[ccp4bb] Imosflm help twinned crystal data

Hi all I am trying to use imosflm in ccp4i2 to re-process my diffraction data, since the autoprocessed data from XDS at the synchotron is not giving me a solution. I think the crystal has decent resolution around 2.5-2.6A. I think the crystal might be twinned however and thus might be making str

[ccp4bb] CCP4i2 COOT no showing model or map?

Has anyone had the issue where they run coot from ccp4i2 on say a refmac5 job and when coot opens the model or even the map do not show up? its just empty? Does anyone know how to fix this and display the model and map? I like ccp4i2 so far more than ccp4 and I did not have this issue with ccp4

[ccp4bb] Data Processing questions

Hi All, I just collected a lot of data for native crystals and Seleno-methionine derivative crystals. I have a couple of questions 1. How do I know which images to process and which ones to exclude which might be radiation damaged and not be good to further process? I have been told it is possib

[ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

Hello all, I have a data collection trip next week and plan to collect data on selenomethionine derivative crystals at the al831 beamline. Are there any resources, tips, tutorials, literature etc. That you can recommend to help me prepare for these experiments. Also is there a way to plug in th

[ccp4bb] In-Silico Structural Biology School - Bari, October 2024

please visit: https://www.gene2structure.it/issb/ https://school2024.cristallografia.org/ Registration deadline: 1st July 2024 For any queries about the school, please contact directly secretar...@gene2structure.it<mailto:secretar...@gene2structure.it> Best wi

[ccp4bb] ECM34 "MS01 - Nucleic acids - protein interactions"

am looking forward to receiving your contributions. The deadline for abstract submission has been extended to May 7th. https://www.ecm34.org/abstracts Best regards Marco Nardini To unsubscribe from the CCP4BB list, click the

Re: [ccp4bb] Crystallographic data table

am not a phenix user typically but may need to for the table function. https://www.dropbox.com/scl/fi/kkl2fu816q5wae1q81u6f/summary.jpg?rlkey=oaz31dhdxoikstw85waan21wg&dl=0 Thank you Marco To unsubscribe from the CC

[ccp4bb] Crystallographic data table

Marco 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 hoste

Re: [ccp4bb] Superimposition save as PDB for ccp4 refmac question

This worked Thanks! 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

[ccp4bb] Superimposition save as PDB for ccp4 refmac question

Hello all, Does anyone know how to save a superimposed pymol or chimerax session as a PDB file in correct format so that I can used it for ccp4 refmac? I am trying to superimpose a protein with DNA bound onto the same protein from a different species without the DNA. I just want the DNA from the

Re: [ccp4bb] Difficult Molecular replacement

https://www.dropbox.com/scl/fi/aqxm6s28mwbvufx5vkt4z/j7pointless.log?rlkey=075kia624ehmtzugnu5n8ymy0&dl=0 Here is a link to the pointless file , thank you for your help! To unsubscribe from the CCP4BB list, click the follow

Re: [ccp4bb] Difficult Molecular replacement

https://www.dropbox.com/scl/fo/pmw9nisdmq53yir2jqcmu/h?rlkey=zaj6cnknkjgkowrzf0vrmqdyf&dl=0 Here is a link to my Molecular replacement and asymmetric unit contents logfiles. I ran Simple molecular replacement phaser MR through ccp4 cloud with my .mtz that was auto-processed at the ALS ligh

Re: [ccp4bb] Difficult Molecular replacement

Hello Todd, I get the best solution for p22121 space group after MR with an LLG score of 640 from phaser. and the Rfree is .4748. However after MR refinement does not lower the Rfree and it appears to make the Rfree worse. The XDS software indicates that my best solution is P21 21 2. Often Phase

[ccp4bb] Difficult Molecular replacement

Hello all, I recently collected data on some plate crystals for a previously uncharacterized protein at the ALS light source. The XDS auto-data processing log output indicates that my resolution is 2.8 angstroms. The protein is a helicase with homologs already in the protein data bank making it

[ccp4bb] Post-Doctoral opportunity in Pavia, Italy

CV and a cover letter to: marco.lolic...@unipv.it Informal inquiries can be also addressed to the same e-mail. Kind Regards, Marco Lolicato -- Marco Lolicato, PhD Associate Professor of Molecular Biology Università di Pavia Dipartimento di Medicina Molecolare Palazzo Golgi / Spallanzani Via

[ccp4bb] Open post-doc position (Xtal-cryoEM)

Messaggio originale Da: "Marco Nardini" Data: 23/nov/2022 07.59.31 Oggetto: Open post-doc position Xtal-cryoEM A: (marco.nardini) Marco Nardini Two years post-doc position (possibly renewable) at the University of Milano (UNIMI), Department of Biosciences R

[ccp4bb] Postdoc position in the Marcia lab (EMBL) - deadline May 31st

submit the application can be found at: https://www.embl.org/jobs/position/GR00182 Thank you! Marco -- Dr. Marco MARCIA Group Leader EMBL Grenoble 71 Avenue des Martyrs, room 254 38042 Grenoble Cedex 09 France phone (lab): 0033-(0)476207634 phone (office): 0033-(0)476207759 fax: 0033-(0

[ccp4bb] Postdoc position in the Marcia lab (EMBL) - deadline Feb 25th

to submit the application can be found at: https://www.embl.org/jobs/position/GR00178 Thank you! Marco -- Dr. Marco MARCIA Group Leader EMBL Grenoble 71 Avenue des Martyrs, room 254 38042 Grenoble Cedex 09 France phone (lab): 0033-(0)476207634 phone (office): 0033-(0)476207759 fax: 0033-(0

Re: [ccp4bb] EMBO Practical Course on Characterization of macromolecular complexes by integrative structural biology

Dear all a kind reminder about this course application deadline, which is approaching now in 2 weeks. Regards Marco On 19/12/2021 16:11, Marco MARCIA wrote: Dear all, please take note of the EMBO course announced below and do not miss its application deadline (Jan 31st)! Kind regards

[ccp4bb] EMBO Practical Course on Characterization of macromolecular complexes by integrative structural biology

Dear all, please take note of the EMBO course announced below and do not miss its application deadline (Jan 31st)! Kind regards, Marco Marcia ** EMBO Practical Course on Characterization of macromolecular complexes by integrative structural biology May 28 - Jun 04, 2022

Re: [ccp4bb] pictures in emails

Dear All, what about linking to any free cloud service for large attachments? Isn't CCP4 7.1 already such a cloud? Best, marco Marco Patrone – PhD Biocrystallography Unit Division of Immunology, Transplantation, and Infectious Disease (DITID) DIBIT – San Raffaele Scientific Institut

Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

, Best wishes Marco Il giorno mar 22 dic 2020 alle ore 17:04 Irwin Selvam < irwin.sel...@postgrad.manchester.ac.uk> ha scritto: > Hi, > > I'd like to reprocess some data that were collected on an Eiger2 detector > at Diamond with Xia2Dials using CCP4i2's GUI. I&#x

[ccp4bb] Postdoc positions at Monash University

development position will heavily focus on image processing but does not need to have prior cryoEM experience, although it would help. Anyone interested, please contact me directly and send me a CV. Cheers Alex -- *Alex de Marco, PhD* Associate Professor Monash University *Dept. of Biochemistry

[ccp4bb] Open position at EMBL Grenoble - Scientific Expert for Eukaryotic Protein Production

/searchjobs/index.php?ref=GR00141&newlang=1&loc Regards Marco -- Dr. Marco MARCIA Group Leader EMBL Grenoble 71 Avenue des Martyrs, room 254 38042 Grenoble Cedex 09 France phone (lab): 0033-(0)476207634 phone (office): 0033-(0)476207759 fax: 0033-(0)476207199 email: mmar...@embl.fr web: https:/

Re: [ccp4bb] Open position at EMBL Grenoble - Scientific Expert for Eukaryotic Protein Production

Dear all a kind reminder about the open position advertised below. Regards Marco On 12/11/2019 09:46, Marco MARCIA wrote: Dear all I am writing to let you know that EMBL Grenoble has an opening for a Scientific Expert for Eukaryotic Protein Production. *Closing date: Jan 15th 2020.* You can

[ccp4bb] Open position at EMBL Grenoble - Scientific Expert for Eukaryotic Protein Production

&newlang=1&loc Regards Marco -- Dr. Marco MARCIA Group Leader EMBL Grenoble 71 Avenue des Martyrs, room 254 38042 Grenoble Cedex 09 France phone (lab): 0033-(0)476207634 phone (office): 0033-(0)476207759 fax: 0033-(0)476207199 email: mmar...@embl.fr web: https://embl.fr/research/uni

[ccp4bb] PhD position in structural biology at EMBL Grenoble

free to share this message with potential candidates. Kind regards Marco Marcia -- _ Dr. Marco MARCIA Group Leader EMBL Grenoble 71 Avenue des Martyrs, room 254 38042 Grenoble Cedex 09 France phone (lab): 0033-(0)476207634 phone (office): 0033-(0)476207759

[ccp4bb] 2-year postdoctoral position available - Structural Microbiology, Institut Pasteur

the position and contacts of a couple of referees to marco (dot) bellinzoni (at) pasteur (dot) fr. Please send applications or informal enquiries no later than June 5. Best regards, Marco === Marco Bellinzoni Unité de Microbiologie Structurale Institut Pasteur 25

[ccp4bb] Prato cryoEM course 2019 (Tuscany) - few sits still available

Institute for Biophysics, Goethe University of Frankfurt. *Timothy Grant*, Janelia Research Campus, Ashburn, VA, USA *Daniel Castano-Diez*, Biozentrum, University of Basel, Basel, Switzerland *Carlos Oscar Sorzano*, National Center for Biotechnology, Madrid, Spain *Alex de Marco*, Monash University

[ccp4bb] cryoEM course in Prato Tuscany

*Daniel Castano-Diez*, Biozentrum, University of Basel, Basel, Switzerland *Carlos Oscar Sorzano*, National Center for Biotechnology, Madrid, Spain *Alex de Marco*, Monash University, Melbourne, Australia *Hans Elmlund*, Monash University, Melbourne, Australia *Dominika Elmlund*, Monash University

[ccp4bb] 3rd International Workshop on Biological Membranes (19-22 August 2018, Helsinki)

This might be of interest to someone: *** Dear All, We would like to remained you that *the early registration deadline (April 15, 2018)* for the 3rd International Workshop on Biological Membranes (19-22 August 2018, Helsinki) is approaching. Registration link: https://www.helsinki.fi/en/c

[ccp4bb] deadline approaching: EMBO Practical Course on Characterization of macromolecular complexes by integrative structural biology

Dear all, please note that the deadline for the EMBO course announced below is approaching soon (Feb 28th). Kind regards, Marco Marcia ** EMBO Practical Course on Characterization of macromolecular complexes by integrative structural biology May 12-19, 2018 EPN campus

[ccp4bb] EMBO Practical Course on Characterization of macromolecular complexes by integrative structural biology

Dear ccp4 community, I would like to remind you of the announcement below. You can now find the complete programme of the Course following the indicated link. Kind regards, Marco Marcia ** EMBO Practical Course on *Characterization of macromolecular complexes by

Re: [ccp4bb] the purification process of protein, used for crystallization

day using this sequence of columns and the reproducible protocol gave consistently well-diffracting crystals. Hope this helps. Ciao, Marco 2017-11-17 13:44 GMT+00:00 Liuqing Chen <519198...@163.com>: > Hello everyone! > I have listened someone suggested that, first

[ccp4bb] cryoEM course in Prato

://simplecryoem.com/Prato/workshop2018.html or should you have any more questions feel free to contact us. Looking forward to see you in Tuscany Alex, Hans and Dominika -- Alex de Marco, PhD Associate Professor Monash University *Dept. of Biochemistry and Molecular Biology

[ccp4bb] EMBO Practical Course on Characterization of macromolecular complexes by integrative structural biology

structural biology of large multisubunit complexes. *Deadline for registration: 28 February 2018* We are looking forward to receiving your applications! Marco on behalf of the organizing committee: Marco Marcia, Montserrat Soler Lopez, Carlo Petosa, Estelle Mossou, Daniele De Sanctis

[ccp4bb] cryoEM course Prato 2018

speakers: *Daniel Castano Diez*, Biozentrum, University of Basel, Basel, Switzerland *Alex de Marco*, Monash University, Melbourne, Australia *Hans Elmlund*, Monash University, Melbourne, Australia *Friedrich Foerster*, University of Utrecht, Utrecht, Netherlands *Timothy Grant*, Janelia Research

[ccp4bb] Post-Doc in RNA-Protein interactions

interactions pharmacologically. This project is a collaboration between Cellzome-GSK and two leading research groups in the field of RNA-protein interaction: the group of Matthias Hentze (EMBL-Heidelberg) and the group of Marco Marcia (EMBL Grenoble). This project offers the opportunity to work in

[ccp4bb] Postdoctoral position at EMBL Grenoble

scientific research organisations in the world. The Headquarters Laboratory is located in Heidelberg (Germany), with additional sites in Grenoble (France), Hamburg (Germany), Hinxton (UK) and Monterotondo (Italy). EMBL is seeking to recruit a postdoctoral researcher to join the group of Marco Marcia

[ccp4bb] Postdoctoral Position at EMBL Grenoble

. Marco Marcia -- _ Dr. Marco MARCIA Yale University, KBT 834 266, Whitney Avenue New Haven, CT - 06511 USA phone (lab): +1-203-432-6370 phone (office): +1-203-432-5546 fax: +1-203-432-5316 email: marco.mar...@yale.edu web: http://www.pylelab.org

Re: [ccp4bb] Invisible atoms in ligands

ors option might be preferable. Hope this helps, Ciao Marco 2014-06-13 10:45 GMT+01:00 Frank von Delft : > Hi all - talking about ligands, a quick question on that old conundrum, > of what to do about invisible atoms -- build them with occ=0, or omit > them? > > For bits o

[ccp4bb] [ccp4] Research Technician Position at EMBL Grenoble

11th. Please, forward this link to anyone you think may be interested. Thank you. Marco -- _ Dr. Marco MARCIA Yale University, KBT 834 266, Whitney Avenue New Haven, CT - 06511 USA phone (lab): +1-203-432-6370 phone (office): +1-203-432-5546 fax: +1-203-432-

Re: [ccp4bb] Room temperature data collection

.* (2013). D*69*, 1617-1632 http://scripts.iucr.org/cgi-bin/paper?S0907444913012274 ). If you want to know more, please check http://diamond.ac.uk/mx-home/ Hope this helps. Ciao, Marco 2014-02-06 9:51 GMT+00:00 Theresa Hsu : > Dear crystallographers > > Just out of curiosity, is it po

[ccp4bb] Postdoctoral position - Structural Microbiology, Institut Pasteur

f referees) by *November 15* to marco.bellinzoni at pasteur.fr. Best, Marco -- == Marco Bellinzoni Unité de Microbiologie Structurale Institut Pasteur 25, rue du Dr. Roux 75724 Paris Cedex 15 France Tel. +33 (0)1 45688608 Fax. +33 (0)1 45688604 ==

Re: [ccp4bb] OT: "Who's Afraid of Peer Review?"

on the intrinsic quality and not from the names on it or from the country. I'm looking forward to see your opinion. Marco Il giorno 09/ott/2013, alle ore 15.00, Miguel Ortiz Lombardia ha scritto: > Hi denizens, > > Now that Biology has gone missing, at least in the programs

[ccp4bb] postdoctoral position available in the Pyle lab at Yale

Dear all on behalf of Prof. Pyle, I would like to inform you that a postdoctoral position is available in our lab at Yale. Please, see the announcement below. Kind regards Marco Marcia The Pyle laboratory at Yale (www.pylelab.org) is looking for an exceptional and highly motivated postdoctoral

[ccp4bb] postdoctoral position available in the Pyle lab at Yale

Dear all on behalf of Prof. Pyle, I would like to inform you that a postdoctoral position is available in our lab at Yale. Please, see announcement below. Kind regards Marco Marcia The Pyle laboratory at Yale (www.pylelab.org) is looking for an exceptional and highly motivated postdoctoral

Re: [ccp4bb] installation in sw or sw64?

, the latest release of ccp4 suite (6.3.0) doesn't require fink and you can install the entire package (coot included) by downloading the .dmg file from ccp4 website. Moreover, if remember correctly, ccp4 6.3.0 doesn't need X11, too. So, you will be safe proceeding this way. Marco

Re: [ccp4bb] How to identify unknow heavy atom??

collecting multiple spectra. HTH Best regards, Marco

[ccp4bb] Random coil protein

andom coil. I would like to express and crystallize the complex between them. I'm wondering if anyone could give me tricks how to express the random coils portion in E. coli and keeping it in a soluble form. Could co-expression help? Thank you in advance, all the best, Marco

Re: [ccp4bb] prescission protease cutting site

Dear McCully, I always used this protease with a cleavage success near to 100% at 4°C over night without shaking. Concerning the construct, I putted the first Met just after the sequence LEVLFQ/GP SSP, so I added only three aminoacids after the cleavage site. All the best, Marco Il

Re: [ccp4bb] XDS question

f I process only the strong spots I have those cell parameters: a=b=96.66 c=112.26alpha=beta=gamma= 90 f I process all the spots I have those cell parameters: a=b=216.4 c=112.4 alpha=beta=gamma= 90 In both cases the space group is I422. Thank you again to all, do you have any other suggestion? Marco

[ccp4bb] XDS question

ttern to have a structure of the apo-protein? Is a good idea discard the strongest spots and try to analyze only the weak spots? If yes, how I can do it? All the best, Marco

[ccp4bb] AutoXDS

Dear all, suggestion how to run autoxds on MAC OSX? I downloaded a script without success...do you know if are there others? Thanks, Marco

[ccp4bb] CNIO International PhD and Postdoctoral Programmes_2011 call

s> Websites: www.cnio.es/postdoc <http://www.cnio.es/postdoc> and www.cnio.es/phd <http://www.cnio.es/phd> -- ------- Marco Mazzorana, PhD Structural Biology and Biocomputing Programme CNIO - Centro Nacional de Investi

[ccp4bb] How to see miller indeces onto images

. The aim is look at particular reflections into the original film and to observe possible intensity modulation. Anyone knows a tool that do it? Thanks. Marco Antonio Seiki Kadowaki Department of Biochemistry and Molecular Biology Universidade Federal do Paraná Curitiba-Pr - Brazil

Re: [ccp4bb] creating new ligand cif file

Hi Paul, you can use PRODRG server at Dundee university ( http://davapc1.bioch.dundee.ac.uk/prodrg/ ) It generates libraries in different formats... you just need to copy/paste in your preferred text editor. HTH Marco Paul Lindblom wrote: Hi all, I need to create a cif file for a new

Re: [ccp4bb] protein purity in SAXS

another dataset at different concentration, essentially because of radiation damage issues. Hope these advices may help you. Regards, Marco --- Marco Mazzorana, PhD Structural Biology and Biocomputing Programme CNIO - Centro Nacional

Re: [ccp4bb] insoluble ligand

. Hope this will help you. Marco