent.ac.uk <mailto:m@kent.ac.uk>. For more details and to apply for this position, please follow the link below: https://www.jobs.ac.uk/job/DJZ951/research-associate Best wishes, Mohinder --- "Whatever you’re meant to do, do it now. The conditions are always impossible.” Doris Lessing --- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Hercules 2025 - deadline Oct 6th!
Dear colleagues, The deadline for the application to HERCULES 2025 is approaching soon! Please find below the announcement for the HERCULES 2025 session. The poster of the school announcement is available here <https://hercules-school.eu/sites/default/files/file/booklets_schedules/Affiche%20HERCULES%202025%20Basse%20Def.pdf> Click here <https://hercules-school.eu/form/application-to-hercules-2025> to apply. *DEADLINE FOR APPLICATION: 6 October 2024* Thanks to spread the word in your laboratory and network. Best regards, Hubert Renevier on behalf of the HERCULES organising committee https://hercules-school.eu/ --- *HERCULES 2025** - European School* /Neutron & Synchrotron Radiation Science since 1991/ *2025 **session**:**/ 9th March - 12th April, 2025/* DEADLINE FOR APPLICATION: 6 October 2024 HERCULES is a European course for PhD students and young researchers using *Neutrons* *and **Synchrotron Radiation* for applications in *Biology*, *Chemistry*, *Physics*, *Hard & Soft Condensed Matter*. The 5-week school includes *lectures* (60%), *hands-on practicals, labs &* *tutorials* (30%), visits, a poster session, group work sessions, ... /*P*//*articipants will spend one week in a partner institution*// in Europe among/: * *ALBA* in Barcelona, Spain * *PETRA III and EU-XFEL* in Hambourg, Germany * *KIT light source *in Karlsruhe, Germany * *SOLEIL *in Saint-Aubin, France This comes in addition to practicals, labs, and tutorials which will take place in Grenoble at *ILL*, *ESRF* and Grenoble Laboratories (*CNRS*, *IBS*). The school includes a common part and two parallel sessions: - /*Physics and chemistry of condensed matter (session A)*/ - /*Biomolecular and soft condensed matter (session B)*/ The school will be held in an hybrid format. Thus, a part-time online participation is also possible, consisting only in following online the lectures held in Grenoble during weeks 1, 2, 3 and 5. *_/Why join Hercules/_/?/* - to *learn new techniques using neutron and synchrotron radiation* - to expand your *theoretical *and* practical *knowledge, /not only for your present research but also for your scientific career/ - to *experiment these techniques* on world-class instruments & beamlines - to *build a network of relations* with fellow young researchers and experienced teachers from all over the World /*Bursaries/reduced costs*/ - A limited number of fellowship grants will be available to reduce registration fees * Full list of lectures: https://hercules-school.eu/general-programme (with links to the dedicated pages) * Download the full 2024 Booklet (lectures, practicals...) <https://hercules-school.eu/sites/default/files/file/booklets_schedules/Hercules2024_Booklet_Web.pdf> *Contact email*: hercu...@hercules-school.eu #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Join RCSB PDB for upcoming events on Advanced Search, BinaryCIF, and extended PDB IDs
Join RCSB PDB for upcoming events on Advanced Search, BinaryCIF, and extended PDB IDs: Virtual Office Hour: RCSB.org and Advanced Search Tuesday October 8, 2024 4:00 pm – 5:00pm Eastern |1:00 pm – 2:00pm Pacific RCSB.org’s Advanced Search feature is a powerful tool for searching the PDB Archive. Want to learn how to better use Advanced Search? Bring questions to our virtual office hour with Rachel Kramer Green, RCSB PDB’s Scientific Support & Customer Service Lead. Registration is required for the Zoom meeting information, but attendance is at no charge. Please sign up at https://go.rutgers.edu/2ueche6f. Webinar: Unlock Rapid Analyses Across the Whole PDB Using BinaryCIF Monday November 4, 2024 2:00 pm – 3:00 pm Eastern | 11:00 am – 12:00 pm Pacific Join our one-hour workshop to future-proof your data analysis with BinaryCIF, a fully interchangeable yet drastically more efficient flavor of the PDBx/mmCIF format. BinaryCIF not only boosts storage efficiency, but also substantially improves parsing speed, making it ideal for large-scale analyses. BinaryCIF is supported by resources such as RCSB PDB, PDBe, and AlphaFold DB. This webinar will benefit bioinformaticians, data scientists, and structural biologists who want to Understand the basics of the PDBx/mmCIF schema Access BinaryCIF files and related APIs on RCSB.org Programmatically consume BinaryCIF data and convert between formats Compute archive-wide statistics across the entire PDB Gain hands-on experience with our Python parser This webinar is part of the ISCBacademy series. <https://www.iscb.org/iscbacademy/home> Registration is required for the Zoom meeting information, but attendance is at no charge. Please sign up at https://go.rutgers.edu/y84mir74. Office Hour: Supporting Extended PDB IDs Thursday, November 7, 2024 2:00 pm – 3:00 pm Eastern | 11:00 am –12:00 pm Pacific The wwPDB anticipates that all four-character PDB IDs will be exhausted by 2028, after which 12-character PDB IDs will be issued. Entries with extended PDB IDs will not be compatible with the legacy PDB file format and will only be available in PDBx/mmCIF format. wwPDB encourages users to transition to the PDBx/mmCIF format as soon as possible. Bring any related questions to our virtual office hour with RCSB PDB's Ezra Peisach. Registration is required for the Zoom meeting information, but attendance is at no charge. Please sign up at https://go.rutgers.edu/p0u1dhuq. Software developers who will need to make updates to code are encouraged to attend. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] [phenixbb] new BUILT of XDS
Dear Kay, so far I am very happy with this version! The issues of the June release do not show up in my case. Best, Tim On Thu, 03 Oct 2024 06:29:48 - kay.diederi...@uni-konstanz.de wrote: > Dear XDS users in the Phenix community, > > as reported by users, and confirmed in a larger-scale comparison by > GlobalPhasing, the BUILT=20240723 of XDS Version 20240630 leads to > problems for some datasets when compared with (the expired) XDS > Version 20230630. (it may be better than the 20230630 version for > other datasets!). > > An improved BUILT=20241002 of the 20240630 version is available (all > platforms) > from https://xds.mr.mpg.de/html_doc/downloading.html for non-commercial > (academic) users (commercial users have their own arrangements). In my/our > testing, it is at least as good as version 20230630, and often better. Please > install and use this instead of BUILT=20240723. If you still find > deficiencies, please contact me or Wolfgang Kabsch - but be prepared to share > the raw data (confidentially, of course). > > To enable comparisons, the old XDS version 20230630 was re-released > for Linux by Wolfgang Kabsch with expiration date 2025-Mar-31; the > link to its XDS_old.tar.gz is at https://xds.mr.mpg.de/ . > > Best wishes, > Kay > ___ > phenixbb mailing list -- pheni...@phenix-online.org > To unsubscribe send an email to phenixbb-le...@phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s -- -- Tim Gruene Head of the Core Facility Crystal Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 https://ccsa.univie.ac.at GPG Key ID = A46BEE1A #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ pgpciGqmm7T4b.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Co-Crystallization with drug molecule
Hi Dr. Gaur, A few questions: 1. Do you know the kinetics (binding constants, etc) of the drug and the protein? 2. Do you know how soluble the drug is in DMSO (is 10 mM the most concentrated?) 3. Is the drug soluble in a mixture of DMSO and water (70% DMSO)? 4. Have you tried crystal soaking experiments? DMSO can poison crystal formation and it can also enhance it as an additive as well as a cryoprotectant. You’ll have to determine how much DMSO you can add and still obtain diffractable crystals under 2.5 Å. My suggestions would be: * Take an apo crystal and transfer it to a drop with the amount of DMSO you plan on adding in your mother liquor and observe (does it wiggle, did it dissolve, does it still diffract?) * Grow your apo crystal in the presence of DMSO and shoot it (did the crystal grow, diffract, etc) * Get the most concentrated sample of your compound and do * Co-crystallization experiments * Soaking experiments * If DMSO is donking up your experiment, try a different solvent, or a lower concentration of DMSO in water. Best, eta *** Eta A. Isiorho, Ph.D. Research Assistant Professor Macromolecular Crystallization Facility Manager CUNY Advanced Science Research Center 85 Saint Nicholas Terrace, 3.352B/3.134 New York, NY 10031 eisio...@gc.cuny.edu<mailto:eisio...@gc.cuny.edu> From: CCP4 bulletin board on behalf of amit gaur Date: Wednesday, October 2, 2024 at 2:51 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Co-Crystallization with drug molecule Hi everyone, I am trying to crystallize a protein with a drug molecule. The protein concentration is 15.5 mg/ml, the drug stock concentration is 10 mM, and the drug is dissolved in DMSO. I am adding the drug to a final concentration of 1 mM in 100 ul of protein, and the DMSO volume is 10 ul for Co-crystallization. I want to know how much DMSO is permissible during co-crystallization with the drug and if DMSO can poison crystal formation. I have not been successful in getting crystals with inhibitors till now, but I obtained crystals of protein without DMSO, and those diffracted to 2.5A. Thanks, Dr. Amit Gaur, Research Scientist Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 1623 15th Street, Troy, NY, 12180 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] AW: [ccp4bb] Co-Crystallization with drug molecule
Dear Amit I did not follow the full thread, just in case this was not covered already some additional considerations: - 10% DMSO (if I understand your CoX setup correctly) is on the high side, we had cases where this was tolerated but more where not - depending on the Kd of your ligand you want to consider going down to 1% / 100µM ligand - with 15mg/ml protein, where are you in terms of mM protein? Figuring this out and considering law of mass action will tell you if your setup leaves you with sufficient occupancy (% ligand bound) - for poorly soluble ligands (and to reduce DMSO) you can use an alternative CoX protocol: incubate diluted protein and diluted ligand (I often use 5-10µM protein and 10x molar excess ligand) and reconcentrate after incubation (eg overnight) - try to use the available apo crystals as seeds! - the above will probably nor work if you have a ligand that is weak (Kd> 1-10µM) AND poorly soluble. In this case the already mentioned strategy of adding solid material to crystal drops is probably your only chance. Good luck! Alex Alexander Pautsch Global NCE Boehringer Ingelheim Pharma GmbH & Co. KG Birkendorfer Str. 65 | 88397 Biberach T +49 (7351) 54-4683 M +49 (151) 15022743 E alexander.paut...@boehringer-ingelheim.com<mailto:alexander.paut...@boehringer-ingelheim.com> [cid:image001.png@01DB1590.DC556720]<https://www.boehringer-ingelheim.com/de/> Pflichtangaben finden Sie unter: hier<https://www.boehringer-ingelheim.com/de/unser-unternehmen/gesellschaften-in-deutschland> Mandatory information can be found at: here<https://www.boehringer-ingelheim.com/de/unser-unternehmen/gesellschaften-in-deutschland> Datenschutzhinweis: Klicken Sie hier<https://www.boehringer-ingelheim.com/de/datenschutz>, um weitere Informationen auf der lokalen Unternehmensinternetseite des betreffenden Landes über Datenschutz bei Boehringer Ingelheim und zu Ihren Rechten zu erhalten. Privacy Notice: Click here<https://www.boehringer-ingelheim.com/de/datenschutz> for more information on the local company website of the respective country about data protection at Boehringer Ingelheim and your rights. Diese E-Mail ist vertraulich zu behandeln. Sie kann besonderem rechtlichem Schutz unterliegen. Wenn Sie nicht der richtige Adressat sind, senden Sie bitte diese E-Mail an den Absender zurück, löschen die eingegangene E-Mail und geben den Inhalt der E-Mail nicht weiter. Jegliche unbefugte Bearbeitung, Nutzung, Vervielfältigung oder Verbreitung ist verboten. / This e-mail is confidential and may also be legally privileged. If you are not the intended recipient please reply to sender, delete the e-mail and do not disclose its contents to any person. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. Von: CCP4 bulletin board Im Auftrag von Tom Peat Gesendet: Mittwoch, 2. Oktober 2024 23:23 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Co-Crystallization with drug molecule CAUTION: Do not click links, scan QR codes, or open attachments unless you trust the sender; this email is from an external sender (outside Boehringer Ingelheim). Hello Amit, In addition to what others have written, if you have some of your compound dry (not in DMSO), then adding this directly to your preformed crystals has worked for us on several occasions. In this instance, one would take a small/ fine pipette tip and dip this into your compound and then touch this to your crystallisation drop. Even if the compound is mostly insoluble, one still gets a little in solution and if this small amount binds to your protein, it is taken out of solution, and more goes into solution (mass action). It is very manual, so you don't want to do a high throughput screen this way, but if you get can get apo crystals and you don't have too many compounds, it can work. Best regards, tom From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Artem Evdokimov mailto:artem.evdoki...@gmail.com>> Sent: Thursday, October 3, 2024 5:42 AM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: Re: [ccp4bb] Co-Crystallization with drug molecule Dear Amit As David already pointed out, all proteins are different and it's hard to say in advance what amount of DMSO may work (or not). An additional concern is that DMSO can also interfere with ligand binding (cases from my personal past history), especially if these inhibitors/ligands are on the weaker side. Solutions: Despite its very high boiling point (189C) DMSO can in fact be evaporated from a small sample of your inhibitor, resulting in more or less solid inhibitor sample that can be re-dissolved in the same DMSO (but higher concentration), some other solvent, or perhaps directly in the protein solution. The latter is sometimes the only way to do this -
[ccp4bb] CCPBioSim Industry Talk - Cresset 23 Oct 2024
Hi all, Our next online talk will be given by Mark Mackey from Cresset at 2pm UK time on Wednesday 23 October 2024. Registration is free but required - details at https://www.ccpbiosim.ac.uk/cresset2024. Title: Adventures in electrostatics - 20 years at Cresset Abstract: In this talk I will present a history of science at Cresset, from our beginnings as ligand-based drug discovery specialists to our current position as a major vendor of computational chemistry software. Along the way I'll touch on molecular electrostatics and why it's critically important, the difficulty of running virtual screening experiments correctly (and the greater difficulty of benchmarking them), the use of water analysis methods for setting up simulations, the difficulties in defining exactly what a bioisostere is, and some of our learnings and results in organising, running and analysing free energy calculations. Best wishes, Sarah To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Co-Crystallization with drug molecule
Hello Amit, In addition to what others have written, if you have some of your compound dry (not in DMSO), then adding this directly to your preformed crystals has worked for us on several occasions. In this instance, one would take a small/ fine pipette tip and dip this into your compound and then touch this to your crystallisation drop. Even if the compound is mostly insoluble, one still gets a little in solution and if this small amount binds to your protein, it is taken out of solution, and more goes into solution (mass action). It is very manual, so you don't want to do a high throughput screen this way, but if you get can get apo crystals and you don't have too many compounds, it can work. Best regards, tom From: CCP4 bulletin board on behalf of Artem Evdokimov Sent: Thursday, October 3, 2024 5:42 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Co-Crystallization with drug molecule Dear Amit As David already pointed out, all proteins are different and it's hard to say in advance what amount of DMSO may work (or not). An additional concern is that DMSO can also interfere with ligand binding (cases from my personal past history), especially if these inhibitors/ligands are on the weaker side. Solutions: Despite its very high boiling point (189C) DMSO can in fact be evaporated from a small sample of your inhibitor, resulting in more or less solid inhibitor sample that can be re-dissolved in the same DMSO (but higher concentration), some other solvent, or perhaps directly in the protein solution. The latter is sometimes the only way to do this - I used to set up drops of DMSO solutions, then evaporate the DMSO in high vacuum (heating helps) with a cryofinger, then set up protein drops on top. This of course requires access to a lyophilizer or something similar. If you have a vial of your solution you can freeze-dry DMSO with water, by first diluting the sample then freeze-drying it. Also water can sometimes crash the substance out (if not water, then perhaps Ether or another solvent where your inhibitor does not dissolve) which makes it easier to redissolve (but there will be a loss of course). Find a friendly chemist nearby and ask then to put your sample in a speedvac on 'high BP' setting Notably, if you're "blessed" with an inhibitor that has the general solubility of a Sony Walkman, once you get rid of the DMSO, you may find out that the damned thing does not want to dissolve in anything else, including your protein solution. This happens a lot during early discovery phases when compounds are not very active (micromolar) and also poorly soluble (also micromolar). This is by far the most frequent cause for failing to co-crystallize (or soak) a ligand of interest. Very frustrating. Some success can be achieved using high DMSO or DMF (DMA also can be good) in your crystallization, or by phase transfer catalysts like Cyclodextrin(s) or appropriately formulated micelles. All of which can also mess up crystallization, needless to say. Best of luck in your endeavors! Artem - Cosmic Cats approve of this message On Wed, Oct 2, 2024 at 2:51 PM amit gaur mailto:cdriamitg...@gmail.com>> wrote: Hi everyone, I am trying to crystallize a protein with a drug molecule. The protein concentration is 15.5 mg/ml, the drug stock concentration is 10 mM, and the drug is dissolved in DMSO. I am adding the drug to a final concentration of 1 mM in 100 ul of protein, and the DMSO volume is 10 ul for Co-crystallization. I want to know how much DMSO is permissible during co-crystallization with the drug and if DMSO can poison crystal formation. I have not been successful in getting crystals with inhibitors till now, but I obtained crystals of protein without DMSO, and those diffracted to 2.5A. Thanks, Dr. Amit Gaur, Research Scientist Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 1623 15th Street, Troy, NY, 12180 ____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Co-Crystallization with drug molecule
Dear Amit As David already pointed out, all proteins are different and it's hard to say in advance what amount of DMSO may work (or not). An additional concern is that DMSO can also interfere with ligand binding (cases from my personal past history), especially if these inhibitors/ligands are on the weaker side. Solutions: Despite its very high boiling point (189C) DMSO can in fact be evaporated from a small sample of your inhibitor, resulting in more or less solid inhibitor sample that can be re-dissolved in the same DMSO (but higher concentration), some other solvent, or perhaps directly in the protein solution. The latter is sometimes the only way to do this - I used to set up drops of DMSO solutions, then evaporate the DMSO in high vacuum (heating helps) with a cryofinger, then set up protein drops on top. This of course requires access to a lyophilizer or something similar. If you have a vial of your solution you can freeze-dry DMSO with water, by first diluting the sample then freeze-drying it. Also water can sometimes crash the substance out (if not water, then perhaps Ether or another solvent where your inhibitor does not dissolve) which makes it easier to redissolve (but there will be a loss of course). Find a friendly chemist nearby and ask then to put your sample in a speedvac on 'high BP' setting Notably, if you're "blessed" with an inhibitor that has the general solubility of a Sony Walkman, once you get rid of the DMSO, you may find out that the damned thing does not want to dissolve in anything else, including your protein solution. This happens a lot during early discovery phases when compounds are not very active (micromolar) and also poorly soluble (also micromolar). This is by far the most frequent cause for failing to co-crystallize (or soak) a ligand of interest. Very frustrating. Some success can be achieved using high DMSO or DMF (DMA also can be good) in your crystallization, or by phase transfer catalysts like Cyclodextrin(s) or appropriately formulated micelles. All of which can also mess up crystallization, needless to say. Best of luck in your endeavors! Artem - Cosmic Cats approve of this message On Wed, Oct 2, 2024 at 2:51 PM amit gaur wrote: > Hi everyone, > > I am trying to crystallize a protein with a drug molecule. The protein > concentration is 15.5 mg/ml, the drug stock concentration is 10 mM, and the > drug is dissolved in DMSO. I am adding the drug to a final concentration of > 1 mM in 100 ul of protein, and the DMSO volume is 10 ul for > Co-crystallization. I want to know how much DMSO is permissible during > co-crystallization with the drug and if DMSO can poison crystal formation. > I have not been successful in getting crystals with inhibitors till now, > but I obtained crystals of protein without DMSO, and those diffracted to > 2.5A. > > Thanks, > > *Dr. Amit Gaur,* > *Research Scientist* > *Center for Biotechnology and **Interdisciplinary Studies,* > *Rensselaer Polytechnic Institute,* > *1623 15th Street, Troy, NY, 12180* > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 of data reprocessing with XDS
Dear Yimin, similar shortcomings were observed with other datasets with XDS VERSION Jun 30, 2024 that was posted on July 23 at https://xds.mr.mpg.de/html_doc/downloading.html . I am sorry for that! The testing of that version had not uncovered this problem. Corrected binaries were posted today at that site, and my (admittedly limited) testing shows them to be as good as, or better than the old (2023) version. Please install and use these binaries. That previous version was made available for comparison purposes as XDS_old.tar.gz, with expiration date 31 Mar 2025, for Linux; download link is at https://xds.mr.mpg.de/ . Hope this helps, Kay On Wed, 2 Oct 2024 16:30:55 +0200, Yimin Hu wrote: >Dear colleagues， > >I ran into a problem when I reprocessed a dataset after switching to XDS >VERSION Jun 30, 2024. > >Processing the dataset with the old XDS I ended up with these statistics: > >RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR >COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano > LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected >Corr > 5.78 167471239 1253 98.9% 7.4% 8.5% > 16745 29.13 7.6%99.9* 20.740 465 > 4.10 299212220 2226 99.7% 8.9% 8.7% > 29921 28.12 9.2%99.8* 90.897 951 > 3.35 400652848 2849 100.0% 10.1% 9.3% > 40065 23.84 10.4%99.8* 30.8411264 > 2.91 442133390 3390 100.0% 13.5% 13.0% > 44213 14.61 14.1%99.8* -100.7171537 > 2.60 542353827 3827 100.0% 24.6% 28.4% > 542359.08 25.5%99.5* -150.6111758 > 2.38 620624270 4270 100.0% 42.5% 57.6% > 620625.40 44.1%98.8* -100.5651973 > 2.20 620764589 4589 100.0% 76.3%111.3% > 620763.06 79.2%97.0*-70.5492138 > 2.06 674374941 4941 100.0% 116.7%176.7% > 674372.03121.3%89.2*-80.5412311 > 1.94 705905226 5268 99.2% 232.1%363.5% > 705790.93241.2%64.3*-40.5112451 >total 447346 32550 32613 99.8% 12.7% 14.4% > 4473339.30 13.2%99.9*-50.621 14848 > > >Reprocessing the dataset with the new version I ended up with the following >statistics though I kept the parameters essentially the same： > > RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR > COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano > LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected >Corr > > 5.80 169321220 1240 98.4% 7.2% 8.5% > 16930 28.65 7.5%99.9* -390.502 459 > 4.12 298882207 2209 99.9% 9.9% 9.3% > 29888 25.46 10.3%99.7* 00.707 945 > 3.37 348172796 2836 98.6% 14.9% 11.7% > 34817 17.63 15.5%99.7*15* 0.9471244 > 2.92 425523268 3347 97.6% 24.5% 23.5% > 42552 10.04 25.5%99.6* -120.5831481 > 2.61 541203811 3816 99.9% 56.8% 69.2% > 541206.14 58.9%98.2* -140.5431750 > 2.38 609224173 4221 98.9% 358.4%464.1% > 609222.93371.4%93.7* -180.4211897 > 2.21 520763861 4566 84.6% -99.9%-99.9% > 520760.00-99.9%66.9* -370.3061566 > 2.06 408233045 4911 62.0% -99.9%-99.9% > 408230.00-99.9%33.3* -390.1961047 > 1.95 347642526 5227 48.3% -99.9%-99.9% > 347640.00-99.9%14.7* -480.072 585 >total 366894 26907 32373 83.1% 28.2% 29.1% > 3668927.57 29.2%99.8* -160.493 10974 > >I tried to tweak several parameters, especially for background subtraction, >but it didn't really help. It would be great if you could give me some >suggestions. Thank you in advance! > >Best, >Yimin > > >-- >Yimin Hu >(Pronouns: she/her) >PhD Student >Department of Protein Evolution >Max Planck Institute for Biology, Tübingen > >#### > >To unsubscribe from the CCP4BB list, click
Re: [ccp4bb] Co-Crystallization with drug molecule
Proteins are individual things. It should be easy to test whether your particular protein is stable and active with a given concentration of DMSO by adding DMSO without the drug molecule. Add the DMSO, then check with light scattering or SAXS for unfolding effects, or perhaps you have a spectroscopic or activity assay you could run. If your protein can tolerate DMSO, you get an added bonus in that DMSO is a cryoprotectant. === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: CCP4 bulletin board on behalf of amit gaur Sent: Wednesday, October 2, 2024 2:51 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Co-Crystallization with drug molecule Hi everyone, I am trying to crystallize a protein with a drug molecule. The protein concentration is 15.5 mg/ml, the drug stock concentration is 10 mM, and the drug is dissolved in DMSO. I am adding the drug to a final concentration of 1 mM in 100 ul of protein, and the DMSO volume is 10 ul for Co-crystallization. I want to know how much DMSO is permissible during co-crystallization with the drug and if DMSO can poison crystal formation. I have not been successful in getting crystals with inhibitors till now, but I obtained crystals of protein without DMSO, and those diffracted to 2.5A. Thanks, Dr. Amit Gaur, Research Scientist Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 1623 15th Street, Troy, NY, 12180 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Co-Crystallization with drug molecule
Hi everyone, I am trying to crystallize a protein with a drug molecule. The protein concentration is 15.5 mg/ml, the drug stock concentration is 10 mM, and the drug is dissolved in DMSO. I am adding the drug to a final concentration of 1 mM in 100 ul of protein, and the DMSO volume is 10 ul for Co-crystallization. I want to know how much DMSO is permissible during co-crystallization with the drug and if DMSO can poison crystal formation. I have not been successful in getting crystals with inhibitors till now, but I obtained crystals of protein without DMSO, and those diffracted to 2.5A. Thanks, *Dr. Amit Gaur,* *Research Scientist* *Center for Biotechnology and **Interdisciplinary Studies,* *Rensselaer Polytechnic Institute,* *1623 15th Street, Troy, NY, 12180* To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 of data reprocessing with XDS
me > suggestions. Thank you in advance! > > Best, > Yimin > > > -- > Yimin Hu > (Pronouns: she/her) > PhD Student > Department of Protein Evolution > Max Planck Institute for Biology, Tübingen ######## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] DelsaMax software
Hello, I am looking for obsolete software from Beckman called DelsaMax. It controls their particle sizer DelsaMax which is also obsolete. Software used to be license free. However, Beckman does not store it for download anymore. If anyone has a copy of it please reach out. Thank You for your help, _ Michal T. Boniecki, Ph.D. Professional Affiliate Department of BMI Manager Protein Characterization and Crystallization Facility University of Saskatchewan 107 Wiggins Rd HLTH 3D30.11 Saskatoon, SK S7N 5E5 Canada tel. (306) 966-2977 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Problem of data reprocessing with XDS
Dear colleagues， I ran into a problem when I reprocessed a dataset after switching to XDS VERSION Jun 30, 2024. Processing the dataset with the old XDS I ended up with these statistics: RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 5.78 167471239 1253 98.9% 7.4% 8.5% 16745 29.13 7.6%99.9* 20.740 465 4.10 299212220 2226 99.7% 8.9% 8.7% 29921 28.12 9.2%99.8* 90.897 951 3.35 400652848 2849 100.0% 10.1% 9.3% 40065 23.84 10.4%99.8* 30.8411264 2.91 442133390 3390 100.0% 13.5% 13.0% 44213 14.61 14.1%99.8* -100.7171537 2.60 542353827 3827 100.0% 24.6% 28.4% 542359.08 25.5%99.5* -150.6111758 2.38 620624270 4270 100.0% 42.5% 57.6% 620625.40 44.1%98.8* -100.5651973 2.20 620764589 4589 100.0% 76.3%111.3% 620763.06 79.2%97.0*-70.5492138 2.06 674374941 4941 100.0% 116.7%176.7% 674372.03121.3%89.2*-80.5412311 1.94 705905226 5268 99.2% 232.1%363.5% 705790.93241.2%64.3*-40.5112451 total 447346 32550 32613 99.8% 12.7% 14.4% 4473339.30 13.2%99.9*-50.621 14848 Reprocessing the dataset with the new version I ended up with the following statistics though I kept the parameters essentially the same： RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 5.80 169321220 1240 98.4% 7.2% 8.5% 16930 28.65 7.5%99.9* -390.502 459 4.12 298882207 2209 99.9% 9.9% 9.3% 29888 25.46 10.3%99.7* 00.707 945 3.37 348172796 2836 98.6% 14.9% 11.7% 34817 17.63 15.5%99.7*15* 0.9471244 2.92 425523268 3347 97.6% 24.5% 23.5% 42552 10.04 25.5%99.6* -120.5831481 2.61 541203811 3816 99.9% 56.8% 69.2% 541206.14 58.9%98.2* -140.5431750 2.38 609224173 4221 98.9% 358.4%464.1% 609222.93371.4%93.7* -180.4211897 2.21 520763861 4566 84.6% -99.9%-99.9% 520760.00-99.9%66.9* -370.3061566 2.06 408233045 4911 62.0% -99.9%-99.9% 408230.00-99.9%33.3* -390.1961047 1.95 347642526 5227 48.3% -99.9%-99.9% 347640.00-99.9%14.7* -480.072 585 total 366894 26907 32373 83.1% 28.2% 29.1% 3668927.57 29.2%99.8* -160.493 10974 I tried to tweak several parameters, especially for background subtraction, but it didn't really help. It would be great if you could give me some suggestions. Thank you in advance! Best, Yimin -- Yimin Hu (Pronouns: she/her) PhD Student Department of Protein Evolution Max Planck Institute for Biology, Tübingen To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Structural biology opportunities at Astex Pharmaceuticals
Dear All, We have a number of positions available in our Molecular Sciences group at Astex Pharmaceuticals, Cambridge UK to help us continue to develop and expand our structural biology capabilities. We are looking for protein scientists, a protein crystallographer and a cryo-EM scientist to join our expanding Discovery Technologies department, supporting projects during all phases of the drug discovery process. Further details of these roles can be found at: https://www.cloudonlinerecruitment.co.uk/Astex/Vacancy.aspx Thanks, Judith Judith Reeks, PhD Associate Director, Discovery Technologies Astex Pharmaceuticals 436 Cambridge Science Park Milton Road, Cambridge CB4 0QA, UK Tel: +44(0)1223 226264 Fax: +44(0)1223 226238 Email: judith.re...@astx.com Website: www.astx.com This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Postdoc position on protein biophysics
Hi, a postdoc position is open in our lab at the Institute for Structural Biology to develop an experimental approach for the determination of the photoinduced structural dynamics of photosensitive biomolecules /in vivo/ using time-resolved X-ray scattering techniques. Here the link to apply: https://emploi.cnrs.fr/Offres/CDD/UMR5075-VALLAN-031/Default.aspx?lang=EN Please share the announcement with whoever potentially interested. Best wishes, Giorgio Schirò To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] FEBS advanced lecture course 'Emerging insights from structural biology into molecular mechanisms of diseases' 27-31 May, 2025
Dear friends and colleagues, It is our pleasure to invite you to join us for a *structural biology* conference “Emerging Insights from Structural Biology into Molecular Mechanisms of Diseases” in Groningen, 27-31 of May 2025! Tailored for early-career scientists, the event features lectures from world-leading experts from both academia and industry, career development sessions, and numerous chances to network with renowned professionals in an inclusive environment. Furthermore you can present your own work through posters or selected talks and engage in discussions that could shape your future research and career. So, if you are passionate about structural biology in a biomedical context, this meeting is not to be missed! The registration opens today! https://molmechdisease2025.febsevents.org Confirmed speakers: Radu Aricescu, Stefan Arold, Jens Carlsson, Larissa Dietz, Ruslan Efremov, Ingo Greger, Inga Hänelt , Maryam Khoshouei, Meytal Landau, Claus Løland, Ulrich Lorenz, Paula Navarro, Arwen Pearson, Aravind Penmatsa, Alexander Sobolevsky, Phill Stansfeld, Sonja Sucic, Joanna Sułkowska, Petrine Wellendorph. Special guests: Jan Riemer and Chris Croft See you in Groningen, Albert Guskov, Katharina Dürr and Dirk Slotboom To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Structural biology opportunities at Astex Pharmaceuticals
Dear all, We have a number of positions available in our Molecular Sciences group at Astex Pharmaceuticals, Cambridge UK to help us continue to develop and expand our structural biology capabilities. We are looking for protein scientists, a cryo-EM scientist and a protein crystallographer to join our expanding Discovery Technologies department, supporting projects during all phases of the drug discovery process. Further details of these roles can be found at https://www.cloudonlinerecruitment.co.uk/Astex/Vacancy.aspx Kind regards Pamela Pamela Williams, DPhil Senior Director, Discovery Technologies Astex Pharmaceuticals 436 Cambridge Science Park Milton Road, Cambridge CB4 0QA, UK Tel: +44(0)1223 226232 Fax: +44(0)1223 226201 Email:pamela.willi...@astx.com Website: www.astx.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
Re: [ccp4bb] Introducing the UNTANGLE Challenge
OK Folks, it has been nine months since I announced this challenge. Some excellent suggestions have been made, and some new tools created for this community, but the UNTANGLE Challenge is still not solved! As additional incentive, I am now officially announcing cash prizes: $1000 (USD) for the first/best solution to level 11. $500 (USD) for the first/best solution to level 10. The instructions, rules and data files otherwise remain the same: https://bl831.als.lbl.gov/~jamesh/challenge/twoconf/ No cheating! (by that I mean, I'm not sending you $500 for just emailing me a copy of the provided best.pdb file. You have to show how you got there from the density). Some good news: If you download the latest Phenix Suite, there are new tools that will help you: % phenix.holton_geometry_validation Calculates my wE score and is generally applicable beyond this challenge data (no, I did not name it, thanks Tom Terwilliger) % phenix.create_alt_conf Makes and optimizes alternate conformer choices (can use a lot of CPU) % phenix.refine new features: fit_altlocs_method=masking , include_altlocs=True and refine_oat=True for improved refinement results when using alt confs in protein and in solvent One recent caveat: As of Phenix version 1.21.2 (build 5419 and later) the ideal non-bond distances for potential hydrogen bonds have been updated. This will make my "weighted Energy" (wE) geometry scores worse than those from earlier versions. So, in fairness to those who put a lot of effort in so far, I will allow wE scores computed with earlier versions of phenix, even if they are built or refined with other programs. Yes, I know this is the CCP4BB, but I have not had any reports of new developments on this front from the CCP4 team. Feel free to chime in here. Thank you all who have tried your hand and made great new tools so far! The path to the ideal, underlying ensemble is clearly a difficult one, but it must exist. And it is a journey worth making if it reveals cooperative motions like those posited in the ground truth of this Challenge. Easily worth $1500. -James Holton MAD Scientsit On 1/21/2024 7:07 AM, Herbert J. Bernstein wrote: Have you considered the impact of tunneling? Your rope crossings are not perfect barriers. On Sat, Jan 20, 2024 at 6:09 PM James Holton wrote: Update: I've gotten some feedback asking for clarity on what I mean by "tangled". I paste here a visual aid: The protein chains in an ensemble model are like these ropes. If these ropes are the same length as the distance from floor to ceiling, then straight up-and-down is the global minimum in energy (left). The anchor points are analogous to the rest of the protein structure, which is the same in both diagrams. Imagine for a moment, however, after anchoring the dangling rope ends to the floor you look up and see the ropes are actually crossed (right). You got the end points right, but no amount of pulling on the ropes (energy minimization) is going to get you from the tangled structure to the global minimum. The tangled ropes are also strained, because they are being forced to be a little longer than they want to be. This strain in protein models manifests as geometry outliers and the automatic weighting in your refinement program responds to bad geometry by relaxing the x-ray weight, which alleviates some of the strain, but increases your Rfree. The goal of this challenge is to eliminate these tangles, and do it efficiently. What we need is a topoisomerase! Something that can find the source of strain and let the ropes pass through each other at the appropriate place. I've always wanted one of those for the wires behind my desk... More details on the origins of tangling in ensemble models can be found here: https://bl831.als.lbl.gov/~jamesh/challenge/twoconf/#tangle -James Holton MAD Scientist On 1/18/2024 4:33 PM, James Holton wrote: Greetings Everybody, I present to you a Challenge. Structural biology would be far more powerful if we can get our models out of local minima, and together, I believe we can find a way to escape them. tldr: I dare any one of you to build a model that scores better than my "best.pdb" model below. That is probably impossible, so I also dare you to approach or even match "best.pdb" by doing something more clever than just copying it. Difficulty levels range from 0 to 11. First one to match the best.pdb energy score an Rfree wins the challenge, and I'd like you to be on my paper. You have nine months. Details of the challenge, scoring system, test data, and available starting points can be found here: https://bl831.als.lbl.gov/~jamesh/challenge/twoconf/ Why am I doing this? We all know that macro
[ccp4bb] Molecular devices Flex station assay plate readers
Hi all Definitely off topic yet I am sure the people in here are super helpful I have a Molecular devices Flex station used for plate assays and stopped working so looking for a third party repair sources in California Does anyone know a good repair service for lab scientific equipment I am out of warranty and the quotes for repair seems very expensive Best regards Pius *Pius Padayatti* To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Resize Coot windows in Ubuntu 24.04 LTS
On 30/09/2024 10:20, Kolenko, Petr wrote: I have a fresh installation of Ubuntu 24.04 LTS and CCP4. In Coot 0.9, I cannot resize additional windows, e.g. check waters, distance measurement, residue info. The only thing I can resize is the main window. Do I miss some library? I have not heard of this problem before. Those non-main widows are transients - maybe you have some config file that says that transients are not resizable - or maybe your window manager does. If you have a fresh (new) CCP4 then I'd be interested to see how Coot 1 behaves (you can find it in the coot_py3 directory). Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Resize Coot windows in Ubuntu 24.04 LTS
Dear colleagues, Apologies, the installation is so fresh that I did not realize that I have the same issue with some other applications. It is most probably not related to the CCP4 package at all. I have to find the solution on my own. Best regards, Petr Od: CCP4 bulletin board za uživatele Kolenko, Petr <9d229ba2f5a3-dmarc-requ...@jiscmail.ac.uk> Odesláno: pondělí 30. září 2024 11:20 Komu: CCP4BB@JISCMAIL.AC.UK Předmět: [ccp4bb] Resize Coot windows in Ubuntu 24.04 LTS E-maily z adresy 9d229ba2f5a3-dmarc-requ...@jiscmail.ac.uk nedostáváte často. Přečtěte si, proč je to důležité<https://aka.ms/LearnAboutSenderIdentification> Dear colleagues, I have a fresh installation of Ubuntu 24.04 LTS and CCP4. In Coot 0.9, I cannot resize additional windows, e.g. check waters, distance measurement, residue info. The only thing I can resize is the main window. Do I miss some library? Best regards, Petr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Resize Coot windows in Ubuntu 24.04 LTS
Dear colleagues, I have a fresh installation of Ubuntu 24.04 LTS and CCP4. In Coot 0.9, I cannot resize additional windows, e.g. check waters, distance measurement, residue info. The only thing I can resize is the main window. Do I miss some library? Best regards, Petr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Downtime of the PDB-REDO and Tortoize servers
Dear CCP4BB-ers, Tomorrow, the 30th of September, we are performing a server upgrade that will temporarily will bring down the PDB-REDO website (https://pdb-redo.eu). The maintenance will begin around 8:00h Amsterdam time and can last several hours. During that time no PDB-REDO jobs can be submitted directly or through the API that is used by CCP4i2 and CCP4-cloud. The PDB-REDO databank will also not be available through the website or in Coot, CCP4mg and other molecular graphics programs. The databank will remain available through rsync (rsync://rsync.pdb-redo.eu/pdb-redo/). The downtime will also affect the Tortoize server (https://pdb-redo.eu/tortoize) that can be used to calculate the Ramachandran Z-score (Rama-Z). However Tortoize is also available in CCP4 as a standalone tool. If you notice any unexpected behaviour in PDB-REDO after we come back online, or if you have any other support request, feel free to reach out to me directly. Best wishes, Robbie Joosten Department of biochemistry The Netherlands Cancer Institute To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] contour level for cryoEM deposition: coot vs chimera
I read somewhere (I don’t have the ref, sorry) that it is because the phases are directly measured in cryoEM (since it is an imaging technique), and they are often more accurate than the phases of crystallographic maps. On this basis, if you can find a structure that has been solved both by cryoEM and crystallography with very accurate experimental phasing, and at comparable resolutions, then these two maps should look more similar in quality than what you would observe when comparing the same cryoEM map to a crystallographic map phased by MR. Cheers, Guillaume On 26 Sep 2024, at 18:56, Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk>> wrote: Another thing I am curious about is how a map can look good at 5.5 sigma because an X-ray one probably wouldn't unless it was atomic resolution. Don't worry if there isn't a simple explanation. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com<mailto:jon.b.coo...@protonmail.com> Sent from Proton Mail Android Original Message On 26/09/2024 11:13, anna anna wrote: Dear all, I am depositing my first cryoEM structure and I am facing the following problem concerning the contour level of the map. Briefly, where do I find the value for the contour level to associate to the uploaded map in Coot? Long story: I worked with coot and I am happy with my map when I set the contour level at 0.115 V = 5.5 rmsd (actually "happy" is not the best definition, I feel quite uncomfortable with this "by feeling" assignment but, to what I understood, this is how it works...). Upon deposition, when I upload maps, a contour level is required but the values from coot are not accepted, I have to provide the contour level relative to the map value, like the one that you set in Chimera. Thus I opened the map in Chimera and I set a contour level "by eye" but the validation report revealed some problems: the total volume of the map is too low and too many residues are highlighted as out of density. Probably I should low the contour level but I don't want to go for a trial-and-error approach, there must be a way to convert the contour level from coot (the one that I used for modelling) in the one required for deposition! Any advice? Thank you, Anna To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Call for access to Synchrotron Beamline Facilities, 2025 - EMBL Hamburg, Germany
We announce the call for synchrotron beamtime applications in biological small-angle X-ray scattering (SAXS), macromolecular crystallography (MX) and X-Ray imaging (XIMG) for the period March - December 2025. The following EMBL beamlines at PETRA III are available: P12 (SAXS, TR-SAXS), P13 (MX) and P14 (MX including the T-REXX endstation and XIMG). Submission of BAG (Block Allocation Group) proposals is encouraged. *Groups applying for beamtime to work on several projects during 2025 are requested to submit their research proposals via a BAG application and not as several individual proposals (even if the BAG only consists of a single research group).* For experiments intending to use the T-REXX endstation, please submit your proposal (BAG or Single) under the T-REXX heading. The deadline for submission of proposals for 2025 is: *_Monday, 4th November 2024 (midnight CET)_*. After this date, the proposals will be evaluated by an external Project Evaluation Committee and the users will be informed about the results of their application(s) in the second half of January 2025. Support for access to the infrastructures is being offered via Instruct-ERIC <https://www.embl.org/about/info/hamburg-access-infrastructures/instruct-eric-funding/>, please contact the User Office for details on how to apply. A detailed description of the three beamlines and links to the electronic proposal forms can be found on our Structural Biology Services page: https://www.embl.org/services-facilities/hamburg/ <https://www.embl.org/services-facilities/hamburg/>. Information about the X-ray imaging facility is available at: www.embl.org/groups/duke <http://www.embl.org/groups/duke>. For additional information and advice regarding submitting a proposal, visit our Access to Infrastructures page <https://www.embl.org/about/info/hamburg-access-infrastructures/>. Please submit your proposal via the EMBL Hamburg user portal: https://smis.embl-hamburg.de <https://smis.embl-hamburg.de/>. Access to the EMBL Hamburg facilities also includes assistance with crystallisation, sample preparation and, in combination with an EMBL beamline visit, with sample characterisation and optimisation. For further general information, please contact the EMBL Hamburg user office: Tel.: +49 40-89902-183/ 311 Email: useroffice (at) embl-hamburg.de For specific information: saxs (at) embl-hamburg.de (small-angle X-ray scattering) mx (at) embl-hamburg.de (macromolecular crystallography) trexx (at) embl-hamburg.de (macromolecular crystallography) imaging (at) embl-hamburg.de (X-Ray imaging) spc (at) embl-hamburg.de (sample preparation and characterisation) With kind regards, EMBL Hamburg User Office To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] contour level for cryoEM deposition: coot vs chimera
There is some more info in the documentation of the corresponding command: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#mapstats ChimeraX and Coot report different numbers probably because they have different defaults: ChimeraX computes statistics on the whole box (per its documentation, and unless you have cropped or masked or otherwise explicitly done something to the map), while Coot might use only the sub-region within a mask? Not sure what the default is for Coot, but Paul’s last message suggests that it might use a mask by default. The sure thing is that these numbers should come out identical (to rounding error maybe) if both programs compute them from the entire box, and you might be able to check this if you can convince Coot to consider the whole box. Cheers, Guillaume On 27 Sep 2024, at 11:42, anna anna mailto:marmottalb...@gmail.com>> wrote: Dear Paul, I am not expert of chimeraX here https://www.cgl.ucsf.edu/chimerax/docs/user/tools/mapstats.html I found this description: Map Statistics reports the minimum, maximum, and mean values, the standard deviation (SD) from the mean, and the root-mean-square (RMS) deviation from zero for volume data (map) models. Here is the output for my model: Map cryosparc_P9_J388_003_volume_map(1).mrc #1, minimum -0.255, maximum 0.4798, mean 0.0002941, SD 0.01472, RMS 0.01472 That's all I can say. PS: I didn't know about moorhen, I am trying it right now! Il giorno gio 26 set 2024 alle ore 18:11 Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk>> ha scritto: Dear Ana, Coot calculates the map rmsd for cryo-EM reconstructions by ignoring the modal values. I suspect that this is not what ChimeraX does. Can you get ChimeraX to tell you what it thinks the map rmsd is? Ideally one should use a mask when calculating the cryo-EM rmsd. Paul. p.s. for a bit of fun, I thought I'd see if I could reproduce the style of representation using moorhen On 26/09/2024 16:30, anna anna wrote: Dear Colin, thank you for the explanation. I followed your advice and indeed, the map is almost identical in coot and chimera. I would like to take this opportunity to ask for further clarification: as suggested by someone else, I should be able to calculate the map value by multiplying the rmsd value of the map by 5.5. The statistics of my map are (from chimera): Map cryosparc_P9_J388_003_volume_map(1).mrc #1, minimum -0.255, maximum 0.4798, mean 0.0002941, SD 0.01472, RMS 0.01472 so 0.01472 multiplied by 5.5 = 0.081 Do you have any idea to account for this difference? Thank you, Anna Il giorno gio 26 set 2024 alle ore 16:21 Colin Palmer - STFC UKRI mailto:colin.pal...@stfc.ac.uk>> ha scritto: Dear Anna, The absolute map value that Coot displays – i.e. the 0.115 in your “0.115 V = 5.5 rmsd” – is the raw value from the map file, and should be equivalent to the “Level” shown in the Volume Viewer in Chimera or ChimeraX (as long as the step value is set to 1). If you set the contour levels to the same number, the map should appear very similar in both programs. Note that when working with cryo-EM maps, you should usually ignore the rmsd value and focus only on the absolute values, because the rmsd will change if the map is masked, cropped or padded and the absolute values won’t. Also note that Coot changes the unit: if it thinks the map is from cryo-EM it shows “V” and if it thinks it is from crystallography it shows “e/A^3”. Sometimes it picks the wrong one, but it doesn’t matter and in both cases the values are the same. Best wishes, Colin From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of anna anna Sent: Thursday, September 26, 2024 11:13 AM To: ccp4bb mailto:ccp4bb@jiscmail.ac.uk>> Subject: [ccp4bb] contour level for cryoEM deposition: coot vs chimera Dear all, I am depositing my first cryoEM structure and I am facing the following problem concerning the contour level of the map. Briefly, where do I find the value for the contour level to associate to the uploaded map in Coot? Long story: I worked with coot and I am happy with my map when I set the contour level at 0.115 V = 5.5 rmsd (actually "happy" is not the best definition, I feel quite uncomfortable with this "by feeling" assignment but, to what I understood, this is how it works...). Upon deposition, when I upload maps, a contour level is required but the values from coot are not accepted, I have to provide the contour level relative to the map value, like the one that you set in Chimera. Thus I opened the map in Chimera and I set a contour level "by eye" but the validation report revealed some problems: the total volume of the map is too low and too many residues are highlighted as out of density. Probably I should low the contour level but I don't want to go for a trial-and-error approach, there must be a way to convert the
[ccp4bb] Membrane Protein Biochemist position UCB
istribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. UCB screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. UCB accepts no liability for any damage caused by any virus transmitted by this electronic mail. (Ref: #*UG1107) [Ref-UG1107] #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] contour level for cryoEM deposition: coot vs chimera
Sorry, I think the answer is on Colin's reply. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android Original Message On 26/09/2024 17:56, Jon Cooper wrote: > Another thing I am curious about is how a map can look good at 5.5 sigma > because an X-ray one probably wouldn't unless it was atomic resolution. Don't > worry if there isn't a simple explanation. > > Best wishes, Jon Cooper. > jon.b.coo...@protonmail.com > > Sent from Proton Mail Android > > Original Message > On 26/09/2024 11:13, anna anna wrote: > >> Dear all, >> I am depositing my first cryoEM structure and I am facing the following >> problem concerning the contour level of the map. >> >> Briefly, where do I find the value for the contour level to associate to the >> uploaded map in Coot? >> >> Long story: I worked with coot and I am happy with my map when I set the >> contour level at 0.115 V = 5.5 rmsd (actually "happy" is not the best >> definition, I feel quite uncomfortable with this "by feeling" assignment >> but, to what I understood, this is how it works...). >> Upon deposition, when I upload maps, a contour level is required but the >> values from coot are not accepted, I have to provide the contour level >> relative to the map value, like the one that you set in Chimera. Thus I >> opened the map in Chimera and I set a contour level "by eye" but the >> validation report revealed some problems: the total volume of the map is too >> low and too many residues are highlighted as out of density. Probably I >> should low the contour level but I don't want to go for a trial-and-error >> approach, there must be a way to convert the contour level from coot (the >> one that I used for modelling) in the one required for deposition! >> >> Any advice? >> >> Thank you, >> Anna >> >> --- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > --- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Assistant/Associate Professor positions in structural biology at Univ. of Iowa
The Department of Biochemistry and Molecular Biology at the University of Iowa College of Medicine is inviting applications for a tenure-track Assistant or Associate Professor position. Successful applicants will be able to establish an independent, extramurally funded research program probing basic or translational aspects of biochemistry. We seek multiple, outstanding individuals working in any area of biochemistry or molecular biology--individuals who will complement our research strengths in metabolism, control of gene expression, DNA replication and repair, and protein structure and function are especially encouraged to apply. See job post here: https://jobs.uiowa.edu/faculty/view/75303 For those interested in cryoEM, the University of Iowa will be getting a Glacios microscope with a Falcon 4i and Selectris in fall 2025. Contact: Rosemary E Stratton - bioc...@uiowa.edu<mailto:bioc...@uiowa.edu> https://medicine.uiowa.edu/biochemistry-molecular-biology/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] contour level for cryoEM deposition: coot vs chimera
Another thing I am curious about is how a map can look good at 5.5 sigma because an X-ray one probably wouldn't unless it was atomic resolution. Don't worry if there isn't a simple explanation. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android Original Message On 26/09/2024 11:13, anna anna wrote: > Dear all, > I am depositing my first cryoEM structure and I am facing the following > problem concerning the contour level of the map. > > Briefly, where do I find the value for the contour level to associate to the > uploaded map in Coot? > > Long story: I worked with coot and I am happy with my map when I set the > contour level at 0.115 V = 5.5 rmsd (actually "happy" is not the best > definition, I feel quite uncomfortable with this "by feeling" assignment but, > to what I understood, this is how it works...). > Upon deposition, when I upload maps, a contour level is required but the > values from coot are not accepted, I have to provide the contour level > relative to the map value, like the one that you set in Chimera. Thus I > opened the map in Chimera and I set a contour level "by eye" but the > validation report revealed some problems: the total volume of the map is too > low and too many residues are highlighted as out of density. Probably I > should low the contour level but I don't want to go for a trial-and-error > approach, there must be a way to convert the contour level from coot (the one > that I used for modelling) in the one required for deposition! > > Any advice? > > Thank you, > Anna > > --- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] contour level for cryoEM deposition: coot vs chimera
Dear Anna, The absolute map value that Coot displays – i.e. the 0.115 in your “0.115 V = 5.5 rmsd” – is the raw value from the map file, and should be equivalent to the “Level” shown in the Volume Viewer in Chimera or ChimeraX (as long as the step value is set to 1). If you set the contour levels to the same number, the map should appear very similar in both programs. Note that when working with cryo-EM maps, you should usually ignore the rmsd value and focus only on the absolute values, because the rmsd will change if the map is masked, cropped or padded and the absolute values won’t. Also note that Coot changes the unit: if it thinks the map is from cryo-EM it shows “V” and if it thinks it is from crystallography it shows “e/A^3”. Sometimes it picks the wrong one, but it doesn’t matter and in both cases the values are the same. Best wishes, Colin From: CCP4 bulletin board On Behalf Of anna anna Sent: Thursday, September 26, 2024 11:13 AM To: ccp4bb Subject: [ccp4bb] contour level for cryoEM deposition: coot vs chimera Dear all, I am depositing my first cryoEM structure and I am facing the following problem concerning the contour level of the map. Briefly, where do I find the value for the contour level to associate to the uploaded map in Coot? Long story: I worked with coot and I am happy with my map when I set the contour level at 0.115 V = 5.5 rmsd (actually "happy" is not the best definition, I feel quite uncomfortable with this "by feeling" assignment but, to what I understood, this is how it works...). Upon deposition, when I upload maps, a contour level is required but the values from coot are not accepted, I have to provide the contour level relative to the map value, like the one that you set in Chimera. Thus I opened the map in Chimera and I set a contour level "by eye" but the validation report revealed some problems: the total volume of the map is too low and too many residues are highlighted as out of density. Probably I should low the contour level but I don't want to go for a trial-and-error approach, there must be a way to convert the contour level from coot (the one that I used for modelling) in the one required for deposition! Any advice? Thank you, Anna ________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] contour level for cryoEM deposition: coot vs chimera
Hello Anna I have no idea why the map format is unacceptable without more details of how you created the file. Presumably it is in ccp4 format, but there are others. Is it a binary file or humanly readable? It's EM so cell dimensions are artificial, etc, I think. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android Original Message On 26/09/2024 11:13, anna anna wrote: > Dear all, > I am depositing my first cryoEM structure and I am facing the following > problem concerning the contour level of the map. > > Briefly, where do I find the value for the contour level to associate to the > uploaded map in Coot? > > Long story: I worked with coot and I am happy with my map when I set the > contour level at 0.115 V = 5.5 rmsd (actually "happy" is not the best > definition, I feel quite uncomfortable with this "by feeling" assignment but, > to what I understood, this is how it works...). > Upon deposition, when I upload maps, a contour level is required but the > values from coot are not accepted, I have to provide the contour level > relative to the map value, like the one that you set in Chimera. Thus I > opened the map in Chimera and I set a contour level "by eye" but the > validation report revealed some problems: the total volume of the map is too > low and too many residues are highlighted as out of density. Probably I > should low the contour level but I don't want to go for a trial-and-error > approach, there must be a way to convert the contour level from coot (the one > that I used for modelling) in the one required for deposition! > > Any advice? > > Thank you, > Anna > > --- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Registration now open for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models
Some of you keen people may have noticed that the button to register is missing from the SW website!! Please use https://cvent.me/bxlPqr to register until it appears. Regards Karen McIntyre CCP4 Project Administrator CCP4 ED&I Champion UKRI-STFC Rutherford Appleton Laboratory Harwell Campus Didcot OX11 0QX Phone: +44 (0) 1235 44 5790 [cid:image001.png@01DB101A.28616FF0] STFC is part of UK Research and Innovation, a public body funded by the UK government. For more information visit www.ukri.org<http://www.ukri.org/> [A grey circle with red text Description automatically generated] Affiliatated Member of the Institute for Continuous Improvement in the Public Sector ***Please note I only work part-time - hours are Monday to Thursday 08:30 to 13:30 and Friday 10:30 to 15:30** From: McIntyre, Karen (STFC,RAL,SC) Sent: Thursday, September 26, 2024 1:15 PM To: CCP4 WG2 ; CCP4 WG1 ; ccp4bb@jiscmail.ac.uk Subject: Registration now open for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models Importance: High Dear all, Registration is now open for the 2025 CCP4 study weekend entitled " Using software, AI and other methods to advance macromolecular models". This year the CCP4 Study Weekend will be held as a hybrid event from the 7th to 9th January 2025, enabling people to choose whether to attend in-person or virtually. The in-person event will be held at the East Midlands Conference Centre, Nottingham, UK. We would like to invite you to another iteration of the ever-popular CCP4 Study Weekend - to start the year 2025 with a lot of fresh ideas, new insights and (hopefully) new friends and contacts to boost. As always it will be an eclectic mix of bleeding-edge science, in-depth presentations, discussion panel, poster-sessions, hands-on tutorials and plenty of opportunities for social interactions. For full details, programme, logistics and registration, please visit the Study Weekend website<https://studyweekend.ccp4.ac.uk/>. There is no better way to start 2025 than to put participation in that exciting meeting at the top of your "New Year's Resolutions" list! Key Dates: * Early bird registration final date: 11 November 2024; * Standard Student bursaries are open to all students registering during early bird period i.e. now until 11 November which cover the cost of registration plus one night accommodation in halls (1 night in hotel will be subsidised for those students choosing to stay in the hotel); * Travel bursaries are available for students and young postdocs studying at overseas labs to help cover cost of travel to UK. The deadline for applications is 31 October 2024; * Registration for in-person delegates closes 4 December 2023 (or earlier if in-person places sell out although you will be able to join the in-person waitlist). * Registration for virtual delegates will close 9 January 2025. Key Timings Diamond MX user meeting will start at 11:00 on 7TH January 2025 CCP4 study weekend 2025 will start at ~17:30 on 7th January 2025 the event will finish at ~16:30 on 9th January 2025 We hope to see you there! Scientific Organisers: Elke De Zitter (Institut de Biologie Structurale, FRANCE) Deborah Harrus (EMBL-EBI, UK) Dorothee Liebschner (Lawrence Berkeley National Laboratory, USA) Administrative Organisers: Karen McIntyre (CCP4, UK) #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Registration now open for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models
Dear all, Registration is now open for the 2025 CCP4 study weekend entitled " Using software, AI and other methods to advance macromolecular models". This year the CCP4 Study Weekend will be held as a hybrid event from the 7th to 9th January 2025, enabling people to choose whether to attend in-person or virtually. The in-person event will be held at the East Midlands Conference Centre, Nottingham, UK. We would like to invite you to another iteration of the ever-popular CCP4 Study Weekend - to start the year 2025 with a lot of fresh ideas, new insights and (hopefully) new friends and contacts to boost. As always it will be an eclectic mix of bleeding-edge science, in-depth presentations, discussion panel, poster-sessions, hands-on tutorials and plenty of opportunities for social interactions. For full details, programme, logistics and registration, please visit the Study Weekend website<https://studyweekend.ccp4.ac.uk/>. There is no better way to start 2025 than to put participation in that exciting meeting at the top of your "New Year's Resolutions" list! Key Dates: * Early bird registration final date: 11 November 2024; * Standard Student bursaries are open to all students registering during early bird period i.e. now until 11 November which cover the cost of registration plus one night accommodation in halls (1 night in hotel will be subsidised for those students choosing to stay in the hotel); * Travel bursaries are available for students and young postdocs studying at overseas labs to help cover cost of travel to UK. The deadline for applications is 31 October 2024; * Registration for in-person delegates closes 4 December 2023 (or earlier if in-person places sell out although you will be able to join the in-person waitlist). * Registration for virtual delegates will close 9 January 2025. Key Timings Diamond MX user meeting will start at 11:00 on 7TH January 2025 CCP4 study weekend 2025 will start at ~17:30 on 7th January 2025 the event will finish at ~16:30 on 9th January 2025 We hope to see you there! Scientific Organisers: Elke De Zitter (Institut de Biologie Structurale, FRANCE) Deborah Harrus (EMBL-EBI, UK) Dorothee Liebschner (Lawrence Berkeley National Laboratory, USA) Administrative Organisers: Karen McIntyre (CCP4, UK) #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] contour level for cryoEM deposition: coot vs chimera
Dear all, I am depositing my first cryoEM structure and I am facing the following problem concerning the contour level of the map. Briefly, where do I find the value for the contour level to associate to the uploaded map in Coot? Long story: I worked with coot and I am happy with my map when I set the contour level at 0.115 V = 5.5 rmsd (actually "happy" is not the best definition, I feel quite uncomfortable with this "by feeling" assignment but, to what I understood, this is how it works...). Upon deposition, when I upload maps, a contour level is required but the values from coot are not accepted, I have to provide the contour level relative to the map value, like the one that you set in Chimera. Thus I opened the map in Chimera and I set a contour level "by eye" but the validation report revealed some problems: the total volume of the map is too low and too many residues are highlighted as out of density. Probably I should low the contour level but I don't want to go for a trial-and-error approach, there must be a way to convert the contour level from coot (the one that I used for modelling) in the one required for deposition! Any advice? Thank you, Anna ######## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] CBMS Structural Biology Workbench
Dear All Reminder the last day of the CBMS Structural Biology workshop features a whole Day PHENIX Workshop starting at 8:30 am (EST) tomorrow, September 26 offered by the PHENIX Team members Dr Pavel Afonine and Dr. Oleg Sobolev. To attend register at register at https://bnl.zoomgov.com/meeting/register/vJItcOqpqzIoE_ErRfyE_f2PdhyDjyXmpGY Vivian To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Structural Biology Postdoc Opportunity in the Pegan Laboratory at UCR
Everyone, The Pegan laboratory is growing, and I am looking for a new postdoc to join us! Please share the below Ad with anyone or group that might be interested. https://medschool.ucr.edu/pegan-laboratory-post-doctoral-researcher-crimean-congo-hemorrhagic-fever<https://urldefense.com/v3/__https:/medschool.ucr.edu/pegan-laboratory-post-doctoral-researcher-crimean-congo-hemorrhagic-fever__;!!OLyWHuc!RBL4-7c8wrKOLRMyGTjKETWySJNle6IOrfHSDPIH_RKU1mwwf3jdpq4ObkKneCBDG1LlinWLdPArfEn9qT6Mlw$> Looking for someone to start any were from this Fall to Springtime. So, open to graduate students planning on graduating up to late next Spring. Scott -- Scott Pegan Professor Associate Dean Pre-Clerkship Medical Education School of Medicine University of California Riverside 205 SOM Research Building 900 University Avenue Riverside, CA 92521-0001 (951) 827 7907 sco...@medsch.ucr.edu<mailto:sco...@medsch.ucr.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Antechamber cannot determine atomic charge for Mn2+ to run PDB2PQR-APBS
Maybe you could try the CCPBioSim mailing list in case someone there could help. Best wishes James On 25 Sep 2024, at 19:19, Medhanjali Dasgupta wrote: Dear all, I am trying to generate the electrostatic surface for a protein that contains Mn in the 2+ state in its active site. I've tried to go about it in two ways but keep getting stuck. 1. If I use chimera or Pymol to use the PDB2PQR-APBS plug in, it cannot find GAFF type for Mn2+ so it cannot run anyechamber to allocate the atomic charge to Mn2+. Am i missing an update? Is there any way to get around this? Can I run antechamber myself to recognise my ion of interest, and then determine the charge, input it into the .pqr file and run APBS? 2. I have used the onkine server hosted at poissonboltzmann.org<http://poissonboltzmann.org/> to run pdb2pqr and apps but run into the problem of not knowing what the atomic charge is for Mn2+. Any ideas? Thanks in advance, Medhanjali To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Antechamber cannot determine atomic charge for Mn2+ to run PDB2PQR-APBS
Dear all, I am trying to generate the electrostatic surface for a protein that contains Mn in the 2+ state in its active site. I've tried to go about it in two ways but keep getting stuck. 1. If I use chimera or Pymol to use the PDB2PQR-APBS plug in, it cannot find GAFF type for Mn2+ so it cannot run anyechamber to allocate the atomic charge to Mn2+. Am i missing an update? Is there any way to get around this? Can I run antechamber myself to recognise my ion of interest, and then determine the charge, input it into the .pqr file and run APBS? 2. I have used the onkine server hosted at poissonboltzmann.org to run pdb2pqr and apps but run into the problem of not knowing what the atomic charge is for Mn2+. Any ideas? Thanks in advance, Medhanjali To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Integrative Structural Biology Seminar
*Dear colleagues,* It is a pleasure to annonce the * Integrative Structural Biology Symposium (ISBIN)* on the integrative use of NMR, cryo-electron microscopy, macromolecular crystallography (static and time-resolved), small-angle X-ray scattering and computation in Barcelona and at the nearby Alba Synchrotron on *November 14 and 15, 2024*. Save the date! Please find the *registration* link at https://indico.cells.es/e/ISBINsymposium There is no registration fee, but attendance could be limited by the capacity of the venue. Please register early not to miss this opportunity. Venues: November 14th: Barcelona Science Park November 15th: Alba synchrotron (30 Km from Barcelona). Transport from/to Barcelona will be provided. An optional visit to the synchrotron facilities is scheduled in the afternoon. Further information on the Spanish Integrative Structural Biology network: https://isbin.org All the best, The organizing committee, I. Usón, ICREA & Dep. Structural and Molecular Biology, IBMB-CSIC, Spain N. Verdaguer, Dep. Structural and Molecular Biology, IBMB-CSIC, Spain M. Solà, Dep. Structural and Molecular Biology, IBMB-CSIC, Spain J. Juanhuix, Head of Life Sciences Section, ALBA Synchrotron Light Source, Spain C. González, Dep. of Biological Physical Chemistry, IQF-CSIC, Spain O. Millet, CIC bioGUNE, Spain M. Pons, Dep. Organic Chemistry, Univ. of Barcelona, Spain -- Maria Solà Deputy director IBMB Dep. Structural and Molecular Biology IBMB-CSIC Baldiri Reixach 15 Barcelona Science Park 08028 BARCELONA Spain Tel: (+34) 93 403 4950 e-mail: maria.s...@ibmb.csic.es To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Postdoctoral Position - Ohio State University
Dear All, Applications are invited for a postdoctoral scientist position in the laboratory of Dr. Krishna Chinthalapudi at the Ohio State University. Our research focuses on the molecular mechanisms governing the *actin cytoskeleton* in health and disease, with particular emphasis on *myosin motors, membrane proteins,* and their regulation by actin cytoskeleton. We use an interdisciplinary approach, integrating *structural biology techniques* such as *cryo-electron microscopy (cryo-EM)* and *X-ray crystallography* with *biochemical*, *biophysical*, and *cell biology* methodologies. *Facilities and Resources: * My lab is equipped with cutting-edge instrumentation, with generous access to the *Titan Krios G3i Cryo-TEM* at the *Center for Electron Microscopy and Analysis (CEMAS)* at OSU. This includes: - BioQuantum imaging filter and K3 direct electron detector. - Phase plates for advanced imaging. - Image spherical aberration corrector. - *Glacios cryo-EM* with Falcon III detector and Ceta-D camera for *MicroED analysis*. *Qualifications:* - Ph.D. in *Structural Biology* or related field. - Strong experience in structural biology is required; prior work with *cryo-EM* is highly desirable. - Enthusiasm for exploring complex biological systems using state-of-the-art tools. *Application Instructions:* To apply, please submit the following: 1. *Curriculum Vitae*. 2. *Cover letter* summarizing your research experience and interests. 3. *Contact information* for two to three references. Please email the application materials to Krishna Chinthalapudi ( krishna.chinthalap...@osumc.edu). Sincerely, Krishna Chinthalapudi, PhD Assistant Professor Columbus, Ohio https://u.osu.edu/chinthalapudilab/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Post-doc position in protein crystallography, epigenetics and drug discovery at the City of Hope
Hi, We currently have a Postdoctoral Fellowship position open in protein crystallography and drug discovery as a joint position in the labs of Dr. Jianjun Chen, Chair of Department of Systems Biology and Dr. Jeff Perry, Assistant Professor in the Department of Molecular Diagnostics and Experimental Therapeutics, at City of Hope Medical Center in Los Angeles, California. The research is focused on fragment, and small molecule-based drug discovery approaches against RNA/DNA epigenetic targets, RNA methylation and post-transcriptional regulation, and includes determining structures of fragment, RNA probe, and small molecule:protein target co-complexes and using biophysical approaches, including thermal shift assays, isothermal calorimetry and/or surface plasmon resonance. For consideration, please send a single PDF that includes your CV, a cover letter briefly highlighting your previous research accomplishments and future research goals, and contact information of three scientific mentors (references) to Dr. Jianjun Chen at jianc...@coh.org and Dr. Jeff Perry at jpe...@coh.org. Thanks, Jeff Perry, Ph.D. Assistant Professor, City of Hope To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Senior Scientist ( X-ray crystallography, CryoEM)
Dear colleagues, I would like to bring to your attention the Senior Scientist position we currently have open in London. Please see the link below at our job site. Senior Scientist Protein and Structural Chemistry, London Discovery job in London, London, United Kingdom | Research & Development jobs at MSD<https://jobs.msd.com/gb/en/job/R312134/Senior-Scientist-Protein-and-Structural-Chemistry-London-Discovery> Please feel free to forward this message to anyone who might be interested in applying. Note, all applicants will need to apply through our jobs site (use link above). Please do not submit any applications directly to me. Best regards, Chitra Shintre Protein and Structural Chemistry MSD London UK Today MSD is a global healthcare leader working to help the world be well. MSD is a tradename of Merck & Co., Inc., Rahway, NJ., U.S.A. Through our prescription medicines, vaccines, biologic therapies, and consumer care and animal health products, we work with customers and operate in more than 140 countries to deliver innovative health solutions. We also demonstrate our commitment to increasing access to healthcare through far-reaching policies, programs and partnerships. For more information, visit www.msd.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] CryoEM Current Practices Webinar this week - 9/26/2024
Dear all, Please join the NIH supported CryoEM centers for our CryoEM Current Practices webinar this week. Time: Thursday, September 26, 2024 at 9 AM pacific / 12 PM eastern time Speaker: Bradley F. Guilliams, Department of Chemistry, Colorado State Title: Cryo-EM of a Cloneable Selenium Nanoparticle All are welcome to attend. Registration is at no-cost, but sign-up is required: https://us02web.zoom.us/webinar/register/WN_MN7mIhghQlenzjKtayffBw Please forward this posting to anyone that may be interested. Information about previous and future talks can be found at https://www.cryoemcenters.org/events/#cryoEM-webinar Best regards, National Center for CryoEM Access and Training To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Phenix.autobuild command problem
Dear Xin, I can see that your input model is from Buccaneer. I would just like to note that there has been recently done a lot of development in the program ModelCraft. It is now recommended to use ModelCraft (available in CCP4i2 or CCP4Cloud) rather than Buccaneer. If I were you, I would also try MrParse in CCP4 or 'Predict and Build: Crystallography' in Phenix for molecular replacement. These programs are very powerful. The input are only the diffraction data and a sequence; models for molecular replacement are prepared automatically from PDB entries and AlphaFold predictions. It may solve your problems relating to the long poly-ala sequnces in your current structure model. Best regards, Martin On 24/09/2024 08:35, zx2...@connect.hku.hk wrote: Dear Kay, Thank you for your reminder. I am encountering the following error messages: Sorry, the segment '' (residues 1:20 of chain 'D') could not be matched to sequence. Matching is required for rebuild_in_place. You might try supplying a different sequence file or no sequence file I have also attached the log file for your reference. Thank you very much for your assistance. Best regards, Xin *From:* CCP4 bulletin board on behalf of zx2...@connect.hku.hk *Sent:* 23 September 2024 09:13 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Phenix.autobuild command problem *This is an external email.* Dear all, I encountered an issue while running the following command with the attached files: BUCCANEER.pdb <https://connecthkuhk-my.sharepoint.com/:u:/g/personal/zx2020_connect_hku_hk/EaiKgmMxOS1Lg9BUIkXYdQcBbM3wshv-ZR1q5ssPpY5bJA> PHASER.1.mtz <https://connecthkuhk-my.sharepoint.com/:u:/g/personal/zx2020_connect_hku_hk/EcGf62NLnX9CmB-TGKn3_-gBKNsv7n-6ipzESzOWAyQR6Q> phenix.autobuild data=PHASER.1.mtz model=BUCCANEER.pdb The error message I received was: Interestingly, this error does not occur when I use the Phenix GUI with the default autobuild configuration. Could anyone help me troubleshoot this command line issue? Thank you very much! Best regards, Xin ---- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> ---- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Phenix.autobuild command problem
Dear Kay, Thank you for your reminder. I am encountering the following error messages: Sorry, the segment '' (residues 1:20 of chain 'D') could not be matched to sequence. Matching is required for rebuild_in_place. You might try supplying a different sequence file or no sequence file I have also attached the log file for your reference. Thank you very much for your assistance. Best regards, Xin From: CCP4 bulletin board on behalf of zx2...@connect.hku.hk Sent: 23 September 2024 09:13 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Phenix.autobuild command problem This is an external email. Dear all, I encountered an issue while running the following command with the attached files: [https://res.public.onecdn.static.microsoft/assets/mail/file-icon/png/generic_16x16.png]BUCCANEER.pdb<https://connecthkuhk-my.sharepoint.com/:u:/g/personal/zx2020_connect_hku_hk/EaiKgmMxOS1Lg9BUIkXYdQcBbM3wshv-ZR1q5ssPpY5bJA> [https://res.public.onecdn.static.microsoft/assets/mail/file-icon/png/generic_16x16.png]PHASER.1.mtz<https://connecthkuhk-my.sharepoint.com/:u:/g/personal/zx2020_connect_hku_hk/EcGf62NLnX9CmB-TGKn3_-gBKNsv7n-6ipzESzOWAyQR6Q> phenix.autobuild data=PHASER.1.mtz model=BUCCANEER.pdb The error message I received was: Interestingly, this error does not occur when I use the Phenix GUI with the default autobuild configuration. Could anyone help me troubleshoot this command line issue? Thank you very much! Best regards, Xin ____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ AUTOBUILD.log Description: AUTOBUILD.log
[ccp4bb] GSK Structural and biophysics positions
Structural and biophysics positions at GSK I am delighted to announce that GSK's Structural Biology CoE, located in Stevenage, UK, has opened recruitment for talented scientists in three distinct areas : Position description GSK<https://jobs.gsk.com/en-gb/jobs/405080?lang=en-us&previousLocale=en-GB> <https://jobs.gsk.com/en-gb/jobs/405080?lang=en-us&previousLocale=en-GB> careers<https://jobs.gsk.com/en-gb/jobs/405080?lang=en-us&previousLocale=en-GB> <https://jobs.gsk.com/en-gb/jobs/405080?lang=en-us&previousLocale=en-GB> websit<https://jobs.gsk.com/en-gb/jobs/405080?lang=en-us&previousLocale=en-GB>e<https://jobs.gsk.com/en-gb/jobs/405080?lang=en-us&previousLocale=en-GB> Role no Link Cryo-EM facility manager 405080 Cryo-EM Facilities Manager in Stevenage, United Kingdom | GSK Careers<https://jobs.gsk.com/en-gb/jobs/405080?lang=en-us&previousLocale=en-GB> Structural biologists with cryo-EM expertise 405085 Structural Biologist with cryo-EM Experience in Stevenage, United Kingdom | GSK Careers<https://jobs.gsk.com/en-gb/jobs/405085?lang=en-us&previousLocale=en-GB> Biophysics Group leader 405079 Biophysics Group leader in Stevenage, United Kingdom | GSK Careers<https://jobs.gsk.com/en-gb/jobs/405079?lang=en-us&previousLocale=en-GB> This is a fantastic opportunity to use your expertise in structural and biophysics sciences to impact drug discovery. You'll work across all modalities - NCE, Antibodies, Oligos, and Vaccines - in a vibrant environment. If contributing to the prevention and treatment of diseases interests you, I encourage you to take a look. We believe the varied talents within our team are what drive innovation and success. So, don't hesitate to let us know where your strengths lie. We look forward to hearing about what skills and perspectives you can bring to our team. Best wishes Chun-wa Chun-wa Chung Head Structural & Biophysical Sciences GSK R&D Stevenage SG1 2NY GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information. GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Phenix.autobuild command problem
Dear all, I encountered an issue while running the following command with the attached files: [https://res.public.onecdn.static.microsoft/assets/mail/file-icon/png/generic_16x16.png]BUCCANEER.pdb<https://connecthkuhk-my.sharepoint.com/:u:/g/personal/zx2020_connect_hku_hk/EaiKgmMxOS1Lg9BUIkXYdQcBbM3wshv-ZR1q5ssPpY5bJA> [https://res.public.onecdn.static.microsoft/assets/mail/file-icon/png/generic_16x16.png]PHASER.1.mtz<https://connecthkuhk-my.sharepoint.com/:u:/g/personal/zx2020_connect_hku_hk/EcGf62NLnX9CmB-TGKn3_-gBKNsv7n-6ipzESzOWAyQR6Q> phenix.autobuild data=PHASER.1.mtz model=BUCCANEER.pdb The error message I received was: Interestingly, this error does not occur when I use the Phenix GUI with the default autobuild configuration. Could anyone help me troubleshoot this command line issue? Thank you very much! Best regards, Xin To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] CASP conference this December
Check out the latest in the post-AlphaFold macromolecular structure prediction and see how the new methods are doing—all while enjoying some of the world’s best beaches! Over 80,000 predictions on about 100 prediction targets have been collected, covering methods for calculation of protein and nucleic acid structure, complexes, structure accuracy, conformational ensembles, and ligand binding (additional 30,000 predictions on 263 targets from pharma). Assessment is underway, but it’s already clear that once again, there are some pretty exciting results! The meeting will be in-person only. Both active participants in the experiment and anyone interested in recent advances in this field are invited to attend! Presentations are expected from independent assessors and from successful structure predictors. Discussions, poster presentations, and a job fair are also planned. Don’t wait, pre-registration closes soon! Visit predictioncenter.org/CASP16 now. Andriy Kryshtafovych for CASP organizers To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] HERCULES SCHOOL 2025: deadline is approaching!
*HERCULES 2025** - European School* /Neutron & Synchrotron Radiation Science since 1991/ *2025 **session**:**/ 9th March - 12th April, 2025/* DEADLINE FOR APPLICATION: 6 October 2024 HERCULES is a European course for PhD students and young researchers using *Neutrons* *and **Synchrotron Radiation* for applications in *Biology*, *Chemistry*, *Physics*, *Hard & Soft Condensed Matter*. The 5-week school includes *lectures* (60%), *hands-on practicals, labs &* *tutorials* (30%), visits, a poster session, group work sessions, ... /*P*//*articipants will spend one week in a partner institution*// in Europe among/: * *ALBA* in Barcelona, Spain * *PETRA III and EU-XFEL* in Hambourg, Germany * *KIT light source *in Karlsruhe, Germany * *SOLEIL *in Saint-Aubin, France This comes in addition to practicals, labs, and tutorials which will take place in Grenoble at *ILL*, *ESRF* and Grenoble Laboratories (*CNRS*, *IBS*). The school includes a common part and two parallel sessions: - /*Physics and chemistry of condensed matter (session A)*/ - /*Biomolecular and soft condensed matter (session B)*/ The school will be held in an hybrid format. Thus, a part-time online participation is also possible, consisting only in following online the lectures held in Grenoble during weeks 1, 2, 3 and 5. *_/Why join Hercules/_/?/* - to *learn new techniques using neutron and synchrotron radiation* - to expand your *theoretical *and* practical *knowledge, /not only for your present research but also for your scientific career/ - to *experiment these techniques* on world-class instruments & beamlines - to *build a network of relations* with fellow young researchers and experienced teachers from all over the World /*Bursaries/reduced costs*/ - A limited number of fellowship grants will be available to reduce registration fees * Full list of lectures: https://hercules-school.eu/general-programme (with links to the dedicated pages) * Download the full 2024 Booklet (lectures, practicals...) <https://hercules-school.eu/sites/default/files/file/booklets_schedules/Hercules2024_Booklet_Web.pdf> *Contact email*: hercu...@hercules-school.eu To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Job opportunity: Senior Scientist at Bicycle Therapeutics - Cambridge, UK
Dear all, I am thrilled to announce an exciting opportunity to join our innovative Structural Biology team at Bicycle Therapeutics - Cambridge, UK. If you are passionate about cutting-edge research and eager to contribute to groundbreaking advancements aimed at improving patients’ lives, please reach out! Follow the link below for the full job description and how to apply Senior Scientist, Structural Biology Best regards, Gustavo | | | | | | | | | | | Senior Scientist, Structural Biology Company Description: Bicycle Therapeutics is a clinical-stage pharmaceutical company developing a novel class of... | | | To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Head of a protein crystallography platform manager (Research engineer position) in Paris, France
Hello,Please could you post on ccp4bb this information about a position for a research engineer in our laboratory?Many thanks. Sincerely, To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 Offre-IR-CPB-09-2024-English.pdf Description: Adobe PDF document Dr Béatrice Golinelli-PimpaneauDirectrice de Recherches CNRSLaboratoire de Chimie des Processus BiologiquesCollège de France11 place Marcelin Berthelot75005 ParisFrance tel: 01 44 27 12 52fax: 01 44 27 14 83beatrice.goline...@college-de-france.frhttps://www.college-de-france.fr/site/chimie-processus-biologiques/index.htm To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
Re: [ccp4bb] Picture request: Evans & Sutherland Picture System 2 (PS2)
Someone has very kindly sent me a very good picture so the problem has now gone away, although I am happy to receive any other pictures out of nostalgic interest ;-0 Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android Original Message On 18/09/2024 22:11, Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > Does anyone have a decent photograph (preferably in colour and in a > crystallographic context) of an E&S PS2 which I could use in an article, > acknowledging the source? There is a very good one on a museum website but > they haven't replied in a few days. I have googled quite a lot and, yes, > Donald Sutherland and Sony PlayStations feature prominently in the results so > far... > > Best wishes, Jon Cooper. > jon.b.coo...@protonmail.com > > Sent from Proton Mail Android > > #### > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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] Picture request: Evans & Sutherland Picture System 2 (PS2)
Does anyone have a decent photograph (preferably in colour and in a crystallographic context) of an E&S PS2 which I could use in an article, acknowledging the source? There is a very good one on a museum website but they haven't replied in a few days. I have googled quite a lot and, yes, Donald Sutherland and Sony PlayStations feature prominently in the results so far... Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] CCP4 v9 installation issue
Dear all The issue with the CCP4 setup manager should be fixed now. If you still see a warning about write permissions, you can hopefully ignore that. Let us know if the problem persists. This error seemed to occur on some Linux distros, but not on all. All the best Ville CCP4 team To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Registration reminder for From first image to final structure with HexAuFoil grids - Tue 24 Sep 11am EST/ 4pm BST
Dear All, A quick reminder to register for the latest in our HexAuFoil webinar series next week. I'm also pleased to share that all registered participants will receive a 20% discount code, so they can try these exciting new grids for themselves! HexAuFoil® ultra-small hole gold grids: from first image to final structure Yehuda Halfon and Sebastian Porav, University of Leeds, UK Registration link: https://attendee.gotowebinar.com/register/2381405188368491349 Register today<https://register.gotowebinar.com/register/2381405188368491349> for our new webinar to hear about some of the first results achieved using HexAuFoil ultrasmall hole gold specimen supports, and discover how to ensure you get the best from your data collection and image processing with these exciting new grids. During the webinar you will learn about: * Sample preparation, grid screening and data collection with Yehuda Halfon of the University of Leeds, UK * Image processing and analysis with Sebastian Porav or the University of Leeds, UK HexAuFoil grids, the revolutionary new sample support, developed by Chris Russo and Katharina Naydenova of the MRC LMB in Cambridge, UK deliver consistent, thin ice across 9 million densely packed 300 nm holes on each grid. They have been commercially available from Quantifoil, part of SPT Labtech for almost 12 months. Register for our webinar to hear about some of the exciting results early users of these grids have achieved, and learn how to optimize your data collection and image processing to make the most of HexAuFoil sample supports in your research. Yehuda Halfon, University of Leeds, UK completed his PhD at the Weizmann Institute of Science in the laboratory of Ada Yonath. He then moved to the ICR in London where he undertook postdoctoral studies in the laboratory of Alessandro Vannini. In December 2021 he moved to the University of Leeds EM facility, where he now works as a CryoEM Scientist. Sebastian Porav, University of Leeds, UK completed his PhD under the supervision of Dr Nicolaie Dragos, and during his studies he worked as a research assistant in the Integrated Laboratory of Electron Microscopy at INCDTIM under the supervision of Dr Lucian Barbu. In February 2021 he moved to the University of Leeds where he now works as a research fellow on structural biology of TRPC ion channels in the laboratory Dr Stephen Muench and Dr Robin Bon. We hope to see some of you there! Thanks Claire Dr Claire Naylor | Product Marketing Manager | Quantifoil Micro Tools GmbH | +49 3641 639 3310 | +44 7790 307052 (direct dial) | In den Brückenäckern 4, 07751 Großlöbichau, Germany [cid:image001.jpg@01DB09B8.7D8DF790]<https://register.gotowebinar.com/register/2381405188368491349> quantifoil.com<https://www.quantifoil.com/> | LinkedIn<https://www.linkedin.com/company/quantifoil/> | Twitter<https://twitter.com/quantifoil> The information contained in this e-mail and any attachments is intended for the named recipient(s) only. It may also be privileged and confidential. If you are not an intended recipient, you must not copy, distribute or take any action in reliance upon it. Please notify the sender immediately by e-mail if you believe you have received this e-mail by mistake and delete this e-mail from your system. No warranties or assurances are made in relation to safety, content and/or any attachments. No liability is accepted for any consequences arising from it. No warranties are given by SPT Labtech Ltd, and no liability is accepted by SPT Labtech Ltd, in relation to any loss arising from reliance placed on the information supplied in this email and attachments, other than those warranties expressly stated in SPT Labtech Ltd's Standard Terms and Conditions of Sale. SPT Labtech Ltd's Standard Terms and Conditions of Sale apply at all times. SPT Labtech Ltd Plc, registered in England no. 3300999, Melbourn Science Park, Cambridge Road, Melbourn, SG8 6HB Tel +44(0)1223 627555, This email has been scanned for viruses and malware by ProofPoint #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] CBMS Lecture Series - CHAPPAZ - Wednesday September 18; 13:30pm
You are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. REMINDER ANTHONY CHAPPAZ Earth and Atmospheric Sciences Central Michigan University WEDNESDAY, September 18, 13:30 (EDT) "Molecular geochemistry of trace elements: Combining synchrotron-based techniques with systematic analyses to study heterogenous systems" Register in advance for this meeting: https://bnl.zoomgov.com/meeting/register/vJIsd-mgqzsuGDHvbSLQg-JnX85sBFha7fs Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https:/gcc02.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.worldtimebuddy.com*2F&data=05*7C01*7Cgenoa.blankenship*40pnnl.gov*7C67ffe754733240e42d3e08da641ba4bc*7Cd6faa5f90ae240338c0130048a38deeb*7C0*7C0*7C637932367171794987*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=aSe2IUSomjge9ZW6zXdQ81fPzxpg8eawtRkoiOEJdXM*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!P4SdNyxKAPE!Fd5kIAbibocFpkUaEbpqZZGm8tw-xiqb5oC4sfOklv6Kbbf-T3RvUobMSLrzyXNbfNVT9vMxJGuY1RsSqbc6MjpIABre1Q$> Abstract: Many redox sensitive trace elements present in organic-rich sedimentary rocks, such as black shales, are (1) recognized critical elements required to sustain the Green Energy Transition and (2) paleo-redox proxies used to reconstruct the Earth’s oxygenation. Either economic geologists exploring the potential of subsurface systems, or deep time geoscientists investigating the first traces of oxygen recorded by geological settings billion years ago, keep applying bulk geochemistry analyses of trace elements. This common approach relies on measuring the concentration and, when possible, the isotope ratio and has led to significant findings. Yet, major limitations, like strong heterogeneities, exist and hamper our capabilities to either develop new sustainable mining methods or capture subtle changes in redox conditions that occurred in ancient oceans. Integrating synchrotron-based techniques to enhance our understanding of trace element geochemistry can lead to major breakthroughs. Three examples focusing on chromium, molybdenum and vanadium geochemistry will be presented during my lecture. = Vivian Stojanoff, PhD Education, Training, Outreach User Program p 1(631) 344 8375 e lifescie...@bnl.gov<mailto:lifescie...@bnl.gov> w https://www.bnl.gov/ps/lifesciences/<https://www.bnl.gov/ps/lsbr/> Address: Center for Biomolecular Structure National Synchrotron Light Source II Building 745 Brookhaven National Laboratory Upton NY 11973 #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Job opportunity: Scientist Position in the X-ray Crystallography Center at St. Jude
Dear all, The Biomolecular X-ray Crystallography Center<https://www.stjude.org/research/departments/structural-biology/biomolecular-xray-crystallography-center.html> at St. Jude Children's Research Hospital<https://www.stjude.org/> is seeking a motivated scientist to provide a central service-level support role in the lab. The Center is housed in the Department of Structural Biology<https://www.stjude.org/research/departments/structural-biology.html> and serves St. Jude researchers in all aspects of X-ray crystallography. The Ideal Candidate will be: * Interested in supporting Center goals towards research, training, and education. * A protein crystallographer with expertise in ligand discovery. * A well-organized team player that is eager to learn and contribute to a highly collaborative environment. Responsibilities: * Perform crystallization, crystal optimization, crystal harvesting, data collection, data processing, structure determination, model building and refinement. * Provide general user support and training in various aspects of crystallography. * Maintain the in-house x-ray diffractometer and train on usage. * Provide user support for remote synchrotron data collection. * Deliver high quality results and clearly communicate results to stakeholders. * Keep detailed records and follow SOPs. * Maintain regular attendance during normal business hours. * Seeking a flexible team player ready to join a fast-paced and scientifically rigorous Center in support of the Structural Biology Department and St. Jude. * Due to the nature of this facility, there will be an occasional need to work onsite during overnight or weekend hours. This is a stably funded position that is not reliant on grant funding. Additionally, St. Jude is located in Memphis, TN, an affordable city with plenty to offer. Direct Applications Here: https://talent.stjude.org/careers/jobs/JR3081?lang=en-us Regards, Darcie Miller, PhD Director, X-ray Crystallography Center Department of Structural Biology St. Jude Children’s Research Hospital 262 Danny Thomas Place, Mail Stop 314 Memphis, Tennessee 38105 Phone: (901) 595-6277 [cid:77a317d8-7990-43fa-b0e5-3959ea333f82] Email Disclaimer: www.stjude.org/emaildisclaimer Consultation Disclaimer: www.stjude.org/consultationdisclaimer To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] SMILES from PDB records (HELP-21524)
Dear Doeke,
Here is the process we recommend:
For now you can get the entire collection of ligand definitions at
http://www.wwpdb.org/data/ccd, using the file
https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
From there you would parse the SMILES from _pdbx_chem_comp_descriptor.
You can also use RCSB.org data API as described at
https://data.rcsb.org/#gql-example-7
Select "OPEN IN EDITOR" and add a chemical descriptor component search
as follows:
{
chem_comps(comp_ids:["NAG", "EBW"]) {
rcsb_id
chem_comp {
type
formula_weight
name
formula
}
pdbx_chem_comp_descriptor {
type
descriptor
}
rcsb_chem_comp_info {
initial_release_date
}
}
}
Then, you can get all IDs either using a "grep data_" command from the
file downloaded above, or by using the RCSB Advanced Search >> Chemical
Attributes >> Chemical IDs(s)>> "is not empty"
<https://www.rcsb.org/search?request=%7B%22query%22%3A%7B%22type%22%3A%22group%22%2C%22logical_operator%22%3A%22and%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22logical_operator%22%3A%22and%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22terminal%22%2C%22service%22%3A%22text_chem%22%2C%22parameters%22%3A%7B%22attribute%22%3A%22rcsb_chem_comp_container_identifiers.comp_id%22%2C%22operator%22%3A%22exists%22%2C%22negation%22%3Afalse%7D%7D%5D%2C%22logical_operator%22%3A%22and%22%7D%5D%2C%22label%22%3A%22text_chem%22%7D%5D%7D%2C%22return_type%22%3A%22entry%22%2C%22request_options%22%3A%7B%22paginate%22%3A%7B%22start%22%3A0%2C%22rows%22%3A25%7D%2C%22results_content_type%22%3A%5B%22experimental%22%5D%2C%22sort%22%3A%5B%7B%22sort_by%22%3A%22score%22%2C%22direction%22%3A%22desc%22%7D%5D%2C%22scoring_strategy%22%3A%22combined%22%7D%2C%22request_info%22%3A%7B%22query_id%22%3A%22757e2e66d52ec03ec085a0c4cc2ba0ba%22%7D%7D>
. Using the "Search API" button will then bring you to:
{
"query": {
"type": "terminal",
"label": "text_chem",
"service": "text_chem",
"parameters": {
"attribute": "rcsb_chem_comp_container_identifiers.comp_id",
"operator": "exists",
"negation": false
}
},
"return_type": "entry",
"request_options": {
"paginate": {
"start": 0,
"rows": 25
},
"results_content_type": [
"experimental"
],
"sort": [
{
"sort_by": "score",
"direction": "desc"
}
],
"scoring_strategy": "combined"
}
}
Please feel free to write to us at i...@rcsb.org if you have any questions.
Sincerely,
Rachel Green
-
*RACHEL KRAMER GREEN, PH.D.*
Scientific Support & Customer Service Lead
RCSB Protein Data Bank
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
rachel.gr...@rcsb.org
rcsb.org <http://rcsb.org/>| facebook
<https://www.facebook.com/RCSBPDB> | twitter
<https://twitter.com/buildmodels>_
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Coronavirus Resources: RCSB.org/covid19 <http://RCSB.org/covid19>
Undergraduates and Graduates: Opportunities for Scientific
Software-focused Summer Research, Gap Year, and Postdoctoral Research:
www.rcsb.org/pages/jobs <http://www.rcsb.org/pages/jobs>
On 9/13/2024 9:28 AM, Hekstra, Doeke Romke wrote:
Hi,
Does anyone have experience (or scripts!) to extract ligand SMILES
from macromolecular PDB records using the PDB data API or from a
library of PDB or mmCIF files? We would greatly appreciate any
pointers to get us started.
Thank you,
Doeke
=
Doeke Hekstra
Assistant Professor of Molecular & Cellular Biology, and of Applied
Physics (SEAS),
Director of Undergraduate Studies, Chemical and Physical Biology
Center for Systems Biology, Harvard University
52 Oxford Street, NW311
Cambridge, MA 02138
Office: 617-496-4740
Admin: 617-495-5651 (Lin Song)
--------
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Re: [ccp4bb] SMILES from PDB records
components.cif file from https://www.wwpdb.org/data/ccd has SMILES strings for all monomers in the PDB. Best, Marcin On Fri, Sep 13, 2024 at 5:28 PM Hekstra, Doeke Romke wrote: > > Hi, > > > > Does anyone have experience (or scripts!) to extract ligand SMILES from > macromolecular PDB records using the PDB data API or from a library of PDB or > mmCIF files? We would greatly appreciate any pointers to get us started. > > > > Thank you, > > Doeke > > > > = > > > > Doeke Hekstra > > Assistant Professor of Molecular & Cellular Biology, and of Applied Physics > (SEAS), > > Director of Undergraduate Studies, Chemical and Physical Biology > > Center for Systems Biology, Harvard University > > 52 Oxford Street, NW311 > > Cambridge, MA 02138 > > Office:617-496-4740 > > Admin: 617-495-5651 (Lin Song) > > > > > > > > > ____ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 #### To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] SMILES from PDB records
I have used this web site to generate SMILES strings from PDB coordinates. You need to strictly examine the output to ensure that you get the proper chirality, bond order and correct number of hydrogens, and if there are discrepancies you may have to edit the string. Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) On Sep 13, 2024, at 10:28 AM, Hekstra, Doeke Romke wrote: EXTERNAL MAIL Hi, Does anyone have experience (or scripts!) to extract ligand SMILES from macromolecular PDB records using the PDB data API or from a library of PDB or mmCIF files? We would greatly appreciate any pointers to get us started. Thank you, Doeke = Doeke Hekstra Assistant Professor of Molecular & Cellular Biology, and of Applied Physics (SEAS), Director of Undergraduate Studies, Chemical and Physical Biology Center for Systems Biology, Harvard University 52 Oxford Street, NW311 Cambridge, MA 02138 Office:617-496-4740 Admin: 617-495-5651 (Lin Song) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!MznTZTSvDXGV0Co!GPbhXSnaWPxjCLmQuuy9EfcXLQsBXcNcyCuHjqJhfqOoNq9ubSUeD9W3yhtZhQ4PtLlYEhJrEOW__WP78mYhm7jtHym8xLQtPMk_omJS$> CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. UT Southwestern Medical Center The future of medicine, today. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] SMILES from PDB records
Hi, Does anyone have experience (or scripts!) to extract ligand SMILES from macromolecular PDB records using the PDB data API or from a library of PDB or mmCIF files? We would greatly appreciate any pointers to get us started. Thank you, Doeke = Doeke Hekstra Assistant Professor of Molecular & Cellular Biology, and of Applied Physics (SEAS), Director of Undergraduate Studies, Chemical and Physical Biology Center for Systems Biology, Harvard University 52 Oxford Street, NW311 Cambridge, MA 02138 Office:617-496-4740 Admin: 617-495-5651 (Lin Song) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Opening: RCSB PDB Director and Tenured Professor of Chemistry and Chemical Biology
-field nuclear magnetic resonance, biomedical research innovation and mass spectrometry, X-ray, and microscopy core facilities. The RCSB PDB Director will leverage collaborative opportunities across units and University core facilities at the Institute for Quantitative Biomedicine—including cryo-electron microscopy and macromolecular mass spectrometry—to drive leadership and innovation in structural biology, making breakthrough innovations at the intersection of chemistry, data science, biology, and medicine. Rutgers is a leading national research university and the State of New Jersey’s preeminent, comprehensive public institution of higher education, committed to building a beloved community through University Equity and Inclusion. Established in 1766, the university is the eighth-oldest higher education institution in the United States. More than 70,000 students and 23,400 full- and part-time faculty and staff learn, work, and serve the public at Rutgers locations across New Jersey and around the world. Our community values leadership, respect, innovation and creativity, research and scholarship, integrity, and teamwork. -- CHRISTINE ZARDECKI Associate Director, RCSB Protein Data Bank Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 E: christine.zarde...@rcsb.org RCSB.org | facebook <https://www.facebook.com/RCSBPDB> | twitter <https://twitter.com/buildmodels> Coronavirus Resources: RCSB.org/covid19 <https://rcsb.org/covid19> Undergraduates and Graduates: Opportunities for Scientific Software-focused Summer Research, Gap Year, and Postdoctoral Research: www.rcsb.org/pages/jobs To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] CryoEM Current Practices Webinar - 06/27/2024
Dear all, Please join the NIH supported CryoEM centers at our next CryoEM Current Practices webinar. Time: Thursday, September 26, 2024 at 9 AM pacific / 12 PM eastern time Speaker: Bradley F. Guilliams, Department of Chemistry, Colorado State Title: Cryo-EM of a Cloneable Selenium Nanoparticle All are welcome to attend. Registration is at no-cost, but sign-up is required: https://us02web.zoom.us/webinar/register/WN_MN7mIhghQlenzjKtayffBw Please forward this posting to anyone that may be interested. Information about previous and future talks can be found at https://www.cryoemcenters.org/events/#cryoEM-webinar Best regards, National Center for CryoEM Access and Training To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] CCP4 v9 installation issue
I didn't dig into the underlying cause, but I can verify your experience, I had similar things happen under Alma Linux 9. Installation works fine under a non-root account. === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: CCP4 bulletin board on behalf of Oliver H. Weiergräber Sent: Thursday, September 12, 2024 4:20 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] CCP4 v9 installation issue Dear community, I am running into an unexpected problem while trying to install CCP4 v9 on a RHEL8 workstation. The installer (run as root) complains about missing write permission for the target directory (a subdirectory of /usr/local), which is simply not true. Both standard Unix permissions and SElinux settings are as expected (and as used successfully in the past). Is it possible that for some reason the v9 installer erroneously checks with the (non-root) user running the graphical interface, instead with the user actually running the installer? Best regards Oliver Weiergräber == Prof. Oliver H. Weiergräber Institute of Biological Information Processing IBI-7: Structural Biochemistry Forschungszentrum Jülich 52425 Jülich, Germany Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 == To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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] Postdoc position available
Dear all, We seek a talented individual to fill a postdoctoral position (at the Central European Institute of Technology (CEITEC), Masaryk University Brno, Czech Republic.) with expertise in the field of cryo-electron microscopy and translation regulation. Ideal candidates should possess a solid foundation in biochemistry or structural biology, particularly in single-particle cryo-electron microscopy or protein crystallography. For more details, please visit our website https://demolab.ceitec.cz/<https://urldefense.com/v3/__https://demolab.ceitec.cz/__;!!Mih3wA!AOeRxrJxz8x48ffs5LR1eOYxXK9xZmU6tKgVqjorEz26LzG1SQy4sfmSCFxPNXCCfawKXR7qpNXTu5fJE6E6NsAeL3NftJ0$> and the postdoctoral position offer https://www.ceitec.eu/postdoctoral-fellow-in-the-research-group-of-gabriel-demo/j500<https://urldefense.com/v3/__https://www.ceitec.eu/postdoctoral-fellow-in-the-research-group-of-gabriel-demo/j500__;!!Mih3wA!AOeRxrJxz8x48ffs5LR1eOYxXK9xZmU6tKgVqjorEz26LzG1SQy4sfmSCFxPNXCCfawKXR7qpNXTu5fJE6E6NsAeM0HjSVI$>. To apply, please submit your CV, along with contact information for three referees, and a brief motivational letter to recruitm...@ceitec.muni.cz. The deadline for applications is September 30th, 2024. Best regards, -- Mgr. Gabriel Demo, PhD. | CEITEC MU Junior Group Leader tel: +420 549 49 7827 e-mail: gabriel.d...@ceitec.muni.cz<mailto:michaela.ambroz...@ceitec.muni.cz> web: www.ceitec.cz<http://www.ceitec.eu/> Masarykova univerzita Central European Institute of Technology Kamenice 5, 625 00 Brno Kancelář A35/1S155 #CEITECScience facebook<https://www.google.com/url?q=https://www.google.com/url?q%3Dhttps://www.facebook.com/CEITEC%26amp;sa%3DD%26amp;ust%3D1573738541933000&sa=D&ust=1573738541948000&usg=AFQjCNG1Zetlph45-JLQLqL3PbgcUtN4Eg> | twitter<https://www.google.com/url?q=https://www.google.com/url?q%3Dhttps://twitter.com/ceitec_brno%26amp;sa%3DD%26amp;ust%3D1573738541933000&sa=D&ust=1573738541949000&usg=AFQjCNHzIySbcz__Cqd3lZGyPgQrbeC39Q> | instagram<https://www.google.com/url?q=https://www.google.com/url?q%3Dhttps://www.instagram.com/ceitec_brno/%26amp;sa%3DD%26amp;ust%3D1573738541933000&sa=D&ust=1573738541949000&usg=AFQjCNHnuEB8QexF1oZPwYPzxJM3EAiVJw> | linkedin<https://www.google.com/url?q=https://www.google.com/url?q%3Dhttps://www.linkedin.com/company/2373756/%26amp;sa%3DD%26amp;ust%3D1573738541933000&sa=D&ust=1573738541949000&usg=AFQjCNEmVc6-Q7xwH8DnslMkU_atrNTY2w> | youtube<https://www.google.com/url?q=https://www.google.com/url?q%3Dhttps://www.youtube.com/user/CEITECcz%26amp;sa%3DD%26amp;ust%3D1573738541933000&sa=D&ust=1573738541949000&usg=AFQjCNEVlkGKz9w6EBf_zJz7OpcQo8f-tA> [E6CD5E50] To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] CCP4 v9 installation issue
Dear community, I am running into an unexpected problem while trying to install CCP4 v9 on a RHEL8 workstation. The installer (run as root) complains about missing write permission for the target directory (a subdirectory of /usr/local), which is simply not true. Both standard Unix permissions and SElinux settings are as expected (and as used successfully in the past). Is it possible that for some reason the v9 installer erroneously checks with the (non-root) user running the graphical interface, instead with the user actually running the installer? Best regards Oliver Weiergräber == Prof. Oliver H. Weiergräber Institute of Biological Information Processing IBI-7: Structural Biochemistry Forschungszentrum Jülich 52425 Jülich, Germany Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 == To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ smime.p7s Description: S/MIME Cryptographic Signature
[ccp4bb] 12th International Workshop on Radiation Damage to Biological Samples, PSI, Switzerland 3rd-5th June 2025.
Workshop Announcement: The 12th International Workshop on Radiation Damage to Biological Samples will be held in person at the Paul Scherrer Institut, Villigen PSI, Switzerland 3rd-5th June 2025. The Workshop will address essential questions and challenges of radiation damage to biological samples during their examination with ionizing radiation. The workshop will cover various X-ray and electron scattering techniques, from crystallography to imaging, and offers ample opportunities for information exchange and discussion among researchers from around the globe. Additionally, participants will have the chance to visit the newly upgraded Swiss Light Source (SLS 2.0) and the Swiss X-ray Free Electron Laser (SwissFEL). Further details will be available shortly. ** If you have suggestions for speakers please send them to elspeth.gar...@bioch.ox.ac.uk<mailto:elspeth.gar...@bioch.ox.ac.uk> or martin.w...@ibs.fr<mailto:martin.w...@ibs.fr> ** Elspeth F. Garman, Professor of Molecular Biophysics (Emerita), Supernumerary Fellow (Emerita), Brasenose College, University of Oxford Postal address: Department of Biochemistry Dorothy Crowfoot Hodgkin Building Oxford, OX1 3QU, U.K E-mail: elspeth.gar...@bioch.ox.ac.uk<mailto:elspeth.gar...@bioch.ox.ac.uk> https://www.bioch.ox.ac.uk/garmangroup - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Workshop on "Temperature in macromolecular crystallo
Dear CCP4 community, of course I got the date wrong: The workshop will happen on Monday, September 23rd 2024... At least you won't have to travel back in time to be able to attend this awesome workshop. Cheers, Dominik Dear CCP4 community, I am excited to announce an upcoming workshop on Temperature-Controlled Crystallography, where we will explore the latest techniques, applications, and advancements, including time-resolved methods and multidimensional serial crystallography approaches. This workshop is an excellent opportunity to discuss challenges and opportunities of macromolecular crystallography at room temperature and beyond, learn from leading experts and engage with cutting-edge research in the field. Speakers include: Marius Schmidt, Gisela Branden, Eike C. Schulz, Alessandra Henkel, Sebastian Günther, Chia-Ying Huan, Daniel Keedy, Michael Thompson and Silvia Russi. The workshop is part of this years SSRL/LCLS Users' Meeting (https://web.cvent.com/event/8c2bdf8d-08a1-41c5-b24e-390d039d9be2/summary) and will take place on Monday, September 9th 2024 from 8 am to 12 pm (PDT). Apart from the exciting workshop the Users' Meeting features a bunch of other very interesting workshops on e.g. data analysis, Application of Cryo-EM in Molecular and Cell Biology, Computational Methods in Structural Biology, Metals in Structural Biology and MFX-HE: Opportunities for High-Throughput Multimodal Structural Studies and Their Computational Challenges, that should be very relevant for this community. If you haven't done so, you can still register here: https://web.cvent.com/event/8c2bdf8d-08a1-41c5-b24e-390d039d9be2/register Looking forward to seeing you all at SLAC in the end of September! Cheers, Dominik -- Dr. Dominik Oberthür CFEL - Center for Free-Electron Laser Science - DESY Coherent Imaging Division Notkestrasse 85 22607 Hamburg Germany phone: +49 (0)40 8998 6394 dominik.oberth...@cfel.de To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Workshop on "Temperature in macromolecular crystallo
Dear CCP4 community, I am excited to announce an upcoming workshop on Temperature-Controlled Crystallography, where we will explore the latest techniques, applications, and advancements, including time-resolved methods and multidimensional serial crystallography approaches. This workshop is an excellent opportunity to discuss challenges and opportunities of macromolecular crystallography at room temperature and beyond, learn from leading experts and engage with cutting-edge research in the field. Speakers include: Marius Schmidt, Gisela Branden, Eike C. Schulz, Alessandra Henkel, Sebastian Günther, Chia-Ying Huan, Daniel Keedy, Michael Thompson and Silvia Russi. The workshop is part of this years SSRL/LCLS Users' Meeting (https://web.cvent.com/event/8c2bdf8d-08a1-41c5-b24e-390d039d9be2/summary) and will take place on Monday, September 9th 2024 from 8 am to 12 pm (PDT). Apart from the exciting workshop the Users' Meeting features a bunch of other very interesting workshops on e.g. data analysis, Application of Cryo-EM in Molecular and Cell Biology, Computational Methods in Structural Biology, Metals in Structural Biology and MFX-HE: Opportunities for High-Throughput Multimodal Structural Studies and Their Computational Challenges, that should be very relevant for this community. If you haven't done so, you can still register here: https://web.cvent.com/event/8c2bdf8d-08a1-41c5-b24e-390d039d9be2/register Looking forward to seeing you all at SLAC in the end of September! Cheers, Dominik -- Dr. Dominik Oberthür CFEL - Center for Free-Electron Laser Science - DESY Coherent Imaging Division Notkestrasse 85 22607 Hamburg Germany phone: +49 (0)40 8998 6394 dominik.oberth...@cfel.de To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
