Re: [ccp4bb] what happened to Molprobity
Dear Martin, Mark and Pedro for your replies which have been helpful. Hopefully, here speaking for the hole community, the disfunctioning of the server is just a temporary problem. All the best, Gerlind On 30/04/2024 13:47, Martin Malý wrote: Ce mail provient de l'extérieur, restons vigilants Dear Gerlind, The MolProbity analysis is included in the 'Multimeric validation' task and also in the refinement task in CCP4i2 - just be sure to have the current version 8.0.019. In Phenix GUI, I can still find such a task: Crystals -> Validation and map-based comparison -> Comprehensive validation (X-ray/Neutron). It's concerning that the MolProbity server does not work today... Best wishes, Martin On 30/04/2024 13:25, Gerlind Sulzenbacher wrote: Dear all, The Molprobity server appears to be not functional from my side. I just installed the latest version of Phenix and the module Molprobity has dissapeared. Can anybody provide information on the latest evolutions of this so precious tool? Thanking you in advance, with best wishes, Gerlind -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 413 94 95 27 E-mail: gerlind.sulzenbac...@univ-amu.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] what happened to Molprobity
Dear all, The Molprobity server appears to be not functional from my side. I just installed the latest version of Phenix and the module Molprobity has dissapeared. Can anybody provide information on the latest evolutions of this so precious tool? Thanking you in advance, with best wishes, Gerlind -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 413 94 95 27 E-mail: gerlind.sulzenbac...@univ-amu.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Assistant Professor in Structural Biology, University of Nebraska-Lincoln
Dear Mark, thank you for your clarification. Thanks also to Adrian for his reply. Indeed, from a European, French point of view, I didn't grasp the American rules. I apologise and wish you all a good evening, Gerlind Obviosely On 15/10/2023 18:05, Mark Wilson wrote: Hi Gerlind, To clarify, the position is tenure-leading, where tenure dossiers are typically submitted in the 5^th year of employment. If tenure is granted, then the position is a continuous appointment. The 9-month language in the ad refers to the academic year-typically faculty can either choose to take their salary over either 9 or 12 months. Faculty can also raise additional funds for salary over the summer via grants. This is common (nearly universal) in the US system. Importantly, this is _/not/_ simply a 9-month contract position, which would not make sense for an Assistant Professor. Best regards, Mark Mark A. Wilson (he/him) Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine St. Lincoln, NE 68588 *From: *Gerlind Sulzenbacher *Date: *Sunday, October 15, 2023 at 10:15 AM *To: *Mark Wilson , CCP4BB@JISCMAIL.AC.UK *Subject: *Re: [ccp4bb] Assistant Professor in Structural Biology, University of Nebraska-Lincoln Non-NU Email Dear Mark, thank you for posting this job offer, probably very interesting for people currently unemployed. Personally, I feel that working conditions and job offers in the scientific field have deteriorated considerably in recent years. I've always been shocked by one-year job offers involving international movements. Now we seem to be down at job offers for 9 months. From a human point of view, I find this extremely worrying. Sorry to pollute the mailing list with my personal opinions. All the best. Gerlind On 15/10/2023 16:46, Mark Wilson wrote: Dear Colleagues, The Department of Biochemistry at the University of Nebraska-Lincoln (UNL) invites applications for a tenure-track nine-month (academic year) faculty position at the rank of Assistant Professor. Areas of particular interest include but are not limited to time-resolved approaches to understanding macromolecular function, multiscale imaging, and integrated computational and experimental approaches to structural biology. Researchers at UNL have collaborations with national user facilities pioneering time-resolved X-ray diffraction techniques and have established a state-of-the-art cryo-EM facility housing a Thermo Scientific Glacios 200 keV Cryo TEM equipped with a Falcon 4i direct electron detector camera, a Selectris zero-loss energy filter, and capability for micro-electron diffraction of crystalline samples. The new cryo-EM facility is part of a strategic growth plan at UNL and complements existing strengths in X-ray crystallography, biophysics, and computation at UNL. Review of applications will begin November 15, 2023 and continue until the position is filled or the search is closed. To view details of the position and the application, go to https://employment.unl.edu, requisition F_230175 or visit https://employment.unl.edu/postings/88408. Click “Apply for this Job” and complete the information form. As an EO/AA employer, the University of Nebraska considers qualified applicants for employment without regard to race, color, ethnicity, national origin, sex, pregnancy, sexual orientation, gender identity, religion, disability, age, genetic information, veteran status, marital status, and/or political affiliation. See https://www.unl.edu/equity/notice-nondiscrimination. Best regards, Mark Mark A. Wilson (he/him) Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine St. Lincoln, NE 68588 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://urldefense.com/v3/__https:/www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!PvXuogZ4sRB2p-tU!Bav1hl7rOBTJ55aiWQJffSIG_gw4KPgMy-qLUQCUbhZ-k4fKBhpQxyMoBersHEFXrgHD558g184sfDS-O5RkYNknP_tYVxXeDQ$> -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 413 94 95 27 E-mail:gerlind.sulzenbac...@univ-amu.fr -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 413 94 95 27 E-mail:gerlind.sulzenbac...@univ-
Re: [ccp4bb] Assistant Professor in Structural Biology, University of Nebraska-Lincoln
Dear Mark, thank you for posting this job offer, probably very interesting for people currently unemployed. Personally, I feel that working conditions and job offers in the scientific field have deteriorated considerably in recent years. I've always been shocked by one-year job offers involving international movements. Now we seem to be down at job offers for 9 months. From a human point of view, I find this extremely worrying. Sorry to pollute the mailing list with my personal opinions. All the best. Gerlind On 15/10/2023 16:46, Mark Wilson wrote: Dear Colleagues, The Department of Biochemistry at the University of Nebraska-Lincoln (UNL) invites applications for a tenure-track nine-month (academic year) faculty position at the rank of Assistant Professor. Areas of particular interest include but are not limited to time-resolved approaches to understanding macromolecular function, multiscale imaging, and integrated computational and experimental approaches to structural biology. Researchers at UNL have collaborations with national user facilities pioneering time-resolved X-ray diffraction techniques and have established a state-of-the-art cryo-EM facility housing a Thermo Scientific Glacios 200 keV Cryo TEM equipped with a Falcon 4i direct electron detector camera, a Selectris zero-loss energy filter, and capability for micro-electron diffraction of crystalline samples. The new cryo-EM facility is part of a strategic growth plan at UNL and complements existing strengths in X-ray crystallography, biophysics, and computation at UNL. Review of applications will begin November 15, 2023 and continue until the position is filled or the search is closed. To view details of the position and the application, go to https://employment.unl.edu, requisition F_230175 or visit https://employment.unl.edu/postings/88408. Click “Apply for this Job” and complete the information form. As an EO/AA employer, the University of Nebraska considers qualified applicants for employment without regard to race, color, ethnicity, national origin, sex, pregnancy, sexual orientation, gender identity, religion, disability, age, genetic information, veteran status, marital status, and/or political affiliation. See https://www.unl.edu/equity/notice-nondiscrimination. Best regards, Mark Mark A. Wilson (he/him) Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine St. Lincoln, NE 68588 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 413 94 95 27 E-mail:gerlind.sulzenbac...@univ-amu.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Call for abstracts: ECM33, MS10 Protein-carbohydrate interactions
Dear all, Pietro Roversi and myself are co-chairing a session at the ECM33 meeting, 23rd-27th of August 2022, Versailles, entitled "Protein-carbohydrate interactions". The abstract deadline has been extended to the 16th of May. We will select 3 abstracts for 20 minutes talk. You can submit your abstracts through the conference website: https://www.ecm33.fr/ Please feel free to forward this to scientists who may want to contribute an abstract, including junior researchers! We are looking forward to the meeting and the abstracts, best wishes, Pietro and Gerlind -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@univ-amu.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] EMBO Practical Course on High throughput protein production and crystallization - deadline 10th of April
Dear colleagues, deadline for registration for the "EMBO Practical Course on High throughput protein production and crystallization", Marseille, is approaching: 10th of April More information below, with best wishes, Gerlind - I am glad to announce the "EMBO Practical Course on High throughput protein production and crystallization", hosted at the laboratory AFMB in Marseille, France, from 4 to 13 July 2022. On behalf of the organizers I would like to ask you to please let your colleagues and students know about our course by posting this information on the notice boards/webpage of your institute. Please feel free to download the course flyer for an A4 printout here: https://meetings.embo.org/files/posters/21-protein-production.pdf The course is intended for PhD students and young researchers using high-throughput methods for expression and crystallization of soluble proteins. The goal is to provide participants with the current knowledge in the use of the most innovative methods in the field. Accommodation and subsistence are covered for accepted applicants. For more information please visite the link below (in case of problems please copy the link into your browser) https://meetings.embo.org/event/21-protein-production -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@univ-amu.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] EMBO Practical Course on High throughput protein production and crystallization, Marseille, July 2022
Dear colleagues, I am glad to announce the "EMBO Practical Course on High throughput protein production and crystallization", hosted at the laboratory AFMB in Marseille, France, from 4 to 13 July 2022. On behalf of the organizers I would like to ask you to please let your colleagues and students know about our course by posting this information on the notice boards/webpage of your institute. Please feel free to download the course flyer for an A4 printout here: https://meetings.embo.org/files/posters/21-protein-production.pdf The course is intended for PhD students and young researchers using high-throughput methods for expression and crystallization of soluble proteins. The goal is to provide participants with the current knowledge in the use of the most innovative methods in the field. Accommodation and subsistence are covered for accepted applicants. For more information please visite the link below (in case of problems please copy the link into your browser) https://meetings.embo.org/event/21-protein-production Best wishes, Gerlind, on behalf of the organizing committee -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@univ-amu.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Erica Saphire speaking at ALS Colloquium in 6 hours
Dear James, thank you so much for putting into place all these outstanding seminars. Here a plead to access not only Erica Saphire's talk, but all the previous talks. I had a look at https://als.lbl.gov/news-events/seminars/, great list of seminars, but no way to access any recording. I know, this plead puts just extra work on you. In case you recorded or you will record, many thanks for sharing, in the limits of legal boundaries. Otherwise, just forget and thanks again for always being there to push forward great science. With best wishes, Gerlind On 08/12/2021 18:38, Gerard Bricogne wrote: Dear James, Thank you for this notification about what should be a captivating and inspiring talk. The time of 3pm PST is a little bit on the rough side for most European would-be listeners: is there a chance of putting in a plea that this talk be recorded and made available on demand, for at least a short period of time, through a link that you would broadcast soon after the event? Thank you in advance! With best wishes, Gerard. -- On Wed, Dec 08, 2021 at 09:06:53AM -0800, James Holton wrote: Greetings all! At 3pm PST Dec 8, 2021 (California time), I managed to get Erica Saphire to speak about her recent work at the ALS Colloquium. It is a forum for users and staff of the Advanced Light Source to communicate with each other about how we use the light. I asked Erica because she is a long-time, highly productive user who is doing some very timely work. Her title: A Global Consortium, Next-Generation SARS-CoV-2 Antibody Therapeutics and Stabilized Spike I think it absolutely brilliant how she's gotten so many different entities to work together. Thought that might be of interest if you have the time! Free and open to all, and I'm not sure if this is being recorded or not. Here are the links: https://lbnl.zoom.us/j/97680529569 https://als.lbl.gov/news-events/seminars/ -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=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@univ-amu.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] help needed with link description
Dear David and Rob, thanks a lot for your help and your suggestions. Following your suggestions I found in Coot the very neat solution "Make link (click 2 atoms ...): Much better than my previous dinosaur approach. Thanks again and all the best, Gerlind On 03/06/2021 20:17, David Briggs wrote: Hi Gerlind, Rob Nicholls gave a talk on how to deal with covalent linkages using AceDrg at CCP4 study weekend in 2020. https://youtu.be/p4oTJ0bjD3M <https://youtu.be/p4oTJ0bjD3M> And Paul Emsley has written up a guide about it... https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html Hopefully these will be useful for you. Good luck, Dave -- Dr David C. Briggs Senior Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == about.me/david_briggs *From:* CCP4 bulletin board on behalf of Gerlind Sulzenbacher *Sent:* Thursday, June 3, 2021 7:10:12 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] help needed with link description External Sender: Use caution. Dear all, I am going litteraly mad (or just old). I would like to make a covalent link between a carbohydrate moiety and and ASP of my well-cheered protein. The identifier for the carbohydrate moiety is MAD, chain C, res number 1. The link is established between C5 of MAD and OD2 of ASP 518, chain A. In the mad_monlib.cif I added the following: data_link_list loop_ _chem_link.id _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 _chem_link.name ASP-MAD ASP . . MAD . . bond_ASP-OD2_=_MAD-C5 # data_link_ASP-MAD # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd ASP-MAD 1 OD2 2 C5 . 1.370 0.040 In the entry PDB file I added the line: LINK OD2 ASP A 518 C5 MAD C 1 The log file of REFMAC tells me INFO: link is found (not be used) dist= 1.370 ideal_dist= 1.370 ch:AAA res: 518 ASP at:OD2 .->ch:CCC res: 1 MAD at:C5 . And the expression "not be used" is certainly the case, as the distance of the covalent bond changes from 1.37 to 1.6 Å. The data resolution is 1.8 Å. If somebody could please point out what I am doing wrong, I'd be very grateful. With best wishes, Gerlind -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@univ-amu.fr To unsubscribe from the CCP4BB list, click the following link: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1data=04%7C01%7C%7C360c620f3de94e6ef46808d926badcf6%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637583406295071625%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=C80B0ezyZ5AAWTgXEeVuLEfSw1QljocDI3Kzz6L9vxU%3Dreserved=0 <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1data=04%7C01%7C%7C360c620f3de94e6ef46808d926badcf6%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637583406295071625%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=C80B0ezyZ5AAWTgXEeVuLEfSw1QljocDI3Kzz6L9vxU%3Dreserved=0> This message was issued to members of https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BBdata=04%7C01%7C%7C360c620f3de94e6ef46808d926badcf6%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637583406295071625%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=ZatbCRXPwhVtvLeYyn%2FHMGFGlYKDG5EzQtytvaorIgg%3Dreserved=0 <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BBdata=04%7C01%7C%7C360c620f3de94e6ef46808d926badcf6%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637583406295071625%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=ZatbCRXPwhVtvLeYyn%2FHMGFGlYKDG5EzQtytvaorIgg%3Dreserved=0>, a mailing list hosted by https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2Fdata=04%7C01%7C%7C360c620f3de94e6ef46808d926badcf6%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637583406295071625%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=KSTwQ%2F9mP4RLd
[ccp4bb] help needed with link description
Dear all, I am going litteraly mad (or just old). I would like to make a covalent link between a carbohydrate moiety and and ASP of my well-cheered protein. The identifier for the carbohydrate moiety is MAD, chain C, res number 1. The link is established between C5 of MAD and OD2 of ASP 518, chain A. In the mad_monlib.cif I added the following: data_link_list loop_ _chem_link.id _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 _chem_link.name ASP-MAD ASP . . MAD . . bond_ASP-OD2_=_MAD-C5 # data_link_ASP-MAD # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd ASP-MAD 1 OD2 2 C5 . 1.370 0.040 In the entry PDB file I added the line: LINK OD2 ASP A 518 C5 MAD C 1 The log file of REFMAC tells me INFO: link is found (not be used) dist= 1.370 ideal_dist= 1.370 ch:AAA res: 518 ASP at:OD2 .->ch:CCC res: 1 MAD at:C5 . And the expression "not be used" is certainly the case, as the distance of the covalent bond changes from 1.37 to 1.6 Å. The data resolution is 1.8 Å. If somebody could please point out what I am doing wrong, I'd be very grateful. With best wishes, Gerlind -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@univ-amu.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Call for candidate for PhD position
Dear all, We are looking for a highly motivated student to be candidate for a PhD position in the field of glycobiology and situated at the interface between bacterial genetics and structural biology. The student will be hosted in two Marseille laboratories, located in proximity of the beautiful Calanque Natural resort. A full description of the call can be found in the attachment. Please feel free to spread the information. Thank you in advance for your time, With best wishes, Gerlind -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@univ-amu.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ PhD-call-glycobiology-Marseille.docx Description: MS-Word 2007 document
Re: [ccp4bb] strange crystals
Dear Dale, A warm thank you for pointing out what I had overseen. And a big thanks to all the others who commented so far, cheers, Gerlind On 16/02/2021 21:19, Dale Tronrud wrote: On 2/16/2021 11:47 AM, Gerlind Sulzenbacher wrote: Dear all, I wonder whether any of you have ever encountered such strange crystals. In the images you can download via the link below, crystal1 looks hollow, crystal2 looks like a cubic crystal embedded within a hexagonal arragement. I don't know the cause of the overall appearance that your cubic crystals are embedded within larger cubic objects. I do know that the projection of a cube, down its three-fold axis, to a plane will create a hexagon. I think that is the case in your second photo. The six-fold symmetry is actually the result of a special view of the same cubes you are seeing elsewhere. Dale Tronrud https://filesender.renater.fr/?s=download=71d70da4-5ea2-4cf3-ae5f-5d89545574ce May be all this is just an optical Fata Morgana. We are waiting for our next synchrotron beam time to see whether, and what kind of diffraction they could provide. In the meanwhile, I leave you with the beauty and may be somebody want's to comment. with best wishes, Gerlind -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@univ-amu.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] strange crystals
Dear all, I wonder whether any of you have ever encountered such strange crystals. In the images you can download via the link below, crystal1 looks hollow, crystal2 looks like a cubic crystal embedded within a hexagonal arragement. https://filesender.renater.fr/?s=download=71d70da4-5ea2-4cf3-ae5f-5d89545574ce May be all this is just an optical Fata Morgana. We are waiting for our next synchrotron beam time to see whether, and what kind of diffraction they could provide. In the meanwhile, I leave you with the beauty and may be somebody want's to comment. with best wishes, Gerlind -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@univ-amu.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Open position - data management in biophysics
. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@univ-amu.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Post-doctoral position in structural glycobiology, AFMB, Marseille
Dear all, a post-doctoral position funded by ANR project GAGOsynth is available for a structural biologist in the team “Structural Glycobiology and Neurobiology” at the AFMB laboratory, Marseille, France. We are seeking for an enthusiastic, highly motivated and creative individual with solid knowledge and expertise in structural biology and biochemistry to investigate the structure-function relationships of enzyme complexes involved in heparan sulfate (HS) biosynthesis in collaboration with the groups of Hugues Lortat-Jacob and Guy Schoehn at IBS (Grenoble, France). In particular, we aim at deciphering how the concerted action of HS biosynthetic enzymes can encode defined oligosaccharide motifs along the polymer to modulate activity of various protein ligands. Candidates must have a recent Ph.D. (or being in the process of completing one) in a relevant field with a demonstrated record of productive research. Experience in protein expression, particularly in eukaryotic cells, in biochemistry, and in X-ray crystallography or single particle cryo-EM is highly desirable. Applicants are invited to submit i) a cover letter describing research interests, ii) a CV and iii) the names and contact details of three references to Yves Bourne (yves.bou...@afmb.univ-mrs.fr)./ / http://www.afmb.univ-mrs.fr/post-doctoral-position,587/ / Application deadline: April 30, 2019/ / -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@afmb.univ-mrs.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Fwd: Re: [ccp4bb] off-screen display window - problem solved
Dear all, a big thanks, especially for the suggestions from Stuart, Phil and Huw. I could solve the problem, but working it the other way around: the option "Displays have separate spaces" on my computer was off. I turned it on, logged out, no result, turned it off, logged out again, and now the windows appear on my screen. Well, the logic behind is not very clear, but at least I know what to do next time it happens, I wish you all a nice day, Gerlind Forwarded Message Subject:Re: [ccp4bb] off-screen display window Date: Tue, 12 Feb 2019 11:29:24 + From: Stuart McNicholas To: Gerlind Sulzenbacher Dear Gerlind, With thanks to Phil Evans and Huw Jenkins there are a couple of suggestions that I've seen passed around: Phil found this on Stack Exchange: "I met this problem before and it's very annoying. Finally, I realized that because the size and resolution of additional monitor are different from my Mac's. Those resulted in a 'non-existing' space between monitors. Sometimes windows would locate in that space and could not be moved. Luckily, I found we can remove the 'non-existing' space by changing settings on Mac. " System Preferences->Mission Control and uncheckDisplays have separate spaces." Then re-login MAC, the problem should be gone." Huw had success with: "I tried that first (as I knew about that one) but it didn't fix it as X11 Full-screen mode was also on. Turning off 'Displays have separate spaces' and Full-screen mode seemed to result in normal behaviour..." Others may know a more definitive solution. Best wishes, Stuart On Tue, 12 Feb 2019 at 11:24, Gerlind Sulzenbacher <mailto:gerlind.sulzenbac...@afmb.univ-mrs.fr>> wrote: Dear members of the community, when I launch ccp4i or Coot on my macbook OSMojave, the graphical window goes off-screen. I had the problem before and it went away by connecting to a new display screen - of course I was pleased about it, but yet I could not understand the logic behind this behaviour. The problem came back when I connected my Macbook to a videoprojector, and since then I do not find a solution. Re-installation of ccp4 and coot did not help. Has anybody encountered the same problem and found a way around? Thanks in advance for your advice, Gerlind -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@afmb.univ-mrs.fr <mailto:gerlind.sulzenbac...@afmb.univ-mrs.fr> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] off-screen display window
Dear members of the community, when I launch ccp4i or Coot on my macbook OSMojave, the graphical window goes off-screen. I had the problem before and it went away by connecting to a new display screen - of course I was pleased about it, but yet I could not understand the logic behind this behaviour. The problem came back when I connected my Macbook to a videoprojector, and since then I do not find a solution. Re-installation of ccp4 and coot did not help. Has anybody encountered the same problem and found a way around? Thanks in advance for your advice, Gerlind -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@afmb.univ-mrs.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] 5th Banff Meeting on Structural Dynamics, 18/19th Febr. - 22nd February 2017
Hi Carlos and friends, somewhere I understood that this discussion was about women in SCIENCE, and not about politics in general. But being a woman myself, maybe I understood wrongly. Thanks Eddie and all the other sensitive people of male gender for bringing up and sustaining this discussion. Happy to see what follows. all the best, Gerlind Le 25/11/16 à 21:05, Carlos Pla Prats a écrit : Like it happened when Trump won the election, someone with a slightly different view will reply and then we will agree to use this board only for science. -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@afmb.univ-mrs.fr
[ccp4bb] PhD position in the laboratory AFMB, Marseille
Dear all, A PhD position within the Marie-Curie (ITN) network is available in the laboratory AFMB (Marseille, France) to work on the mRNA capping machinery of Alphaviruses. A detailed description of the topic and eligibility can be found at the following link http://hactar.phrmy.cf.ac.uk/antivirals/node/13#overlay-context=node/7 Interested candidates should contact Bruno Coutard (bruno.cout...@afmb.univ-mrs.fr) Best regards, Gerlind -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@afmb.univ-mrs.fr
[ccp4bb] Registration deadline upcoming: EMBO Practical Course on HTP Methods for Protein Production and Crystallization
Dear all, just a reminder that the deadline for application for the EMBO Practical Course on HTP Methods for Protein Production and Crystallization to be held in Marseille, France, from 29 June to 8 July 2015 is Tuesday, 7th of April. For more information and for application, please visit: http://events.embo.org/15-htp-protein/ Best wishes, Gerlind Sulzenbacher, on behalf of the Organizers -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@afmb.univ-mrs.fr
[ccp4bb] EMBO Practical Course on HTP Methods for Protein Production and Crystallization
EMBO Practical Course on HTP Methods for Protein Production and Crystallization Marseille, France, 29 June to 8 July 2015 Deadline for application: 7 April 2015 Dear Colleagues, I am glad to announce the EMBO Practical Course on High Throughput methods for protein production and crystallization hosted at the laboratory AFMB in Marseille, France, from 29 June to 8 July 2015. We would be glad if you could inform your colleagues and students about the course. The course is intended for PhD students and young researchers using highthroughput methods for expression and crystallization of soluble proteins. The goal is to provide participants with the current knowledge in the use of the most innovative methods in the field. For more information and for application, please visit: http://events.embo.org/15-htp-protein/ Best wishes, Gerlind Sulzenbacher, on behalf of the Organizers -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@afmb.univ-mrs.fr
[ccp4bb] EMBO Practical Course on HTP Methods for Protein Production and Crystallization, Marseille, 4-13 July
EMBO Practical Course on HTP Methods for Protein Production and Crystallization AFMB, France, 4 to 13 July 2011 Deadline for application: 15 April 2011 (has been extended) Dear Colleague, I am glad to announce the EMBO Practical Course on High Throughput methods for protein production and crystallization hosted at the laboratory AFMB in Marseille, France, from 4 to 13 July 2011. On behalf of the organizers I would like to ask you to please let your colleagues and students know about our course by posting this information on the notice boards of your institute. Please feel free to download the course flyer for an A4 printout here: http://events.embo.org/11-HTP/postera.pdf The course is intended for PhD students and young researchers using highthroughput methods for expression and crystallization of soluble proteins. The goal is to provide participants with the current knowledge in the use of the most innovative methods in the field. There is no registration fee and accommodation and subsistence are covered for accepted applicants. Scientists from industry will be required to pay a fee of € 1000. A detailed programme will be available very soon. For more information and for application, please visit: http://events.embo.org/11-HTP/ Best wishes, Gerlind Sulzenbacher on behalf of the Organizers -- Gerlind Sulzenbacher Architecture et Fonction des MacromolÈcules Biologiques UMR6098 CNRS, UniversitÈ de Provence, UniversitÈ de la MÈditerranÈe Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@afmb.univ-mrs.fr -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
