[ccp4bb] CALL FOR ABSTRACTS - Microsymposium about Infectious and Neglected Diseases at ECM34
Dear all, the deadline to submit abstracts for the ECM34 (https://www.ecm34.org/ <https://urldefense.com/v3/__https://www.ecm34.org/__;!!JFdNOqOXpB6UZW0!rr_W_RwZSuO_xlF_2iV_gbbed0-A3SCRJJnhojzJebGCRf24FR93Cq4en2GaW3-DGwsilon7jB4ySFUV9guLTdlovr2oaDuPVQ$>) which will take place in Padua, Italy (Aug 26-31, 2024) has been extended until May 7th. You are particularly invited to submit your abstracts for the Microsymposium 5, which will take place in the afternoon of Aug 27. We look forward to receiving your proposals addressing interesting structural studies about macromolecular systems involved in *infectious and neglected diseases*. See you in Padua, Federico Forneris and Pedro Alzari [image: LOGO-UNIPV] <https://portale.unipv.it> *Federico Forneris, PhD* Vice-Rector for Research, University of Pavia <https://portale.unipv.it> President of the INF-ACT Foundation <http://www.inf-act.it/> Advisory board member of the Institute for Transformative Innovation Research (ITIR) <https://www.itir.io/> Coordinator of the joint IUSS-UniPV PhD Program in Biomolecular Sciences and Biotechnologies <https://www.iusspavia.it/en/education/doctoral-programmes/biomolecular-sciences-and-biotechnology> Coordinator of the UniPV M.S. Program in Molecular Biology and Genetics <https://molecularbiologyandgenetics.cdl.unipv.it/en> The Armenise-Harvard Laboratory of Structural Biology Dept. Biology and Biotechnology "Lazzaro Spallanzani" via Ferrata 9A - 27100 Pavia (Italy) T. +39 0382 985228 http://fornerislab.unipv.it https://twitter.com/fornerislab 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] help identifying unknown density
Any chances for some guadinium leftover from a refolding protocol? See second line in fig 1 here, quite similar stacking: http://www.mdpi.com/1420-3049/20/5/9214/htm Best, F. Federico Forneris, PhD The Armenise-Harvard Laboratory of Structural Biology Dept. Biology and Biotechnology University of Pavia Via Ferrata, 9 I-27100 Pavia - ITALY http://fornerislab.unipv.it -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Stephen Cusack Sent: lunedì 9 ottobre 2017 17:40 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] help identifying unknown density Dear All, �� I am refining the crystal structure of an E. coli expressed protein at 2.65 A resolution. The crystals grew in 0.1 M MES pH6, 0.7 M sodium formate pH 6. Ni-NTA was used in the purification. There are four molecules in the asymmetric unit. A particular histidine in each molecular has clear, strong extra density which looks like a metal bonded to an imidazole nitrogen (distance approx 2 A) with three other co-ordinating atoms in a triangular planar arrangement (see attached screen shot for unbiased extra density, atoms are only put in the density for illustrative purposes). Has anyone seen anything like this ? Any suggestions ? thanks very much Stephen -- ** Dr. Stephen Cusack, FRS Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL) Group leader in structural biology of protein-RNA complexes and viral proteins ** Email: cus...@embl.fr Website: http://www.embl.fr Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123 Fax:(33) 4 76 20 7199 Postal address: EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue des Martyrs, 38000 Grenoble, France **
[ccp4bb] Cryo-EM School2017 in Pavia: Deadline Extended, but few places remaining
Dear all, Few places are still available for the AIC School "Bridging the gap between Cryo-EM and Crystallography". http://www.cristallografia.org/aicschool2017 We have decided to extend the bursary registration deadline until May 30th, 2017. We wish to remind applicants that have received official sponsorship from the International Union for Crystallography (IUCr) which allows us to offer travel bursaries and awards to outstanding participants based on their CV and motivation letters. This school will offer the opportunity to young researchers in biochemistry or structural biology at the PhD/postdoctoral level to approach the fundamental questions arising from the cryo-EM experiment setup. Central topics will include evaluation sample suitability for analysis and its preparation, choice of appropriate instrumentation for single particle, tomography or electron diffraction approaches, data processing and interpretation of results. A showcase of recent results will contour the tutorial sessions. We are confident that this event will be an excellent opportunity for many scientists who want to approach and learn the basics of cryo-electron microscopy. For information, program and registration details please visit http://www.cristallografia.org/aicschool2017. More specific enquiries can be discussed via e-mail to my address or to aicsch...@cristallografia.org We look forward to hosting you in Pavia and discuss about Cryo-EM in September. On behalf of all school organizers, Very best wishes, F. Federico Forneris, PhD The Armenise-Harvard Laboratory of Structural Biology Dept. Biology and Biotechnology University of Pavia Via Ferrata, 9 I-27100 Pavia - ITALY <http://fornerislab.unipv.it/> http://fornerislab.unipv.it
[ccp4bb] AIC Cryo-EM international School 2017 - Deadlines approaching!
Dear all, this is the second announcement of the International School "Bridging the Gap between Cryo-EM and Crystallography" that will be held in Pavia, 3-7 September 2017. http://www.cristallografia.org/aicschool2017 This school will offer the opportunity to young researchers in biochemistry or structural biology at the PhD/postdoctoral level to approach the fundamental questions arising from the cryo-EM experiment setup. Central topics will include evaluation sample suitability for analysis and its preparation, choice of appropriate instrumentation for single particle, tomography or electron diffraction approaches, data processing and interpretation of results. A showcase of recent results will contour the tutorial sessions. The school program is almost finalized and, given the enthusiastic reply from speakers, tutors and the applicants who already registered until now, we are confident this event will be an excellent opportunity for many scientists who want to approach and learn the basics of cryo-electron microscopy. We have received official sponsorship from the International Union for Crystallography (IUCr) which allows us to offer travel bursaries and awards to outstanding participants based on their CV and motivation letters. DEADLINE FOR BURSARY APPLICATIONS: May 15th, 2017. For information, program and registration details please visit http://www.cristallografia.org/aicschool2017. More specific enquiries can be discussed via e-mail to my address or to aicsch...@cristallografia.org We look forward to hosting you in Pavia and discuss about Cryo-EM in September. On behalf of all school organizers, Very best wishes, F. Federico Forneris, PhD The Armenise-Harvard Laboratory of Structural Biology Dept. Biology and Biotechnology University of Pavia Via Ferrata, 9 I-27100 Pavia - ITALY <http://fornerislab.unipv.it/> http://fornerislab.unipv.it
[ccp4bb] Announcement: Cryo-EM School in Italy
Dear Colleagues, we are pleased to announce the 2017 edition of the Italian Association for Crystallography (AIC) International Crystallography School (AICS2017). This year's school title will be "Bridging the gap between cryo-EM and crystallography". The school will be held in Pavia, Italy, from 3 to 6 September 2017. AICS2017 "Bridging the gap between cryo-EM and crystallography" will offer the opportunity to young researchers in biochemistry or structural biology at the PhD/postdoctoral level to approach the fundamental questions arising from the cryo-EM experiment setup. Central topics will include evaluation of sample suitability for analysis and its preparation, choice of appropriate instrumentation for single particle, tomography or electron diffraction approaches, data processing and interpretation of results. A showcase of recent results will contour the tutorial sessions. We already received enthusiastic confirmation from numerous speakers and sponsors. A preliminary program, as well as registration and practical information can be found at: http://www.cristallografia.org/aicschool2017 We are making every effort to keep registration fees as low as possible and we offer a very convenient package including school attendance, 4-night accommodation in historical University Colleges in Pavia (check-in: Sunday, 3 September; check-out: 7 September), lunches and coffee breaks from 4 to 6 September, welcome party on September 3rd, social dinner on September 5th, and a booklet containing copies of the slides used during the lectures for 400 EUR. A number of student bursaries will be available to cover the registration fee in full or partially. The deadline for bursary application is 15 May 2017. AIC associates will get 50 EUR discount on the registration fee. Deadline for registration: 15 June 2017. Please note that, should we receive a large number of registrations, we may adopt a "first to come, first to serve policy". We look forward to welcoming you in Pavia. The scientific organizing committee: Federico Forneris (University of Pavia) Andrea Mattevi (University of Pavia) Filippo Mancia (Columbia University) Martino Bolognesi (University of Milan) Mauro Gemmi (Italian Institute of Technology) Beatrice Vallone (Sapienza University of Rome) Contact for additional information: <mailto:aicsch...@cristallografia.org> aicsch...@cristallografia.org Best, F. Federico Forneris, PhD The Armenise-Harvard Laboratory of Structural Biology Dept. Biology and Biotechnology University of Pavia Via Ferrata, 9 I-27100 Pavia - ITALY <http://fornerislab.unipv.it/> http://fornerislab.unipv.it
[ccp4bb] Postdoctoral fellowship on structural biology of eukaryotic complexes in Pavia (Italy)
The Department of Biology and Biotechnology of the University of Pavia (Italy) is announcing a new postdoctoral programme on a few selected strategic topics. With an above-average salary, successful postdoctoral fellows will potentially be considered for tenure-track positions at the end of the fellowships which are for two years with possible extension to third year. One of the topics will be on stuctural and biophysical studies of eukaryotic multiprotein complexes and membrane proteins. Expertise in protein expression using insect and/or mammalian cells is essential. Proven experience with expression and purification of membrane protein targets will be a plus. The language of the application will be English, however knowledge of (or commitment to learn) Italian language is highly recommended. The fellowships will be assigned on a competitive basis by an external advisory panel and successful candidates will expectedly have a strong CV. Applicants should have a PhD in Molecular Biology, Crystallography, Biophysics or a related area, and relevant publications, and must be under 35 years old. The Department of Biology and Biotechnology of the Univerisity of Pavia (Italy) has a strong division in structural biology with two highy integrated and well-equipped laboratories led by Dr. Federico Forneris and Prof. Andrea Mattevi, as illustrated at www.unipv.it/biocry. Pavia is a lovely university town in the north of Italy with very good life quality. Interested candidates should request details about application procedure, detailed topics and deadlines to federico.forne...@unipv.it or andrea.matt...@unipv.it no later than October 10th. Best, F. Federico Forneris, PhD --- The Armenise-Harvard Laboratory of Structural Biology Department of Biology and Biotechnology University of Pavia Via Ferrata, 9 27100 Pavia - Italy http://fornerislab.unipv.it http://www.unipv.it/biocry/index.php?page=investigators#forneris
[ccp4bb] postdoctoral position available
Dear all, We seek to appoint a Post-doctoral Training Fellow to join the newly established Armenise-Harvard Laboratory of structural biology at the University of Pavia. The group will focus on the molecular characterization of extracellular ligand and receptors involved in synapse formation using a combination of techniques including structural biology, biochemistry and biophysics. More information on http://www.unipv.it/biocry/fornerislab/ The position will be initially available for one year and may be extended upon positive evaluation. The application should include curriculum vitae, publications, a cover letter explaining research interests and fit for the position. Please also include a minimum of two personal references (name, email and phone number). The application should be sent via e-mail to Dr. Federico Forneris (f.forne...@uu.nl). Review of applications will begin immediately and the position will remain open until filled. Best, F. Federico Forneris, PhD --- Crystal and Structural Chemistry Bijvoet Center for Biomolecular Research - Utrecht University Padualaan 8 3584 CH UTRECHT - The Netherlands Tel. +31 (0) 30 253 4179 - Fax +31 (0) 30 253 3940 http://www.crystal.chem.uu.nl/~forneris/ http://www.unipv.it/biocry/fornerislab/
Re: [ccp4bb] using pymol for making movie of change in protein structure
Hi, A quick and efficient option for morphing between multiple states (structure A --> structure B) defined by separate PDB structures is using UCSF chimera. The program will generate a user-defined number of intermediate pdb models that can be saved and used in Pymol. Best, Federico Forneris, PhD --- Crystal and Structural Chemistry Bijvoet Center for Biomolecular Research - Utrecht University Padualaan 8 3584 CH UTRECHT - The Netherlands Tel. +31 (0) 30 253 2868 - Fax +31 (0) 30 253 3940 http://www.crystal.chem.uu.nl/group-gros/ From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of sonali dhindwal Sent: mercoledì 21 marzo 2012 15:52 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] using pymol for making movie of change in protein structure Dear All, My query is slightly out of scope of ccp4. I need some suggestions for making movie using pymol to show conformation of a reactive site loop, through the use of three crystal structure which are available showing this change. I have seen many people present the structural information in the form of movie, to show how the ligands come and the flexible residues moves giving change in the active site by movement of the flexible loops. I found emovie and installed the plugin but pymol installed on my system doesnt support the morph feature. Can someone please help in suggesting some other tool and tutorial for the same. Thanks in advance. Regards
Re: [ccp4bb] protein stain, B-PER
Hi, if you use pLysS E coli strains and you're working with soluble cytoplasmic proteins, a couple of cycles of freeze-thawing in LN2 will break your cells pretty well with high protein recovery, without the need of extra exotic chemicals added to your mixture. Just put some DNAse to avoid excess viscosity of your sample and get rid of nonspecifically bound DNA. If the cells are not pLysS, the same method works fine if you add to your lysis buffer a bit of lysozyme and do a couple more cycles. Regarding protein stain, here's my suggestion for a 5-minute clean, efficient stain-destain protocol (with microwave, though): - after running your gel, put it in a glass beaker or even better in one of those low-profile glass containers used to make ice baths, filled with ~1 cm of deionized water - microwave the gel for 1 minute, max power (on my microwave, 1000W) -wash out the water, then add 40 ml of PageBlue. Cover your container with a paper towel (do not seal it), and microwave 3 times for 15 seconds at maximum power (1000W), gently shaking the container between the cycles. The blue stain should never boil. If you see that it starts boiling, reduce the length of the cycles. - collect back the blue stain solution, rinse the gel with water (again, 1 cm in the container), and microwave for 30 seconds. Change the water again 1-2 times. its done, low background, ready for imaging. In my hands, the whole procedure takes less than 5 minutes and gives beautiful gels. The PageBlue solution that we use (Fermentas) is much more sensitive than standard coomassie R250 and can be re-used an incredible number of times. This makes this staining solution cheap despite the cost of a 1L bottle (I am staining 3-4 gels per week and Ive been using the same 50ml tube of PageBlue for the last 3 months at least). Without the microwave, the same solution works well if you stain 10' and destain in water for about 1 hour. HTH, Federico Forneris, PhD --- Crystal and Structural Chemistry Bijvoet Center for Biomolecular Research - Utrecht University Padualaan 8 3584 CH UTRECHT - The Netherlands Tel. +31 (0) 30 253 2868 - Fax +31 (0) 30 253 3940 http://www.crystal.chem.uu.nl/group-gros/ -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Thomas Edwards Sent: giovedì 15 marzo 2012 15:24 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] protein stain, B-PER Dear BB, Apologies for being mildly off topic. Maybe. 1. We are trying to express (in E. coli) a protein which appears to be quite sensitive to mechanical disruption. We have ordered some B-PER (Pierce - "B-PER Bacterial Protein Extraction Reagents are designed to extract soluble protein from bacterial cells without harsh chemicals or mechanical procedures like sonication"), but would like to try a variety of similar things if possible. Any advice from the community out there? Anybody know what goes into B-PER or similar things (I know there's some Dnase and lysosyme in there but which detergents are compatible with Ni, GST, how much do you need etc)?? 2. Staining SDS gels. There are various concerns from lab members about safety re methanol in stains, microwaving stains etc etc. "Instant Blue" claims to have none of these problems. Quote: "Protein gel staining takes around 15 minutes without the need to wash, fix, microwave or destain". But again, I'd like to try things to see if they work for us (before spending cash - yes, I am spending averse !). Anybody any suggestions for quick, non-fix, non-methanol, non-microwave, nondestain protein gel stains? Have tried home made colloidal coomassie but our protocol still requires fixes and washes that made it not really worth while. Happy to collate thoughts on replies offline and post summary. Many thanks Ed T.A.Edwards Ph.D. Deputy Director Astbury Centre for Structural Molecular Biology Lecturer in Biochemistry Garstang 8.53d University of Leeds, Leeds, LS2 9JT Telephone: 0113 343 3031 http://www.bmb.leeds.ac.uk/staff/tae/ -- No one should approach the temple of science with the soul of a money changer. ~Thomas Browne
Re: [ccp4bb] [OT] which column to use in SLS/MALS instruments
Hi Sebastiano, we are very happy with the SEC columns from Wyatt coupled to our FPLC/MALLS machine. http://www.wyatt.com/solutions/hardware/sec-columns-for-multi-angle-light-sc attering.html The separation range is (more or less) comparable to GE standard spdx 200/75/superose 6, and the columns are rock solid. The quality of separation is excellent in analytical runs, we routinely use them loading sample volumes of 10-25 microliters at concentrations around 1mg/ml. We did not encounter reproducibility problems/column damage so far with buffers at pH in the 6-8.5 range (8.5 is actually the high pH limit recommended by Wyatt). HTH Best, Federico Forneris, PhD --- Crystal and Structural Chemistry Bijvoet Center for Biomolecular Research - Utrecht University Padualaan 8 3584 CH UTRECHT - The Netherlands Tel. +31 (0) 30 253 2868 - Fax +31 (0) 30 253 3940 http://www.crystal.chem.uu.nl/group-gros/ -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sebastiano Pasqualato Sent: martedì 8 marzo 2011 14:04 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] [OT] which column to use in SLS/MALS instruments Dear all, I was wondering if somebody could help me out by suggesting the "best" column to be used in a Static Light Scattering (I guess it would be the same for a Multi Angle Light Scattering) instrument. We were suggested using a silica-based column, with very high separation properties, but it seems that these columns are highly sensitive to (even slightly) basic pH's. Even running the column in PBS, it looks like injecting samples at pH 8.0 ruins the column resin, making it unusable. On the other hand, GE Healthcare columns would require a huge amount of material to be loaded. What are you guys using in your instruments? Thanks a lot in advance for the feedback, best, ciao Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990
[ccp4bb] [Off-Topic] Ultracentrifuge: AirFuge vs. Conventional
Dear CCP4bbers, We are in the process of buying a new ultracentrifuge to spin our samples over 150.000 x g. Obviously, price is a relevant variable and for this reason we are also evaluating the Airfuge from Beckman. We would like to have some feedbacks from Airfuge users, to understand what are the powers and the limits of this machine compared to a "conventional" ultracentrifuge. Obviously, a summary of all answers will be posted here on the bb. Thank you in advance, Federico Forneris -- Dept. of Genetics and Microbiology University of Pavia Via Ferrata, 1 27100 - Pavia (Italy) http://www.unipv.it/biocry/
[ccp4bb] R: [ccp4bb] ccp4i unable to read mtz files
Check permissions of your TEMPORARY directories. When MTZ files are loaded,
some dumping actions are done in those dirs. I encountered the same problem
with SuSE 10.2 and solved changing permissions in /tmp/[users] directories.
HTH
regards,
Federico Forneris
--
Dept. of Genetics and Microbiology
University of Pavia
Via Ferrata, 1
27100 - Pavia (Italy)
http://www.unipv.it/biocry/
Da: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Per conto di Harry M.
Greenblatt
Inviato: giovedì 14 giugno 2007 13.00
A: CCP4BB@JISCMAIL.AC.UK
Oggetto: Re: [ccp4bb] ccp4i unable to read mtz files
BS"D
what was the error? Was the .mtz file copied from a Windows
machine by any chance?
Flip
No. All these files are produced by various flavours of Unix.
The error was a window that said:
"CCP4i encountered an error when trying to extract the data from
{myfile}.mtz..."
Yes, these are network accounts.
This also occurs in my account, so it is specific to the machine, not to a
user.
Thanks
Harry
-
Harry M. Greenblatt
Staff Scientist
Dept of Structural Biology [EMAIL PROTECTED]
Weizmann Institute of Science Phone: 972-8-934-3625
Rehovot, 76100 Facsimile: 972-8-934-4159
Israel
