Re: [ccp4bb] secondary structure assignment to sequence
Dear Vitali, I used to do it with Stride server. https://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py Hope this helps, Best wishes, Marc https://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py — Marc GRAILLE, PhD DR1-CNRS Head of the team: “Translation and degradation of eukaryotic mRNAs” Laboratoire de Biologie Structurale de la Cellule (BIOC); UMR7654; CNRS ÉCOLE POLYTECHNIQUE 91128 PALAISEAU CEDEX FRANCE 📞: +33 (0)1 69 33 48 90 https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes Responses to emails are not expected outside of your normal working hours.  > Le 13 nov. 2024 à 13:14, Vitali James a écrit : > > Dear User, > Is there any tool that can assign the secondary structure to the sequence of > protein in the PDB. > In the past I have used a 2Struc: the secondary structure server, but it's > not available any more. > Is there any easy way to list the sequence and ss below the sequence of > provided PDB models. > best > J. Vitali > > 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] Server to find structural similarity between nucleic acid structures
Hello, I am looking for a server that finds structural similarities between the structure of an RNA and all RNA structures present in the PDB, pretty much like DALI or PDB-eFold do for proteins. Does anyone know if such server exists? Thanks a loot for your help, Best wishes, Marc — Marc GRAILLE, PhD DR1-CNRS Head of the team: “Translation and degradation of eukaryotic mRNAs” Laboratoire de Biologie Structurale de la Cellule (BIOC); UMR7654; CNRS ÉCOLE POLYTECHNIQUE 91128 PALAISEAU CEDEX FRANCE 📞: +33 (0)1 69 33 48 90 https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes Responses to emails are not expected outside of your normal working hours.  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] Alternatives to X
Dear colleagues, I take advantage of Tim's message about the fact that responsible people have resigned from X. I really enjoyed Twitter (which I discovered rather late) because it was a great tool for announcing news from my laboratory, but also for keeping abreast of recent publications or pre-publications related to my research interests. I notice that many scientists have deserted X in recent months. Can anyone suggest user-friendly alternatives used by the scientific communities to announce recent publications or news in their fields? Best wishes, Marc — Marc GRAILLE, PhD DR1-CNRS Laboratoire de Biologie Structurale de la Cellule (BIOC; Ex-Laboratoire de Biochimie) UMR7654 du CNRS Head of the team: “Translation and degradation of eukaryotic mRNAs” ÉCOLE POLYTECHNIQUE 91128 PALAISEAU CEDEX FRANCE 📞: +33 (0)1 69 33 48 90 : marc.grai...@polytechnique.edu <mailto:marc.grai...@polytechnique.edu> / Twitter : @GrailleLab <https://twitter.com/GrailleLab> https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes — > Le 2 déc. 2023 à 10:15, Tim Grüne a écrit : > > Hi Mark, > responsible people are resigning from X. > Cheers, > Tim > > Am 01.12.2023 23:24, schrieb Mark J. van Raaij: >> just came across this critique of that paper on Twitter: >> This exciting paper shows AI design of materials, robotic synthesis. >> 10s of new compounds in 17 days. But did they? This paper has very >> serious problems in materials characterisation. In my view it should >> never have got near publication. Hold on tight let's take a look 😱 >> [1] >> Robert Palgrave (@Robert_Palgrave) on X [1] >> twitter.com [1] >> but I'm not enough of an expert to judge - perhaps some >> characterizations were wrong and a lot of the paper does stand. >>> On 1 Dec 2023, at 20:51, Bryan Lepore wrote: >>> Adding to that literature list a bit outside : >>> Merchant, A., Batzner, S., Schoenholz, S.S. _et al._ >>> Quote: >>> "... we show that graph networks trained at scale can reach >>> unprecedented levels of generalization, improving the efficiency of >>> materials discovery by an order of magnitude. " >>> Scaling deep learning for materials discovery. >>> _Nature_ (2023), November >>> https://doi.org/10.1038/s41586-023-06735-9 >>> - >>> 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 >> Links: >> -- >> [1] https://twitter.com/Robert_Palgrave/status/1730358675523424344 > > -- > -- > Tim Gruene > Head of the Centre for X-ray Structure Analysis > Faculty of Chemistry > University of Vienna > > Phone: +43-1-4277-70202 > > 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/ 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] Looking for a post-doc with solid knowledge in cryo-EM
The Graille lab is interested in understanding how epitranscritomic marks are deposited on RNAs and influence RNA translation and decay as well as cell proliferation and organ development. We currently use a combination of various experimental approaches : molecular biology, biochemistry, cell biology and structural biology. We are willing to develop cryo-EM studies on human ribosomes as well as on complexes between RNA modifying enzymes and their substrates. The lab has access to an in-house cryo-EM platform equipped with a LEICA EM-GP sampler plunger to prepare grids and a Titan THEMIS cryo-electron microscope (200 kV). Access to Titan KRIOS machines is possible on French or European facilities. This project will be realized at the Laboratory of Structural Biology of the Cell (BIOC) from Ecole Polytechnique (Institut Polytechnique de Paris - IPP; Palaiseau; France), a leading French institute that combines top-level research, academics, and innovation at the cutting-edge of science and technology. The laboratory is located 40 minutes by train from Paris City centre. The campus offers all the equipments to perform various activities (music, theater…) or sports: swimming pools, 8 tennis courts, several football, badminton, tennis table, volleyball and basketball pitches, climbing walls, … The lab is looking for a candidate with solid knowledge in cryo-EM. The successful candidate will work in close collaboration with the team of Dr Schmitt and Mechulam, who have developed a strong expertise in cryo-EM since more than ten years. The selected candidate will apply to various local (Institut Polytechnique de Paris), national (charities such as FRM) or international (EMBO, Marie Curie, …) calls to get a post-doctoral fellowships to join the lab. The applicants should be preparing or hold a PhD degree with demonstrated knowledge in cryo-EM analysis of macromolecular complexes. Planned start date : Spring 2024. Working knowledge of the English language (scientific, oral and written) is necessary, but knowledge of French is not required as the team regularly hosts people from different countries. Enthusiasm, motivation and willingness to contribute to a dynamic and enjoyable working environment are very important qualities. The candidate should show autonomy, but a successful integration into the team projects is essential. Applications (including a detailed CV, summary of your current project and relevant skills and a contact information of two/three references) or information requests should be sent to Marc Graille (marc.grai...@polytechnique.edu). Website: http://bioc.polytechnique.fr/spip.php?rubrique117&lang=en <http://bioc.polytechnique.fr/spip.php?rubrique117&lang=en> Twitter : @GrailleLab — Marc GRAILLE, PhD DR1-CNRS Laboratoire de Biologie Structurale de la Cellule (BIOC; Ex-Laboratoire de Biochimie) UMR7654 du CNRS Head of the team: “Translation and degradation of eukaryotic mRNAs” ÉCOLE POLYTECHNIQUE 91128 PALAISEAU CEDEX FRANCE 📞: +33 (0)1 69 33 48 90 : marc.grai...@polytechnique.edu <mailto:marc.grai...@polytechnique.edu> / Twitter : @GrailleLab <https://twitter.com/GrailleLab> https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes — 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 with fonts in Coot
Hi Mark and Martin, I tried both and they all fixed my problem. thanks a lot for your suggestions. Best wishes, Marc — Marc GRAILLE, PhD DR1-CNRS Laboratoire de Biologie Structurale de la Cellule (BIOC; Ex-Laboratoire de Biochimie) UMR7654 du CNRS Head of the team: “Translation and degradation of eukaryotic mRNAs” ÉCOLE POLYTECHNIQUE 91128 PALAISEAU CEDEX FRANCE 📞: +33 (0)1 69 33 48 90 : marc.grai...@polytechnique.edu <mailto:marc.grai...@polytechnique.edu> / : @GrailleLab <https://twitter.com/GrailleLab> https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes — > Le 23 févr. 2021 à 12:33, Mark Brooks a écrit : > > Hi Marc, > I hope you're well. Have you updated Xquartz recently? This may help > after what appears to be a major update to Big Sur. > > CCP4 7.1 and freshly installed XQuartz 2.8.0_rc1 https://www.xquartz.org > <https://www.xquartz.org/> work on Big Sur 11.2.1 for me with no font errors. > > Kind regards, > > Mark > > On Tue, 23 Feb 2021 at 04:28, Marc Graille <mailto:marc.grai...@polytechnique.edu>> wrote: > Dear colleagues, > > I have recently upgraded my Apple OS from Catalina to Big Sur. > I am afraid, it was not the most brilliant idea I had those last days. > > When trying to run coot, I have the following message : > (coot-bin:25140): Pango-CRITICAL **: No fonts found: > This probably means that the fontconfig > library is not correctly configured. You may need to > edit the fonts.conf configuration file. More information > about fontconfig can be found in the fontconfig(3) manual > page and on http://fontconfig.org <http://fontconfig.org/> > > > and Coot display looks like that : > > > > Does anyone else faced the same problem? > Is there any easy way to solve this issue? > I can recognize the icons but I don’t remember exactly were all Coot options > are in the various Menus. > > Thanks a lot for your help. > > Yours, > > Marc > > — > Marc GRAILLE, PhD > DR1-CNRS > Laboratoire de Biologie Structurale de la Cellule (BIOC; Ex-Laboratoire de > Biochimie) > UMR7654 du CNRS > > Head of the team: “Translation and degradation of eukaryotic mRNAs” > > ÉCOLE POLYTECHNIQUE > 91128 PALAISEAU CEDEX > FRANCE > 📞: +33 (0)1 69 33 48 90 > > : marc.grai...@polytechnique.edu > <mailto:marc.grai...@polytechnique.edu> / : @GrailleLab > <https://twitter.com/GrailleLab> > https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes > > <https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes> > — > > > > > 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] possible solution with Phaser
Dear Luca, few possibilities: 1) Consider that you may have only 3 monomers in the asymmetric unit and not 4 as suggested from Matthew’s coefficient. Which are the R and Rfree values if you refine this model with only 3 molecules? 2) When you look at the crystal packing on the correctly placed monomers (let’s call them A, B and C), is one of them (imagine C) forming a similar homodimer as AB with another monomer C according to the crystal symmetry? 3) Following up on Ethan’s suggestion, if you see extra-density that could correspond to part of the 4th monomer, you can try to use the 2Fo-Fc electron density map to locate the 4th molecule using MolRep and its option “Search in a map”. In this case, feed MolRep with the coordinates of the 3 correctly placed monomers as fixed model. It worked many times in my case. Hope this helps. Marc — Marc GRAILLE, PhD DR1-CNRS Laboratoire de Biologie Structurale de la Cellule (BIOC; Ex-Laboratoire de Biochimie) UMR7654 du CNRS Head of the team: “Translation and degradation of eukaryotic mRNAs” ÉCOLE POLYTECHNIQUE 91128 PALAISEAU CEDEX FRANCE 📞: +33 (0)1 69 33 48 90 : marc.grai...@polytechnique.edu <mailto:marc.grai...@polytechnique.edu> / : @GrailleLab <https://twitter.com/GrailleLab> https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes — > Le 6 janv. 2021 à 08:38, Luca Mazzei a écrit : > > Hi all, > > I am struggling with the MR of a homo-dimer using Phaser. Matt_coeff strongly > suggests the presence of 4 mol per asym unit (space group P6222). The results > after a search of 4 mol per asymmetric unit of my monomer are the following: > > ** SINGLE solution > > ** Solution written to SOL file: phaser_3f6v_A1_MOLREP.sol > > ** Solution written to PDB file: phaser_3f6v_A1_MOLREP.1.pdb > ** Solution written to MTZ file: phaser_3f6v_A1_MOLREP.1.mtz >Solution annotation (history): >SOLU SET RFZ=3.9 TFZ=8.5 PAK=3 LLG=65 TFZ==10.0 RFZ=2.6 TFZ=17.0 PAK=3 > LLG=326 TFZ==29.8 (& TFZ==22.5 & TFZ==19.7) > LLG+=(326 & 529 & 593) LLG=795 TFZ==5.4 PAK=5 LLG=795 TFZ==5.4 PAK=5 > LLG=795 TFZ==5.4 >SOLU SPAC P 62 2 2 >SOLU 6DIM ENSE autoMR EULER 125.3 60.8 300.2 FRAC 0.17 -0.13 0.08 > BFAC -9.34 #TFZ==10.0 >SOLU 6DIM ENSE autoMR EULER 305.4 60.8 300.2 FRAC 0.27 -0.16 0.08 > BFAC -5.29 #TFZ==29.8 >SOLU 6DIM ENSE autoMR EULER 294.7 119.1 120.3 FRAC 0.45 0.01 0.26 > BFAC 0.34 #TFZ==22.5 >SOLU 6DIM ENSE autoMR EULER 305.5 61.6 300.1 FRAC 0.11 -0.16 0.08 > BFAC 29.19 #TFZ==5.4 >SOLU ENSEMBLE autoMR VRMS DELTA -0.2463 #RMSD 0.93 #VRMS 0.79 > > It seems (also looking at the maps) that it correctly places three monomers > out of four. How can I use this information to improve the search of the > fourth monomer using the same template model? > > Thanks in advance for your help, > > Best regards > > Luca Mazzei > > Luca Mazzei - PhD > Laboratory of Bioinorganic Chemistry > Department of Pharmacy and Biotechnology (FaBiT) > Alma Mater Studiorum - University of Bologna > Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy > Tel: +39 0512096235 > > > > > > 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] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)
Dear Auto,with such crystals diffracting like rocks, it can be useful to collect two datasets. One at “low" resolution (up to 3A) using low exposure time and/or low dose to avoid overloads and a second at higher resolution (1A in your case) using higher dose. Then, merge those two datasets into a single one using all reflections from the “low resolution” dataset and for instance data from 5 to 1A for the high resolution data (to exclude overloads). It may improve the Rmeas values at low resolution.My two cents.Marc Marc GRAILLE, PhDDirecteur de recherche CNRSLaboratoire de BiochimieECOLE POLYTECHNIQUE - UMR7654 CNRS91128 PALAISEAU CEDEXFRANCE To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 Phone : +33 (0)1 69 33 48 90 – Fax : +33 (0)1 69 33 49 09Email: marc.grai...@polytechnique.eduTeam: Translation and degradation of eukaryotic mRNAshttps://portail.polytechnique.edu/bioc/recherche/couplage-entre-la-traduction-et-la-degradation-des-arnm-chez-les-eucaryotesTeam supported by the ATIP-Avenir CNRS program Le 9 oct. 2018 à 19:12, Guto Rhys <guto.r...@bristol.ac.uk> a écrit :Hi all,I have a 1.05 Angstrom dataset that I was able to phase but the refined model only has an Rfree of approximately 0.25. The dataset includes 1800 images and, as the crystal did not suffer significantly from radiation damage, comprises all 360 deg. Auto-processing pipelines at diamond light source all suggest I222. I have also indexed the data in iMOSFLM, which has the highest-symmetry Laue group that is least penalised of I422. Subsequent scaling and merging in AIMLESS strongly indicates that I222 is the likely space group (see below). I have ran the refined model through ZANUDA, which has similar R values to lower symmetry space groups (see below). The output from Phenix Xtriage does not find any specific crystal pathologies and if twinning is present it is very low (2 to 4%, see below). The difference map suggests that the model accounts for nearly all the density. Any ideas or direction would be greatly appreciated.Best,GutoAIMLESS Summary Overall InnerShell OuterShellLow resolution limit 27.75 27.75 1.07High resolution limit 1.05 5.75 1.05Rmerge (within I+/I-) 0.050 0.078 0.466Rmerge (all I+ and I-) 0.051 0.080 0.536Rmeas (within I+/I-) 0.055 0.086 0.591Rmeas (all I+ & I-) 0.054 0.085 0.613Rpim (within I+/I-) 0.023 0.034 0.359Rpim (all I+ & I-) 0.017 0.028 0.288Rmerge in top intensity bin 0.049 - - Total number of observations 107950 779 1972Total number unique 11315 88 486Mean((I)/sd(I)) 19.7 46.2 1.8Mn(I) half-set correlation CC(1/2) 0.998 0.994 0.796Completeness 99.1 99.2 90.4Multiplicity 9.5 8.9 4.1Anomalous completeness 98.1 100.0 79.1Anomalous multiplicity 5.0 6.4 2.2DelAnom correlation between half-sets -0.067 0.286 0.097Mid-Slope of Anom Normal Probability 0.789 - - Estimate of maximum resolution for significant anomalous signal = 1.14A, from CCanom > 0.15Estimates of resolution limits: overall from half-dataset correlation CC(1/2) > 0.30: limit = 1.05A == maximum resolution from Mn(I/sd) > 1.50: limit = 1.05A == maximum resolution from Mn(I/sd) > 2.00: limit = 1.07A Estimates of resolution limits in reciprocal lattice directions: Along h axis from half-dataset correlation CC(1/2) > 0.30: limit = 1.06A from Mn(I/sd) > 1.50: limit = 1.09A Along k axis from half-dataset correlation CC(1/2) > 0.30: limit = 1.11A from Mn(I/sd) > 1.50: limit = 1.13A Along l axis from half-dataset correlation CC(1/2) > 0.30: limit = 1.05A == maximum resolution from Mn(I/sd) > 1.50: limit = 1.05A Anisotropic deltaB (i.e. range of principal components), A^2: 6.40Average unit cell: 29.12 29.26 55.50 90.00 90.00 90.00 Space group: I 2 2 2Average mosaicity: 0.36AIMLESS Laue Group prediction Laue Group Lklhd NetZc Zc+ Zc- CC CC- Rmeas R- Delta ReindexOperator= 1 I m m m *** 0.987 6.25 9.19 2.94 0.92 0.29 0.07 0.49 0.0 [h,k,l] 2 I 1 2/m 1 0.004 4.36 9.32 4.96 0.93 0.50 0.07 0.30 0.0 [-h,-k,l] 3 I 1 2/m 1 0.004 4.14 9.24 5.10 0.92 0.51 0.07 0.30 0.0 [k,-h,l] 4 I 1 2/m 1 0.004 4.05 9
Re: [ccp4bb] Density for an unknown ligand
Dear Wei,to get more information on this putative “butterfly-like” ligand, you can perform non-denaturing and denaturing mass spectrometry. This should give you the molecular weight of this compound, which most probably comes from E. coli and co-purifies with your protein of interest. In parallel, you could imagine to purify this compound by HPLC purification. Based on the shape and the details on the density, it might be rich in aromatic rings and then reversed-phase column might be useful. If you end up with enough material, you could try NMR to get info on this ligand.Before performing such experiments, you should definitely check whether this ligand binds to a conserved region of your protein such as a putative active site. If this molecule binds to a region formed by poorly conserved residues, you have to consider whether this is important or not to know precisely the identity of this compound. I mean biologically important. Ideally, this would of course be important to model the correct ligand in the electron density but I am sure it will not be the first structure deposited at the PDB with unattributed density or an unknown ligand.HTH,Best wishes,MarcLe 29 nov. 2016 à 09:26, Wei Liu <we...@me.com> a écrit :Hi all, Thanks for all answers and suggestions to my question regarding the density for an unknown ligand. Many people raised a possibility that the density corresponding molecule might locate at a two-fold symmetry axis, but I am quite sure to rule out this possibility. I tried to placed a molecule of biphenyl sulfide, which can roughly fit into one half of the density in question, and performed one round of refinement. As shown in the attached picture, strong residual density still exist in the rest half, where no symmetry atoms can be seen. So apparently a real molecule rather than an artifact lied in this structure, but I am still wondering from where such a molecule comes and strongly binds to our protein, E. coli or impurities in the crystallization conditions, as Prem suggested, and if there is any experimental methods to identify this compound. Looking forward to more suggestions.BestWei Marc GRAILLE, PhDDirecteur de recherche CNRSLaboratoire de BiochimieECOLE POLYTECHNIQUE - UMR7654 CNRS91128 PALAISEAU CEDEX Phone : +33 (0)1 69 33 48 90 – Fax : +33 (0)1 69 33 49 09 Email: marc.grai...@polytechnique.eduTeam: Translation and degradation of eukaryotic mRNAshttps://portail.polytechnique.edu/bioc/recherche/couplage-entre-la-traduction-et-la-degradation-des-arnm-chez-les-eucaryotesTeam supported by the ATIP-Avenir CNRS program
[ccp4bb] Graphics cards for Coot, Pymol, Chimera on MacBook Pro Laptop
Hello, I would like to buy a MacBook Pro laptop that will allow me among others to solve structures, build models and visualize electron density maps using Pymol, Coot or Chimera. I have the choice between between Intel Iris Pro (5200 series) and Intel Iris Pro + Nvidia GT 750M for the graphics cards but I don’t know which one is fine for the programs I want to run. Can some of you share advices/feedback with me? Thanks a lot for your answer. Best wishes, Marc Dr Marc GRAILLE Directeur de recherche CNRS Team: Translation and degradation of eukaryotic mRNAs Team supported by the ATIP-Avenir CNRS program Laboratoire de Biochimie ECOLE POLYTECHNIQUE - UMR7654 CNRS 91128 PALAISEAU CEDEX Phone : +33 (0)1 69 33 48 90 – Fax : +33 (0)1 69 33 49 09 Office 033012B Email: marc.grai...@polytechnique.edu http://bioc.polytechnique.fr/spip.php?rubrique117
[ccp4bb] 2 years Post-doc position near Paris (France)
Post-doctoral position “Structural studies of post-transcriptional / translational modification enzymes”. Location: Palaiseau, Ecole Polytechnique, near Paris (30 minutes by regular trains), France A 2 years post-doctoral position, funded by the ANR (French National Research Agency), is available at Laboratory of Biochemistry, Ecole Polytechnique-CNRS (France). The successful candidate will work in a young and dynamic international team headed by Dr Marc Graille. He/She should have a PhD in protein biochemistry/structural biology. Expertises in cloning, protein purification and X-ray crystallography are required. Experience in RNA production and purification as well as in protein complexes reconstitution will be very much appreciated. The project aims at studying structural aspects of protein-protein and protein-RNA complexes involved in the post-transcriptional/translational modifications of eukaryotic factors involved in mRNA translation. It will be realized in collaboration with groups studying the role of these complexes in yeast or human cells. To address these questions, the successful candidate will use a large panel of biochemical (protein expression and purification, enzymology, pull-down, …) and biophysical methods (X-ray crystallography, ITC, MALLS, fluorescence, …), which are all implemented in the host laboratory (Laboratory of Biochemistry, Ecole Polytechnique-CNRS). The lab is also equipped with a state-of-the art crystallization platform (Tecan and Mosquito crystallization robots plus an automatic system for crystallization plates imaging) and is located 2 km away from the French synchrotron SOLEIL, which offers regular access to protein crystallography beam lines (Proxima-1 and 2). Recent publications from Dr Graille’s group related to the project: Létoquart et al, PNAS, in press. Figaro et al, Mol. Cell. Biol., 2012 Graille et al, Biochimie, 2012 (review) Liger et al, Nuc. Acids Res., 2011. van den Elzen et al; Nat. Struct. Mol. Biol, 2010 More information can be found on our website: http://bioc.polytechnique.fr/spip.php?rubrique117&lang=en . The Laboratory of Biochemistry has a long standing expertise in the study of translational apparatus and is located on the multidisciplinary “Ecole Polytechnique” campus, one of the most selective and prestigious French “Grande Ecole”, which attracts top undergraduate and graduate students worldwide. Ecole Polytechnique is located 25 km south from Paris and as regular train connections to Paris city centre (30 minutes). The campus offers all the equipments to perform various activities (music, theatre, …) or sports: swimming pools, 8 tennis courts, several football, volleyball and. basketball pitches, climbing walls, … More info on the campus can be found at : http://www.polytechnique.edu/en . Net annual salary: around 24,500€ minimum. Starting : 2015, depending on availability of selected candidate. Duration: 24 months. Applications (including CV, resume describing your relevant skills and a list of three references) or information requests should be sent to Marc Graille (marc.grai...@polytechnique.edu). Dr Marc GRAILLE Directeur de recherche CNRS Team: Translation and degradation of eukaryotic mRNAs Team supported by the ATIP-Avenir CNRS program Laboratoire de Biochimie ECOLE POLYTECHNIQUE - UMR7654 CNRS 91128 PALAISEAU CEDEX Phone : +33 (0)1 69 33 48 90 – Fax : +33 (0)1 69 33 49 09 Office 033012B Email: marc.grai...@polytechnique.edu http://bioc.polytechnique.fr/spip.php?rubrique117
[ccp4bb] Post-doc position in Structural Biology of RNA decay components near Paris (France)
Post-doctoral position in Structural biology of RNA decay components. Location: Orsay, near Paris (45 minutes by regular trains), France A 2,5 years post-doctoral position, funded by the ANR (Agence Nationale pour la Recherche), is available to study structural aspects of protein-protein and protein-RNA complexes involved in eukaryotic mRNA decay. For this purpose, the successful candidate will combine structural biology methods (X-ray crystallography and small angle X-ray scattering) together with biophysical approaches (ITC, DSC, MALLS, fluorescence polarization, CD, …). All these technologies are currently available at the state-of the-art structural biology and biophysical platforms implemented in the host institute IBBMC (Institute for Biophysics and Molecular and Cellular Biochemistry, CNRS & University Paris-Sud), i.e. 3 nanodrop crystallization robots (Tecan, Cartesian and Mosquito), a Formulatrix crystal imager, an ITC200, an in-house SAXS apparatus, … . The lab is also well equipped for protein production in E. coli or eukaryotic systems (P. pastoris and baculovirus) and protein purification (several AKTA purification systems). The project will be carried-out under the supervision of Dr Marc Graille at IBBMC (Orsay, Paris-Sud University, France) in close collaboration with Dr Dominique Durand (IBBMC) for SAXS studies and Dr Séraphin (IGBMC, Illkirch, France) for functional studies. For recent publications related to the subject by Dr Graille and co-workers, see van den Elzen et al; Nat. Struct. Mol. Biol, 2010; Henri J et al, J. Biol. Chem., 2010; Rispal D et al, RNA, 2011 & Liger D, et al, Nuc. Acids Res., 2011. The IBBMC, an institute from CNRS and University Paris-Sud (one of the largest and most renowned French universities), is located in a green and timbered campus, 25km south from Paris. The lab is within 10 minutes walk from the train station, with regular connections to Paris city centre (45 minutes). The IBBMC is 2km away from the recently built French synchrotron SOLEIL, where we have regular access to protein crystallography (Proxima-1) and SAXS (Swing) beamlines. The successful candidate will have a PhD in protein biochemistry, biophysics, or structural biology. He/she should express strong interest in working at the interface between physics and biology. Expertise in RNA production and purification will be very much appreciated. Net annual salary: around 27,000€. Starting from January 2012. Duration: 30 months. Applications (including CV, covering and reference letters) or information requests should be sent to Marc Graille (marc.grai...@u-psud.fr ) and Dominique Durand (dominique.dur...@u-psud.fr) before 15th of September, 2011. Dr Marc Graille, CR1-CNRS, Equipe "Fonction et Architecture des Assemblages Macromoléculaires" IBBMC, CNRS UMR8619, Bât. 430 Université Paris-Sud 91405 ORSAY Tel: 33 (0)1 69 15 31 57 / Fax: 33 (0)1 69 85 37 15
[ccp4bb] MALLS equipment: SUMMARY
Dear all, here is a summary of the few responses that I have got from my posting on MALLS equipment suggestions. 2 labs have WYATT miniDawn system. One is connected to an Agilent HPLC. Seems to be quite good. 1 lab has a Waters equipment connected to an Akta FPLC, which seems to be more appropriate than Akta purifier because on this latter, the pumps have a very short "oscillation" time, creating some serious noise. More advices are still welcome. Yours Marc -- Marc Graille, PhD Yeast Structural Genomics, IBBMC CNRS UMR8619 Bat 430 Universite Paris Sud 91405 Orsay Cedex NEW PHONE NUMBER Tel: (33) 1 69 15 31 57 Fax: (33) 1 69 85 37 15
[ccp4bb] MALLS equipment
Dear all, we are interested in the multiangle laser light scatterring (MALLS) methodology but we do not know exactly which is the best system on the market. We plan to use it in a cold room (8°C) combined to an Akta Purifer system. Thanks to all in advance for sharing with us your expertise. Sincerely -- Marc Graille, PhD Yeast Structural Genomics, IBBMC CNRS UMR8619 Bat 430 Universite Paris Sud 91405 Orsay Cedex NEW PHONE NUMBER Tel: (33) 1 69 15 31 57 Fax: (33) 1 69 85 37 15
[ccp4bb]
Hi, We had success using a testosterone hemisuccinate derivative which is much more soluble. For details, see: Drevelle et al; J Mol Biol. 'jour', 'J Mol Biol.');> 2006 Apr 28;358(2):455-71 Hope this helps!! Marc KUMARASWAMI MUTHIAH a écrit : Anybody tried to cocrystallize the protein-progesterone or estrogen complexes, if so how do you go about the solubility of these compounds? Progesterone is only soluble in 50% chloroform or 100% DMSO and the dilution of this stock is not possible as chloroform falls out of solution. Lots of papers out there used soaking with progesterone or expressed the protein in the presence of progesterone. Any suggestions would be appreciated. Thanks Rediscover Hotmail®: Now available on your iPhone or BlackBerry Check it out. <http://windowslive.com/RediscoverHotmail?ocid=TXT_TAGLM_WL_HM_Rediscover_Mobile1_042009> -- Marc Graille, PhD Yeast Structural Genomics, IBBMC CNRS UMR8619 Bat 430 Universite Paris Sud 91405 Orsay Cedex NEW PHONE NUMBER Tel: (33) 1 69 15 31 57 Fax: (33) 1 69 85 37 15
[ccp4bb] Turbo in stereo
Hi all, First of all, let me apoligize for this off-topic question but I would like to use Turbo in stereo to build structures but unfortunately, I am unable to do so. I have stereo for pymol, coot and O but not for Turbo, which is my favourite program at the moment. I am running Ubuntu Hardy heron 8.04 and my graphics card is a NVIDIA Quadro FX3700. I have tried to edit my xorg.conf file but without any success. Thank you very much for suggestions! Cheers, Marc -- Marc Graille, PhD Yeast Structural Genomics, IBBMC CNRS UMR8619 Bat 430 Universite Paris Sud 91405 Orsay Cedex NEW PHONE NUMBER Tel: (33) 1 69 15 31 57 Fax: (33) 1 69 85 37 15
