Re: [ccp4bb] Michael Rossmann (1930-2019)
During the few years that I had the opportunity to work with Michael Rossmann, I found him to be not only a great scientist but a fine and humble gentleman, who will be missed. -Daniel On Tue, May 14, 2019 at 9:13 PM Hasan, Syed Saif wrote: > Dear Colleagues, > > > It is with profound sadness that I must announce the passing away of Prof. > Michael Rossmann earlier today on May 14th 2019 in West Lafayette IN. > Michael was a giant in the field of structural biology with a lot of > “firsts” to his credit including the structure of lactate dehydrogenase and > the discovery of the Rossmann fold, the first common cold virus structure, > and the first Dengue and Zika virus structures to name just a few. Michael > made seminal contributions to methods development in structural > biology including the development of molecular replacement. > > > A memorial service is being planned at the University Place in West > Lafayette, Indiana, on May 24th. > > > Please see Purdue University’s press release ( > https://www.purdue.edu/newsroom/releases/2019/Q2/renowned-purdue-university-scientist-michael-rossmann-dies.html), > with a note from President Mitch Daniels. > > > Michael will forever be missed. > > Saif > > > S. Saif Hasan, PhD > > > Assistant Professor > Department of Biochemistry and Molecular Biology, University of Maryland > School of Medicine, 108 N. Greene St., Baltimore, MD 21201 > > AND > > Center for Biomolecular Therapeutics (CBT), 9600 Gudelsky Drive, > Rockville, MD 20850 > > > Fellow > > Institute for Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky > Drive, Rockville, MD 20850 > Phone: 240-314-6396 > Fax: 240-314-6225 > > https://www.ibbr.umd.edu/profiles/s-saif-hasan > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] On estimating Unit Structure Factor distribution
Dear Pavel, This is great, thank you so much! I shall try it ASAP. Thank you much for the very kind help. Best wishes, Em qua, 15 de mai de 2019 às 17:52, Pavel Afonine escreveu: > Hi Andre, > > here is the link to cctbx-based code that computes Uhkl according to your > formula below, using model mean B and F000 that accounts for atomic model > and bulk-solvent: > > https://www.dropbox.com/sh/g7sp7pqxst4ldj0/AAD1whlVD2mvAGoRa5jOF-fla?dl=0 > > I leave it up to you to read and understand the script, as well as > ensuring it works as you expect (bug-free!). I hope it exemplifies enough > for you to pick up from there and modify it the way you wish. The only test > I did is I made sure it runs and outputs and MTZ file! > > Good luck, > Pavel > > On Wed, May 15, 2019 at 3:20 PM Andre LB Ambrosio > wrote: > >> Dear all, >> >> We seek to calculate the distribution of Unitary Structure Factors, Uhkl, >> from a few datasets (at different maximum resolutions) for which the >> corresponding atomic models are already available at the PDB; this >> according to the formula (6.4), in the 2nd edition of Jan Drenth´s book: >> >> Uhkl = exp[B*(sin^2(theta)/lambda^2)] x FOBShkl / F(000) >> >> Hence, the following questions: >> >> - Is there any macromolecular crystallography software that can compute >> Uhkl as above, or equivalent? >> >> - If not, would it be more correct to use the Wilson-B or the mean B from >> the final model? >> >> - How can F(000) be best estimated from the final model, which is not >> necessarily always the most complete or best refined? Should we simply add >> together the number of electrons for all the atoms refined in the >> asymmetric unit (protein + ligands + solvent)? >> >> Many thanks in advance and best wishes, >> >> -- >> Andre LB Ambrosio >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> > -- Andre LB Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] On estimating Unit Structure Factor distribution
Hi Andre, here is the link to cctbx-based code that computes Uhkl according to your formula below, using model mean B and F000 that accounts for atomic model and bulk-solvent: https://www.dropbox.com/sh/g7sp7pqxst4ldj0/AAD1whlVD2mvAGoRa5jOF-fla?dl=0 I leave it up to you to read and understand the script, as well as ensuring it works as you expect (bug-free!). I hope it exemplifies enough for you to pick up from there and modify it the way you wish. The only test I did is I made sure it runs and outputs and MTZ file! Good luck, Pavel On Wed, May 15, 2019 at 3:20 PM Andre LB Ambrosio wrote: > Dear all, > > We seek to calculate the distribution of Unitary Structure Factors, Uhkl, > from a few datasets (at different maximum resolutions) for which the > corresponding atomic models are already available at the PDB; this > according to the formula (6.4), in the 2nd edition of Jan Drenth´s book: > > Uhkl = exp[B*(sin^2(theta)/lambda^2)] x FOBShkl / F(000) > > Hence, the following questions: > > - Is there any macromolecular crystallography software that can compute > Uhkl as above, or equivalent? > > - If not, would it be more correct to use the Wilson-B or the mean B from > the final model? > > - How can F(000) be best estimated from the final model, which is not > necessarily always the most complete or best refined? Should we simply add > together the number of electrons for all the atoms refined in the > asymmetric unit (protein + ligands + solvent)? > > Many thanks in advance and best wishes, > > -- > Andre LB Ambrosio > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] On estimating Unit Structure Factor distribution
Dear James, Many thanks for this! I will follow all the suggestions described above. With best wishes, Andre. Em qua, 15 de mai de 2019 às 14:59, Holton, James M < jmhol...@slac.stanford.edu> escreveu: > The CCP4 program you are looking for is "cad". Using the "SCALE" keyword > you can apply an overall positive or negative B factor to any mtz data > set. Negative B factors are sharpening, which is what you are trying to do. > > There is also another program called "ecalc", which is specifically > designed for computing normalized structure factors like "U", which is > closely related to "E". > > As for which B factor to apply? Ostensibly the Wilson B factor and the > average atomic B factor should be the same number. The Wilson B, however, > is prone to systematic errors arising from how you decide which resolution > range to fit. There are also details about the distribution of B factors > in the model and the relative abundance of different atomic numbers. > However, I've always found these considerations dwarfed by the errors in > estimating the Wilson B. Depending on what you are trying to accomplish, > you might want to raise your B factor a bit anyway to reduce the overall > noise. > > > As for F000, another article describing its estimation is here: > https://doi.org/10.1073/pnas.1302823110 > > Script from that publication for calculating F000 is here: > https://bl831.als.lbl.gov/END/RAPID/scripts/find_F000.com > > This script requires the CCP4 Suite and the Phenix Suite version 1.6 or > lower. This was the last version of phenix.refine that reported k_sol and > B_sol for the bulk solvent. Without these, you cannot calculate the number > of electrons in the bulk solvent. > > Alternately, if you have run refmac you can look through the log for the > string: "Partial structure1: scale = " > The "scale =" and "B =" numbers that follow are the k_sol and B_sol for > the bulk solvent. You can then provide these numbers on the command line > of the find_F000.com script above. Then again, if you have already run > refmac it might be simpler to provide the MSKOUT command-line parameter to > refmac. This will output the bulk solvent as a CCP4 map file. Once you > have that, all you need to do is run "mapdump" to report the average value > of the electron density in this map. You multiply this by the k_sol value > from the log and then multiply by the unit cell volume and you now have the > number of electrons in the bulk solvent. Add up all the atomic numbers in > your PDB file (including hydrogen) and you have the rest of the electrons > in your unit cell. The sum of all electrons in one unit cell is F000. > > HTH > > -James Holton > MAD Scientist > > On 5/15/2019 5:52 AM, Andre LB Ambrosio wrote: > > Dear Pavel, thank you so very much for the prompt feedback. > That would be extremely useful if you could script the Uhkl calculation in > CCTBX. > With best regards, > Andre. > > Em qua, 15 de mai de 2019 às 09:47, Pavel Afonine > escreveu: > >> Hi Andre, >> >> >>> - Is there any macromolecular crystallography software that can compute >>> Uhkl as above, or equivalent? >>> >> >> I estimate this can take about 10 minutes to script in CCTBX. I can write >> a script for you, if interested, and send off list. >> >> >>> - If not, would it be more correct to use the Wilson-B or the mean B >>> from the final model? >>> >> >> I'd guess mean B from the model is a better estimate. >> >> - How can F(000) be best estimated from the final model, which is not >>> necessarily always the most complete or best refined? Should we simply add >>> together the number of electrons for all the atoms refined in the >>> asymmetric unit (protein + ligands + solvent)? >>> >> >> See my previous email. >> >> Pavel >> >> > > > -- > Andre LB Ambrosio > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > -- Andre LB Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] On estimating Unit Structure Factor distribution
The CCP4 program you are looking for is "cad". Using the "SCALE" keyword you can apply an overall positive or negative B factor to any mtz data set. Negative B factors are sharpening, which is what you are trying to do. There is also another program called "ecalc", which is specifically designed for computing normalized structure factors like "U", which is closely related to "E". As for which B factor to apply? Ostensibly the Wilson B factor and the average atomic B factor should be the same number. The Wilson B, however, is prone to systematic errors arising from how you decide which resolution range to fit. There are also details about the distribution of B factors in the model and the relative abundance of different atomic numbers. However, I've always found these considerations dwarfed by the errors in estimating the Wilson B. Depending on what you are trying to accomplish, you might want to raise your B factor a bit anyway to reduce the overall noise. As for F000, another article describing its estimation is here: https://doi.org/10.1073/pnas.1302823110 Script from that publication for calculating F000 is here: https://bl831.als.lbl.gov/END/RAPID/scripts/find_F000.com This script requires the CCP4 Suite and the Phenix Suite version 1.6 or lower. This was the last version of phenix.refine that reported k_sol and B_sol for the bulk solvent. Without these, you cannot calculate the number of electrons in the bulk solvent. Alternately, if you have run refmac you can look through the log for the string: "Partial structure1: scale = " The "scale =" and "B =" numbers that follow are the k_sol and B_sol for the bulk solvent. You can then provide these numbers on the command line of the find_F000.com script above. Then again, if you have already run refmac it might be simpler to provide the MSKOUT command-line parameter to refmac. This will output the bulk solvent as a CCP4 map file. Once you have that, all you need to do is run "mapdump" to report the average value of the electron density in this map. You multiply this by the k_sol value from the log and then multiply by the unit cell volume and you now have the number of electrons in the bulk solvent. Add up all the atomic numbers in your PDB file (including hydrogen) and you have the rest of the electrons in your unit cell. The sum of all electrons in one unit cell is F000. HTH -James Holton MAD Scientist On 5/15/2019 5:52 AM, Andre LB Ambrosio wrote: Dear Pavel, thank you so very much for the prompt feedback. That would be extremely useful if you could script the Uhkl calculation in CCTBX. With best regards, Andre. Em qua, 15 de mai de 2019 às 09:47, Pavel Afonine mailto:pafon...@gmail.com>> escreveu: Hi Andre, - Is there any macromolecular crystallography software that can compute Uhkl as above, or equivalent? I estimate this can take about 10 minutes to script in CCTBX. I can write a script for you, if interested, and send off list. - If not, would it be more correct to use the Wilson-B or the mean B from the final model? I'd guess mean B from the model is a better estimate. - How can F(000) be best estimated from the final model, which is not necessarily always the most complete or best refined? Should we simply add together the number of electrons for all the atoms refined in the asymmetric unit (protein + ligands + solvent)? See my previous email. Pavel -- Andre LB Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] On estimating Unit Structure Factor distribution
Dear Pavel, thank you so very much for the prompt feedback. That would be extremely useful if you could script the Uhkl calculation in CCTBX. With best regards, Andre. Em qua, 15 de mai de 2019 às 09:47, Pavel Afonine escreveu: > Hi Andre, > > >> - Is there any macromolecular crystallography software that can compute >> Uhkl as above, or equivalent? >> > > I estimate this can take about 10 minutes to script in CCTBX. I can write > a script for you, if interested, and send off list. > > >> - If not, would it be more correct to use the Wilson-B or the mean B from >> the final model? >> > > I'd guess mean B from the model is a better estimate. > > - How can F(000) be best estimated from the final model, which is not >> necessarily always the most complete or best refined? Should we simply add >> together the number of electrons for all the atoms refined in the >> asymmetric unit (protein + ligands + solvent)? >> > > See my previous email. > > Pavel > > -- Andre LB Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] On estimating Unit Structure Factor distribution
Hi Andre, > - Is there any macromolecular crystallography software that can compute > Uhkl as above, or equivalent? > I estimate this can take about 10 minutes to script in CCTBX. I can write a script for you, if interested, and send off list. > - If not, would it be more correct to use the Wilson-B or the mean B from > the final model? > I'd guess mean B from the model is a better estimate. - How can F(000) be best estimated from the final model, which is not > necessarily always the most complete or best refined? Should we simply add > together the number of electrons for all the atoms refined in the > asymmetric unit (protein + ligands + solvent)? > See my previous email. Pavel To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] On estimating Unit Structure Factor distribution
Hi Andre, - How can F(000) be best estimated from the final model, which is not > necessarily always the most complete or best refined? Should we simply add > together the number of electrons for all the atoms refined in the > asymmetric unit (protein + ligands + solvent)? > the text here explains how to do this: "On the analysis of residual density distributions on an absolute scale" http://phenix-online.org/newsletter/CCN_2012_07.pdf Also, there is a Phenix tool to do this: phenix.f000 Good luck, Pavel To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] On estimating Unit Structure Factor distribution
At the title, please read Unitary, not Unit. Apologies. Em qua, 15 de mai de 2019 às 09:09, Andre LB Ambrosio escreveu: > Dear all, > > We seek to calculate the distribution of Unitary Structure Factors, Uhkl, > from a few datasets (at different maximum resolutions) for which the > corresponding atomic models are already available at the PDB; this > according to the formula (6.4), in the 2nd edition of Jan Drenth´s book: > > Uhkl = exp[B*(sin^2(theta)/lambda^2)] x FOBShkl / F(000) > > Hence, the following questions: > > - Is there any macromolecular crystallography software that can compute > Uhkl as above, or equivalent? > > - If not, would it be more correct to use the Wilson-B or the mean B from > the final model? > > - How can F(000) be best estimated from the final model, which is not > necessarily always the most complete or best refined? Should we simply add > together the number of electrons for all the atoms refined in the > asymmetric unit (protein + ligands + solvent)? > > Many thanks in advance and best wishes, > > -- > Andre LB Ambrosio > -- Andre LB Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] On estimating Unit Structure Factor distribution
Dear all, We seek to calculate the distribution of Unitary Structure Factors, Uhkl, from a few datasets (at different maximum resolutions) for which the corresponding atomic models are already available at the PDB; this according to the formula (6.4), in the 2nd edition of Jan Drenth´s book: Uhkl = exp[B*(sin^2(theta)/lambda^2)] x FOBShkl / F(000) Hence, the following questions: - Is there any macromolecular crystallography software that can compute Uhkl as above, or equivalent? - If not, would it be more correct to use the Wilson-B or the mean B from the final model? - How can F(000) be best estimated from the final model, which is not necessarily always the most complete or best refined? Should we simply add together the number of electrons for all the atoms refined in the asymmetric unit (protein + ligands + solvent)? Many thanks in advance and best wishes, -- Andre LB Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] Research Associate (Fixed Term) at the MRC Mitochondrial Biology Unit, University of Cambridge
Posting on behalf of Dr Edmund Kunji: The University of Cambridge wishes to appoint a Postdoctoral scientist to join the research group of Dr Edmund Kunji in the MRC Mitochondrial Biology Unit of the University of Cambridge. The postholder will work within a programme focussed on mitochondrial transporters. Transport processes are crucial for the functioning of mitochondria and mutations in transport proteins cause of a wide range of metabolic, neuromuscular and developmental diseases. Basic molecular understanding of their structure and mechanism is required to understand their role in health and disease. The goal of the project is to study their structures in different conformational states by electron cryo-microscopy and/or x-ray crystallography. The post-holder will participate in every stage of the process, from the generation of expression strains or cell lines, isolation of mitochondria, purification and sample preparation, data acquisition and processing, and structure model building and interpretation. There will also be an opportunity to study their role and mechanism using a wide range of biochemical and biophysical techniques. This project is part of a collaborative SNF Sinergia grant together with Profs. Hediger and Lochner of the University of Bern. Candidates will have a PhD in Structural Biology/Biophysics or related disciplines, and a track record of research achievements. Knowledge of protein purification and experience in structural biology are essential. Further details about the job may be found here: http://www.jobs.cam.ac.uk/job/21519/ The MRC Mitochondrial Biology Unit is a world-renowned centre for mitochondrial research. Additional information can be found at www.mrc-mbu.cam.ac.uk. Fixed-term: The funds for this post are available for 3 years in the first instance. The closing date for applications is Wednesday 12th June 2019 with interview date yet to be confirmed. Informal enquiries may be made to Dr Edmund Kunji (e...@mrc-mbu.cam.ac.uk). To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] CCPBioSim annual conference 2019, 4-6 Sept, Bristol
>From CCPBioSim. Note that the theme for the invited speakers is synthetic >biology and biomolecular design, but contributed talks and posters can be on >any aspect of biomolecular modelling and simulation. m Dear All, We are pleased to announce that registration is now open for the 7th Annual CCPBioSim Conference - Frontiers in Biomolecular Simulation. Details and the link to the registration page can be found at http://www.ccpbiosim.ac.uk/ccpbiosim2019. The 7th annual meeting of CCP-BioSim is organised jointly with the Molecular Graphics and Modelling Society and will have the theme of Modelling and Simulation for Synthetic Biology. The conference will showcase important advances in biomolecular modelling and simulation tools, technologies, interplay with experiment, and applications to biomolecular design and synthetic biology. The conference will be taking place at the University of Bristol on 4-6 September 2019, with the following invited speakers: Prof. Charlotte Deane, University of Oxford, UK Dr. Sarel Fleishman, Weizmann Institute of Science, Rehovot, Israel Prof. Syma Khalid, University of Southampton, UK Prof. Modesto Orozco, IRB Barcelona, Spain Dr. Fabio Parmeggiani, University of Bristol, UK Dr. Katarzyna Świderek, Universitat Jaume I, Valencia, Spain Dr. Per-Olof Syrén, KTH Royal Institute of Technology, Stockholm, Sweden Submissions for contributed posters and talks are highly encouraged. Whilst the conference specifically highlights the use of modelling and simulation for biomolecular design and synthetic biology, presentations across the broad area of biomolecular simulation and modelling are very welcome. On behalf of the organizing committee, Marc van der Kamp (University of Bristol, co-chair) Adrian Mulholland (University of Bristol, co-chair) Sarah Harris (University of Leeds) Ross Anderson (University of Bristol) Sarah Fegan (STFC, Daresbury) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
