Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

Wankowicz From: CCP4 bulletin board on behalf of Krieger, James M Sent: Monday, May 13, 2024 10:22 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility It definitely is impressive but it also has clear limitations On 13

Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

AIL.AC.UK Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility I tried it yesterday and I was really shocked by how fast it is. When I was preparing to submit my second job, the first one was already finished, which made me think that I was definitely doing something

Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

Is it just me who is really impressed by it? Am I missing something? Get Outlook for Android<https://aka.ms/AAb9ysg> From: CCP4 bulletin board on behalf of Rafael Marques Sent: Monday, May 13, 2024 3:13:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4b

Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

I tried it yesterday and I was really shocked by how fast it is. When I was preparing to submit my second job, the first one was already finished, which made me think that I was definitely doing something wrong. Probably I was...Best wishes Rafael Marques On 13 May 2024 09:53, Harry Powell

Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

Hi Harry, Thanks for sharing this. I already read and endorsed the letter. However, I do have a comment - since one of the letter signatories was a reviewer of the paper, wouldn't the shortcomings described in the letter be grounds for rejection of the manuscript? Best regards, Pedro On

[ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

Hi folks This arrived in my inbox this morning, and I believe that it may provoke some discussion… Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν Best wishes! Harry >From: Stephanie Wankowicz >Sent: Saturday, May 11, 2024 3:31 PM >To: James Fraser ; Pedro Beltrao >

[ccp4bb] Fwd: REMINDER -- EMBO practical course (8th-12th July, 2024) on time-resolved serial macromolecular crystallography (TR-SX) at French-Alps

Dear Everyone! A quick reminder for the deadline to register to our EMBO course on Time-resolved serial macromolecular crystallography! Deadline is in 1 week! Please hurry up to be a part of this excellent brand new course (details given below). Bests, shibom On behalf of *Scientific

[ccp4bb] Fwd: Sixth ESRF-INSTRUCT workshop on sample preparation for cryo-EM, May 28-30, 2024

- Dear all, Quick reminder that the last date to register for the ESRF-INSTRUCT hands-on workshop on sample preparation for cryo-EM is approaching (7th April). The registration link is below.

[ccp4bb] Fwd: [ccp4bb] mmCIF files from PDB format for AlphaFill

Hi Harry, Unfortunately, I did not see that the latest binary update was from 2008. I do not have access to any newer binaries for Linux, as I'm on MacOS. Maybe you can use the MineProt software from the quote I mentioned previously to (in a roundabout way) accomplish the CIF file generation?

[ccp4bb] Fwd: postdoc post at world-renowned Astbury Centre, in Leeds, UK

-- Forwarded message - From: Helen McAllister Date: Fri, 16 Feb 2024 at 13:10 Subject: [CCP4] Please could you advertise another post for us? To: c...@listserv.stfc.ac.uk Dear Sirs, Please could you advertise the following post on your website? (This is by coincidence the

[ccp4bb] Fwd: Open Position (tenure track) - Scientist in Neutron Spectroscopy - at PSI/LNS

Prof. em. Gebhard F.X. Schertler Strukturbiologie ETH Zürich ERC Investigator Head of Biology and Chemistry Division Paul Scherrer Institut OSRA 007 CH-5232 Villigen PSI gebhard.schert...@psi.ch phone +41 56 310 4265 Anfang der weitergeleiteten Nachricht: Von:

[ccp4bb] Fwd: [CCP4] Postdoc position currently available in Leeds

-- Forwarded message - From: Helen McAllister Date: Tue, 5 Dec 2023 at 11:57 Subject: [CCP4] Postdoc position currently available in Leeds To: c...@listserv.stfc.ac.uk Dear Sirs, Please would it be possible to advertise the job below to your members for us? (You may need to

[ccp4bb] Fwd: Post-Doctoral Position in Integrative structural biology of sarcomeric cytoskeleton in @EMBL Grenoble

Dear All, We are recruiting a highly motivated a highly motivated*Post-Doctoral Scientist *to join**our teamat EMBL Grenoble, interested in the molecular mechanisms underlying the architecture and assembly of muscle sarcomeres, particular Z-discs. We use a multidisciplinary approach to

Re: [ccp4bb] Fwd: radiation damage and image discard

Thanks, Clemens, yet more program/literature to study (and to come)! Jorge On 10/31/23 12:41, Clemens Vonrhein wrote: Dear Jorge, as Harry mentioned, autoPROC [1] will automatically exclude image ranges that are significantly worse than the rest (i.e. add mostly noise). This could be due to

Re: [ccp4bb] Fwd: radiation damage and image discard

Dear Jorge, as Harry mentioned, autoPROC [1] will automatically exclude image ranges that are significantly worse than the rest (i.e. add mostly noise). This could be due to radiation damage, badly centred crystals or anything else. The so-called "fitness parameter" it uses takes multiplicity and

[ccp4bb] Fwd: radiation damage and image discard

Hi, Well, it seems there are already many good indications to study and to work on. Thanks, Oliver, Kay, Harry and Graeme! Now, brain and hands on! Jorge Forwarded Message ... Dear all, I have found many fundamental studies on image processing and

[ccp4bb] Fwd: Position open in the HILIFE Instruct-FI cryoEM unit for a research technician - please distribute

Daer All, FYI, we have a job opening in CryoEM for research technician in Helsinki. Best, Tommi Tommi Kajander, Ph.D. Head of Unit, Protein crystallisation INSTRUCT-HiLIFE Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O. Box 65) 00014 Helsinki, Finland p. +358-50-4480991

[ccp4bb] Fwd: Post-doc opportunity in integrative structural biology (Carlomagno Group, University of Birmingham)

Dear All, Please see the link below for details about a post-doc (Research Fellow) position available in the field of integrative structural biology, based in the group of Prof. Teresa Carlomagno at the University of Birmingham. Research Fellow in Integrative Structural Biology, School of

[ccp4bb] Fwd: Crystallographic Computing School

Dear all Those of you who are travelling to Melbourne for the IUCr Congress and General Assembly in August may be interested in this (which finishes in time to get to the opening ceremony of the main Congress). To get an idea of the content of the workshop, you may wish to look at tetails of

Re: [ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2

To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2 -- Forwarded message - From: Nicholas Clark mailto:ndcla...@buffalo.edu>> Date: Mon, Feb 6, 2023 at 6:44 AM Subject: Re: [ccp4bb] Issues with Coot an

[ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2

-- Forwarded message - From: Nicholas Clark Date: Mon, Feb 6, 2023 at 6:44 AM Subject: Re: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2 To: Julia Griese Julia, I have the same issue with PyMOL. After it opens the blank session, if you return to the file explorer

[ccp4bb] Fwd: Register for the Antiviral Drug Discovery (AViDD) Open Science Forum virtual meeting Wed 15 Feb 11.00A ET

Hello all - slightly off-topic, but many BB readers will find the talks at this forum of direct or indeed indirect interest. They will run monthly, for as long as the AViDD awards run (currently middle 2025), and will cover topics of antiviral drug discovery and development, from early

[ccp4bb] RES: [ccp4bb] Fwd: Re: [ccp4bb] Calculate charge on protein surface

"A sorte acompanha uma mente bem treinada" De: Jon Cooper<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk> Enviado:quinta-feira, 29 de dezembro de 2022 13:20 Para: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>

Re: [ccp4bb] Fwd: Re: [ccp4bb] Calculate charge on protein surface

Dear Boaz I think your original answer must have been steganographic ;-0 Maybe white text on a white background ;-? Anyway, I can see it below now that I have started typing this reply, and advice is excellent. My answer to Rafael's question would be to look at apbs:

[ccp4bb] Fwd: Re: [ccp4bb] Calculate charge on protein surface

Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel -- Forwarded message -- From: בעז שאנן Date: Dec 28, 2022 17:13 Subject: Re: [ccp4bb] Calculate charge on protein surface To: Rafael Marques Cc: Hi In ucsf-chimera you can "walk" with the

[ccp4bb] Fwd: Postdoc position in crystallography-driven drug discovery, Yue Lab at Newcastle University

A reminder of the below postdoc position in crystallography-driven drug discovery at Newcastle University, with deadline in a week (*Friday 18th November*) Best wishes *Wyatt Yue* Professor of Structural Biology Biosciences Institute Faculty of Medical Sciences Newcastle University NE2 4HH

[ccp4bb] Fwd: [ccp4bb] Another folding AI

Begin forwarded message: From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>> Subject: Re: [ccp4bb] Another folding AI Date: November 5, 2022 at 12:13:04 PM EDT To: "Nave, Colin (DLSLtd,RAL,LSCI)" mailto:colin.n...@diamond.ac.uk>> As notable a scientist as Maxwell was, he also has been

[ccp4bb] Fwd: Postdoctoral Fellow position at University of Texas Health Science Center San Antonio

My research group at UT Health San Antonio is looking for a creative and self-motivated Postdoctoral Fellow to study the structures and mechanisms of nucleic acid enzymes. We will use X-ray crystallography, cryoEM, and enzyme biochemistry to address basic

[ccp4bb] Fwd: Reminder: CryoEM Centers Webinar Series starts in 1 day

This presentation might help. The live webinar is over but you might find the recorded version sometime time later. Good luck John Begin forwarded message: > From: Zoom > Date: July 20, 2022 at 6:13:22 AM HST > To: "j.hasty" > Subject: Reminder: CryoEM Centers Webinar Series starts in 1 day

[ccp4bb] Fwd: job opening: Scientist, X-ray Crystallography - San Diego, CA

*Scientist, X-ray Crystallography - San Diego, CA* Pharmaceuticals *Job Description * Janssen Research & Development, L.L.C., a division of Johnson & Johnson's Family of Companies is recruiting for a Scientist, X-ray Crystallography, located in La Jolla, CA! At the Janssen Pharmaceutical

Re: [ccp4bb] Fwd: ACA2022: Travel Grant Application Deadline March 31, 2022

This may be a good one for you as well. And they have travel award due mar 31. Yang > On Mar 16, 2022, at 4:04 PM, Anna Gardberg wrote: > > There is a travel award opportunity for students and postdocs to attend ACA > 2022 in Portland, Oregon, July 29 - August 2, 2022. I encourage you to

[ccp4bb] Fwd: ACA2022: Travel Grant Application Deadline March 31, 2022

There is a travel award opportunity for students and postdocs to attend ACA 2022 in Portland, Oregon, July 29 - August 2, 2022. I encourage you to apply! The application deadline closes in two weeks. -Anna S. Gardberg, PhD ACA Meeting Committee Odyssey Pharmaceuticals -- Forwarded

[ccp4bb] Fwd: Postdoctoral Research Associate in Chemical Biology at YSBL

Dear colleagues We have the following position available in the Davies Group at York Structural Biology Laboratory, UK: https://jobs.york.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=3885_web_page_id=468064 Applications are invited for either a Research Fellow or a Postdoctoral

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Fwd: [ccp4bb] Validation of structure prediction

, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 From: CCP4 bulletin board on behalf of F.Xavier Gomis-Rüth Sent: Tuesday, December 21, 2021 5:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] [ccp4bb

Re: [ccp4bb] Fwd: [ccp4bb] Validation of structure prediction

4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: [ccp4bb] Validation of structure prediction Dear all, this is by far not the general case in our hands. Depending on which AlphaFold protocol is used, the resulting models have locally disfavourable geometries–including clashes–, impossible chain crossovers, etc. I wo

[ccp4bb] Fwd: [ccp4bb] Validation of structure prediction

Dear all, this is by far not the general case in our hands. Depending on which AlphaFold protocol is used, the resulting models have locally disfavourable geometries–including clashes–, impossible chain crossovers, etc. I would definitively recommend everybody to go through the model in detail

[ccp4bb] Fwd: [ccpem] Tenure track scientist position at PSI (focus on cryo-ET)

Prof. Gebhard F.X. Schertler Structural Biology ETH Zürich D-BIOL Head of Biology and Chemistry Division Paul Scherrer Institut Laboratory of Biomolecular Research, LBR OSRA 007 CH-5232 Villigen PSI gebhard.schert...@psi.ch phone +41 56 310 4265 Anfang der

[ccp4bb] Fwd: 3 postdoc positions on structure-based drug discovery in the Yue lab at Newcastle University

A reminder of the below 3 postdoc openings in the Yue lab at Newcastle University 7 more days to apply Deadline Monday 13 December -- Forwarded message - From: Wyatt W. Yue Date: Mon, 29 Nov 2021 at 11:10 Subject: 3 postdoc positions on structure-based drug discovery in the

[ccp4bb] Fwd: [ccpem] registration deadline extended until tomorrow - Cellular Structural Biology & Bioimaging symposium, Oct 26-27, 2021

Prof. Gebhard F.X. Schertler Structural Biology ETH Zürich D-BIOL Head of Biology and Chemistry Division Paul Scherrer Institut Laboratory of Biomolecular Research, LBR OSRA 007 CH-5232 Villigen PSI gebhard.schert...@psi.ch phone +41 56 310 4265 Anfang der

[ccp4bb] Fwd: Building Dna rna duplex

Hi everyone, I am working on refinement of a protein-NA complex. It has a dna-rna duplex. How do we build a dna rna duplex in coot. I was able to optimize the RNA chain using Rcrane, is there a similar tool to work on DNA chain? Could anyone please suggest a better way for the refinement of

[ccp4bb] Fwd: asking opinion to all friends here

Hi Bulletin members My question is relatively general regarding some protein engineering The aim is to design a peptide of approx length 25 nm mostly helical in nature that can conduct current. The ends of the peptide have to have some properties that it can bind to metal electrodes

[ccp4bb] Fwd: [ccpem] Glutamate receptor cryo-EM at the MRC LMB

Hi everyone, I’m forwarding this position in structural biology and drug development at the LMB in Cambridge with my former PhD supervisor, Ingo Greger, in collaboration w AstraZeneca in case anyone is interested who is not on CCPEM. It’s a very dynamic, interdisciplinary group that I highly

[ccp4bb] Fwd: Abstract submission deadline extended to 2 June - PSB Symposium "Frontiers in Bioimaging", 1-2 July 2021

Dear all, Please note that the abstract submission deadline for the PSB Symposium "Frontiers in Bioimaging" (1-2 July 2021) has been extended to *Wednesday 2 June*. For further information:

Re: [ccp4bb] Fwd: Please register - Phenix Workshops - April 7 & 14

Dear Dr Moriarty, Thank you so much. Looking forward for this meeting. Kind regards, Rini Chaturvedi On Thu, Apr 8, 2021 at 12:11 AM Nigel Moriarty wrote: > Rini > > It appears you are 30 minutes out but it is still early. Phenix Workshops > will be recorded. As with the last two virtual

Re: [ccp4bb] Fwd: Please register - Phenix Workshops - April 7 & 14

Rini It appears you are 30 minutes out but it is still early. Phenix Workshops will be recorded. As with the last two virtual workshops, they will be posted on YouTube. A simple search there will reveal all. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and

Re: [ccp4bb] Fwd: Please register - Phenix Workshops - April 7 & 14

Dear Dr Moriarty, Thank you for sharing the Phenix workshop link. Will it be possible for the recording of the sessions to be shared in the CCP4BB mail? The given time for the workshop i.e *3.45 pm PDT* which will be around *3.45 am* in India (*IST*) and it would be difficult for us to be

[ccp4bb] Fwd: Thank you for registering - Phenix Workshops - April 7 & 14

Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/-0001-8857-9464

[ccp4bb] Fwd: Please register - Phenix Workshops - April 7 & 14

Forward in case it was not circulated. Sorry if it's a repeat. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax :

[ccp4bb] Fwd: [ccp4bb] Co-crystallization and thermal shift assay

Hello, we had an interesting case in the lab many years ago... Using the shift-assay, a student managed to identify conditions that markedly stabilized the protein of interest. To cut a long story short, in the end it turned out conditions were identified that gave monomers while the

[ccp4bb] Fwd: Fw: Human Resources Advertisement: Lecturer/Lecturer below the bar in Protein Biochemistry

Dear all I'd like to draw attention of interested candidates to the opportunity as listed below. We are targeting excellent candidates in protein biochemistry, bioinformatics or bioprocessing. Yours sincerely *Professor Tewfik Soulimane* Head of School, Natural Sciences Head of

[ccp4bb] Fwd: [ccp4bb] Postdoc position, Plant Hormone Transporting Membrane Proteins (Denmark)

in case it might be of interest for someone @CNB: > Begin forwarded message: > > From: Bjørn Panyella Pedersen > Subject: [ccp4bb] Postdoc position, Plant Hormone Transporting Membrane > Proteins (Denmark) > Date: 5 February 2021 at 17:20:38 GMT+1 > To: CCP4BB@JISCMAIL.AC.UK > Reply-To: Bjørn

Re: [ccp4bb] Fwd: CCP4i2 Export and Deposition task

Hello, if you are depositing the structure, a workaround might just be to use: https://pdb-extract.wwpdb.org/ I suspect that was obvious, sorry! Cheers, Jon. Cooper Original Message On 26 Nov 2020, 17:56, Nikolas wrote: > Hi all, > > I am trying to prepare and export the

Re: [ccp4bb] Fwd: CCP4i2 Export and Deposition task

Dear Nikolas I have the exact same problem Joel On Nov 26, 2020, at 20:00, Nikolas wrote:  Hi all, I am trying to prepare and export the files for a structure solved in CCP4i2 but so far the only tasks available are the "Prepare and validate" and "Merge experimental data .." tasks. I have

[ccp4bb] Fwd: CCP4i2 Export and Deposition task

Hi all, I am trying to prepare and export the files for a structure solved in CCP4i2 but so far the only tasks available are the "Prepare and validate" and "Merge experimental data .." tasks. I have tried to look for the tutorial but both the icon and the input page illustrated are different from

[ccp4bb] Fwd: CCP4i2 Export and Deposition task

Hi all, I am trying to prepare and export the files for a structure solved in CCP4i2 but so far the only tasks available are the "Prepare and validate" and "Merge experimental data .." tasks. I have tried to look for the tutorial but both the icon and the input page illustrated are different from

[ccp4bb] Fwd: [ccp4bb] AW: Kevin Denkmann lädt Sie zur Zusammenarbeit auf 'Rechnungen' ein.

Agreed. In fact, as a matter of course, when die Rechnung arrives I endeavor to head for die Tur… > > > >> On 20 Oct 2020, at 10:23 AM, Schreuder, Herman /DE >> wrote: >> >> Looks more like crowd-phishing to me!  >> The original message did not make it through my spam filter and it may

[ccp4bb] Fwd: Call for MX beamtime proposals at HZB, BESSY II, deadline extended to September 06, 2020

Dear all, the next MX-proposal application deadline has been extenden to September 06, 2020 As usual, all proposals will be handled by our electronic user portal GATE, https://www.helmholtz-berlin.de/pubbin/hzbgate Hereby we would like to invite the submission of new proposals for

Re: [ccp4bb] Fwd: Refmac error

ively. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Eugene > Krissinel > Sent: Friday, May 29, 2020 12:47 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Fwd: Refmac error > > Dear Nadine, > > Many thanks for sharing your proje

Re: [ccp4bb] Fwd: Refmac error

Dear Nadine, Many thanks for sharing your project with me on CCP4 Cloud. The reason for Refmac failure is absolutely clear: the previous Coot job exported PDB file, using commas (wie im besten Deutsch) instead of periods (as we would expect in best English) for all float-point numbers. You can

[ccp4bb] Fwd: Re: What refinement programs are fully Open Source?

Hi Pietro! As for free and open-source (GPLv3 license) refinement software, I am developing Vagabond. https://vagabond.hginn.co.uk It is based on refining bond torsion angles in an ensemble of related structures which also captures flexibility (no B factors!). There are no restraints, only

Re: [ccp4bb] External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

Guys, Thanks for all the help. I figured out what's wrong with the sequence file. I had accedently entered an "X' to one of the sub-chains. Cheeres ! Gihan To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

, this is not a mutation at all but points to the origin of this virus. /Michel. From: CCP4 bulletin board On Behalf Of Carter, Charlie Sent: March 21, 2020 7:48 AM To: CCP4BB@JISCMAIL.AC.UK Subject: External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19 Begin forwarded message: From: "char

[ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

Begin forwarded message: From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>> Subject: Re: [ccp4bb] CCP4BB vs COVID19 Date: March 21, 2020 at 8:07:53 AM EDT To: James Holton mailto:jmhol...@lbl.gov>> Brilliant post, James. Thanks so much! I also find what you describe interesting,

[ccp4bb] Fwd: [ccp4bb] Fw: protein protein interactions

Dear Careina, I would recommend you our partner-specific binding site predictor: BIPSPI, that uses as input 2 sequences or 2 pdb files and proposes the binding site of the two partners. http://bipspi.cnb.csic.es/xgbPredApp/ Kind regards, Ruben Quoting "careinaedgo...@yahoo.com"

[ccp4bb] Fwd: Open scientist position at the EMBL-Grenoble - Project leader for ID30A/MASSIF-1 beamline upgrade

Dear all, Just a quick reminder that the closing date for applications is in one week (Feb 7th). We have an open scientist position at the EMBL-Grenoble for a Project leader to oversee our contribution to the upgrade of the fully automated ID30A/MASSIF-1 macromolecular crystallography

Re: [ccp4bb] Fwd: [ccp4bb] suggestions on small proteins that for a complex

FliS and FliC Artem On Sun, Nov 10, 2019, 03:42 Gianluca Cioci wrote: > ps: the 3D structure > of the complex should > be solved at high resolution > > ;o) > > > > > Dear All, > > I am looking for examples of two small proteins A and B that can form a > tight complex AB. > Each protein

[ccp4bb] Fwd: [ccp4bb] suggestions on small proteins that for a complex

ps: the 3D structure of the complex should be solved at high resolution ;o) Dear All, I am looking for examples of two small proteins A and B that can form a tight complex AB. Each protein should be straightforward to express in E.coli, well folded and stable in the isolated form. Also, if

[ccp4bb] Fwd: CCP4i2 London Road Show

Reminder One week to London CCP4i2 Road show.  Places still available. *CCP4 i2 Road Show, London* There will be a CCP4 Road Show for use of the i2 interface on Tuesday 12th November, at Birkbeck College. *Time:* 14:00 - 16:00 for the main workshop with about an hour afterwards for those

[ccp4bb] Fwd: [Labmanagers] CCP4i2 London Road Show

Reminder Two weeks to London CCP4i2 Road show.  Places still available. *CCP4 i2 Road Show, London* There will be a CCP4 Road Show for use of the i2 interface on Tuesday 12th November, at Birkbeck College. *Time:* 14:00 - 16:00 for the main workshop with about an hour afterwards for those

[ccp4bb] Fwd: Retinal Proteins Conferences - Historical Website

Prof. Gebhard F.X. Schertler Structural Biology ETH Zürich D-BIOL Head of Biology and Chemistry Division Paul Scherrer Institut Laboratory of Biomolecular Research, LBR OFLC 109 CH-5232 Villigen PSI gebhard.schert...@psi.ch phone +41 56 310 4265 Anfang der

[ccp4bb] Fwd: [3dem] Postdoctoral Position at NNF-CPR University of Copenhagen

Dear Colleagues just a kindly reminder, the application deadline is the 18th August, Those interested, please apply through the link provided below https://candidate.hr-manager.net/ApplicationInit.aspx/?cid=1307=18997=149912=5=false Best regards G. Dear colleagues, We are seeking an

[ccp4bb] Fwd: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to Zn2+

-- Forwarded message - From: Daniel M. Himmel, Ph. D. Date: Mon, Aug 5, 2019 at 12:45 PM Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to Zn2+ To: Pentagonal phosphate geometry would be a transition state, except that three oxygens

[ccp4bb] Fwd: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

Begin forwarded message: From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>> Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 Date: July 19, 2019 at 1:32:53 PM EDT To: Patrick Loll mailto:pjl...@gmail.com>> Hi Pat, I, too have fallen into this rabbit hole while Mark

[ccp4bb] Fwd: [ccp4bb] AKTA FPLC fractionation peak by peak

Thank you both for your answers! *Upasana* - the chromatogram was randomly selected to ilustrate the point - we do a careful equilibration of the column and degas the mobile phase(s) before starting. I'm not really sure what you mean by oligomeric state of the protein - we are working with

[ccp4bb] Fwd: Domainex is hiring a Structural Biologist

Posted on behalf of Domainex. Begin forwarded message: From: Stefanie Reich mailto:s.re...@domainex.co.uk>> Date: 31. May 2019 at 17:04:20 CEST To: "ccp4bb@jiscmail.ac.uk" mailto:ccp4bb@jiscmail.ac.uk>> Subject: Domainex is hiring a Structural Biologist

[ccp4bb] Fwd: Open PhD position UiO Protein Biochemistry

Forwarded on behalf of Sandip Kanse, University of Oslo: Forwarded Message Subject: Open PhD position UiO Protein Biochemistry Date: Fri, 26 Apr 2019 08:52:06 +0200 From: Sandip Kanse To: Ute Krengel PHD RESEARCH FELLOW IN PROTEIN BIOCHEMISTRY UNIVERSITY OF OSLO, NORWAY.

[ccp4bb] Fwd: SFX beamline scientist position at the SwissFEL

Somehow the link changed, here is the updated one. https://www.psi.ch/en/pa/job-opportunities/27905-beamline-scientist Best meitian Begin forwarded message: From: Meitian Wang mailto:meitian.w...@psi.ch>> Subject: SFX beamline scientist position at the SwissFEL Date: 18 April 2019 at 10:32:01

Re: [ccp4bb] Fwd: [ccp4bb] SO4 or PO4

This can be done at Diamond I23 beamline. https://doi.org/10.1016/j.nimb.2016.12.005 Best regards, Jan Dne 16.02.2019 v 18:49 Patrick Loll napsal(a): > S has about 0.56 anomalous electrons at 8 keV, whereas P has about > 0.44. This is a small difference between two weak signals—unlikely to >

[ccp4bb] Fwd: [ccp4bb] SO4 or PO4

S has about 0.56 anomalous electrons at 8 keV, whereas P has about 0.44. This is a small difference between two weak signals—unlikely to give a clear result. If you could get to the sulfur & phosphorus edges, then you could (in principle) answer this, but that’s a very hard experiment to

[ccp4bb] Fwd: Head of Membrane Protein Science opportunity available at fast-growing biotech company

Forwarding a job advertisement Please contact the person here copied Lorin -- Forwarded message - From: Lorin Raats Date: Tue, Feb 12, 2019 at 6:53 AM Subject: Head of Membrane Protein Science opportunity available at fast-growing biotech company It would be great to get in

[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

Re: [ccp4bb] Fwd: dry Shipper made in China

If you buy a used one, or the one from Biobase China make a quality check before. Loosing crystals during shipment means loosing money (accounting for all the efforts that went in producing the crystals).  I once got a protocol from Terese Bergfors at Uppsala University". It consists of what

Re: [ccp4bb] Fwd: dry Shipper made in China

Dry shippers are often featured on auction sites for used equipment and sometimes can be found for huge discounts... Artem - Cosmic Cats approve of this message On Fri, Jan 25, 2019 at 8:36 AM Muhammad Imran wrote: > Dear Community members, > > We wanted to buy molecular dimension dry

[ccp4bb] Fwd: 2 EMDB Job Opportunities at EMBL-EBI

Please see the following job opportunities available with our colleagues at EMDB. Kind Regards, David Armstrong Forwarded Message Subject:2 EMDB Job Opportunities at EMBL-EBI Date: Tue, 22 Jan 2019 10:46:19 + From: Osman Salih To: 'David Armstrong'

[ccp4bb] Fwd: Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

Sorry for spamming the CCP4BB with this e-mail meant for Kay, only - I accidentally used the "Reply All" button instead of the "Reply" button ... ;-) Anyway, I wish the CCP4 community a Happy New Year! Cheers, Dirk. Forwarded Message Subject: Re: [ccp4bb] OT: Nvidia 3D

[ccp4bb] Fwd: Re: [ccp4bb] phase behavior (slightly off-topic)

Dear Eugene, the additive is a metal-polyanion with a net charge of 6- ... yes, NaCl affects largely the solubility of the anions, however, the LLPS appears within a rather large protein concentration range (10-50 mg/ml = 0.7 - 3.5 mM) in the presence of e.g. 0.1, 0.5, 1.0, 2.5 and 5.0 mM

[ccp4bb] Fwd: [ccp4bb] VERY old mtz file..

Begin forwarded message: From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>> Subject: Re: [ccp4bb] VERY old mtz file.. Date: November 14, 2018 at 10:16:23 AM EST To: Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>> I’ve found this thread to be most interesting and out of near

[ccp4bb] Fwd: Re: [ccp4bb] coiled-coil "degree"

My /acknowledgements/ to all that have replied to my question. So many interesting inputs and points to software; I will be checking in the next days. I will comment upon just some of the observations. As far as we can, we try to take as "asymmetric unit content" what is "expected" (or

[ccp4bb] Fwd: [ccp4bb] Sulphate or phosphate? (Armin's figures)

Begin forwarded message: [cid:image001.png@01D42A41.AE0B8B60] To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Fwd: Re: [ccp4bb] suggestion of crystallization optimization

hey Liu ... you got all wonderful suggestion, and they may be time consuming. Meantime, you may work on the crystals in hand, and follow the suggestions as mentioned above. >From my experience, i can tell you that crystal age is also an important parameter. I will shoot it as soon as i see it in

[ccp4bb] Fwd: Senior Laboratory Technician - Protein Purification - in the Medicines Discovery Institute at Cardiff University.

We are advertising for a Senior Laboratory Technician Protein Purification in the Medicines Discovery Institute at Cardiff University, UK. The goal of the newly-established Medicines Discovery Institute in Cardiff is to translate world-leading research on scientific understanding of disease

[ccp4bb] Fwd: Re: [ccp4bb] suggestion of crystallization optimization

Good suggestions here.  In situ proteolysis is a new one on me... Sent from my Verizon, Samsung Galaxy smartphone Original message From: Artem Evdokimov Date: 6/5/18 1:24 PM (GMT-06:00) To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] suggestion of crystallization

[ccp4bb] Fwd: [ccp4bb] suggestions on a microscope for Crystallography

-- Forwarded message -- From: Daniel M. Himmel, Ph. D. Date: Wed, Mar 7, 2018 at 12:23 AM Subject: Re: [ccp4bb] suggestions on a microscope for Crystallography To: Chandramohan Kattamuri My best experience was with Leica

[ccp4bb] Fwd: Fwd: Beamline Scientist position available at the EMBL-Grenoble for the ID23-2 and/or ID29 MX beamlines at the ESRF

Dear all, We have an opening for a highly motivated scientist in the Synchrotron Crystallography team at the EMBL Grenoble Outstation. This team works in close collaboration with the ESRF Structural Biology Group in the operation and development of high performance structural biology

[ccp4bb] Fwd: Crystallography job opportunities at HarkerBio in Buffalo, NY

Hello community. HarkerBIO is structural biology-focused biotechnology company based in Buffalo, NY with a close relationship to the renowned Hauptman-Woodward Medical Research Institute. We are rapidly growing and are seeking to quickly fill a few open crystallography/structural biology

Re: [ccp4bb] Fwd: [ccp4bb] how to improve the diffraction quality of the crystals and avoid icerings

Hi, Yuvraj, I can suggest two methods: 1) collect a dataset at room temperature 2) crystallize your protein in cryoconditions. That is add 25 % of glycerol to your crystallization conditions and perform small optimization in terms of precipitant concentration. 2017-12-29 7:55 GMT+03:00 Prem

[ccp4bb] Fwd: [ccp4bb] how to improve the diffraction quality of the crystals and avoid icerings

-- Forwarded message -- From: Prem Prakash Date: Fri, Dec 29, 2017 at 10:22 AM Subject: Re: [ccp4bb] how to improve the diffraction quality of the crystals and avoid icerings To: zaigham mahmood khan Hi, Yuvraj Initially I also

[ccp4bb] Fwd: X-ray Lab Manger Birbeck University of London- Permanent Post

A reminder this vacancy closes on Sunday. There is a vacancy for an X-Ray Laboratory Manager at the Institute for Structural and Molecular Biology at Birkbeck/UCL based at Birkbeck, University of London. see https://tinyurl.com/y7jgfmr5 This is a permanent University Funded post. A brief

[ccp4bb] Fwd: divulgacao bolsa, obrigada

Dear all I'd like to draw your attention to the postdoc position in protein crystallography, currently open in my group at UCIBIO-NOVA (Faculty of Science and Technology, NOVA University of Lisbon, Portugal). I am a young PI interested in protein-ligand interactions for structural-based drug

[ccp4bb] Fwd: Postdoc in Cryo-EM of Membrane Proteins at the Max Planck Institute for Biophysics

Forwarded Message > Dear colleagues,  > > My group is looking for a postdoc interested in doing subtomogram averaging > on membrane proteins.  > > Naturejob post:  > https://www.nature.com/naturejobs/science/jobs/626553-postdoc-in-cryo-em-of-membrane-proteins-in-situ > >

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