Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

On Fri, 17 May 2024 08:27:02 -0700, James Holton wrote: ... > >With a bit of a caveat on how many photons/pixel you need for stable >background subtraction. XDS starts having issues around 1 photon/pixel >or less, and DIALS claims to be able to get to 0.01 photons/pixel, but I >have not

Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

Hi, > What if instead of images we just collected a list of x-y coordinates of > photon hits vs time? This is how the Tristan detector works, it is based on timepix3 chips and the data is a read as time stamped x-y co-ordinates + counts and then diffraction images are reconstructed from this

Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

Hello, > What if instead of images we just collected a list of x-y coordinates of > photon hits vs time? This already exists, but for electrons: https://doi.org/10.1107/S205225252000929X This is the technology in Falcon4 detectors. The advantage is that it allows you to decide how to slice

Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

A few follow-up questions I got out-of-band: how did you get to the 1:1 relationship between Bijvoet ratio and dose? I got this from fitting a straight line to Table 1 of Banu's 2004 paper: 10.1107/S0907444904007917 Is this a rough estimate based on a singular result?  Of course it is!  This

Re: [ccp4bb] Unable to send a query email to supp...@proteindiffraction.org

Dear all, After half an year from the original Shivani's message, I am having the same problem. Please has anybody successfully deposited data there recently or has any idea how to reach the admins? Cheers, Martin On 14/11/2023 00:16, Shivani Sharma wrote: I deposited some raw data on the

Re: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC

Dear All Thank you for the detailed response. I will implement the suggested fixes and report back on a later date. Kind regards, Otsile -Original Message- From: CCP4 bulletin board On Behalf Of Bernhard Lohkamp Sent: Wednesday, May 15, 2024 9:11 PM To: CCP4BB@JISCMAIL.AC.UK Subject:

Re: [ccp4bb] Computational crystallography in 2024

Hi Lucas This one? https://www.iucr.org/resources/commissions/crystallographic-computing/schools/kyoto-2008-crystallographic-computing-school IUCr’s Commission on Crystallographic Computing still holds these - next one (probably) in Alberta! Harry > On 16 May 2024, at 01:51, Lucas Bleicher

Re: [ccp4bb] Computational crystallography in 2024

On 16/05/2024 01:51, Lucas Bleicher wrote: -- Dear all, I've been outside of the field for a few years (I have very fond memories of the 2008 Crystallographic Computing School, but did a lot of different stuff since then), but I'd love to come back and figured this would be the best place to

[ccp4bb] Computational crystallography in 2024

Dear all, I've been outside of the field for a few years (I have very fond memories of the 2008 Crystallographic Computing School, but did a lot of different stuff since then), but I'd love to come back and figured this would be the best place to ask - what are the go-to resources today for those

Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

Thank you to all who provided helpful suggestions so far. A few things I'd recommend for this particular beamline (which I have been running for 20+ years) Do NOT collect one wavelength at a time. This was a good strategy on old beamlines with noisy detectors and slow, drifty monochromators.

Re: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC

On 15/05/2024 19:03, Paul Emsley wrote: On 13/05/2024 17:38, Otsile Mojanaga wrote: *From:*Otsile Mojanaga *Sent:* Monday, May 13, 2024 3:29 PM *To:* Paul Emsley *Subject:* RE: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC Dear Paul/All Thank

Re: [ccp4bb] a dinosaur asks ... PDB format query

The old BNL PDB format documents are available at https://www.wwpdb.org/documentation/file-format I looked at the Feb 1992 document to be certain that my memory was correct [I am 6 days shy of 82 and am reassured that my recollection was,in fact, correct] for information about the

Re: [ccp4bb] a dinosaur asks ... PDB format query

It says in aforementioned docs: "Alignment of one-letter atom name such as C starts at column 14, while two-letter atom name such as FE starts at column 13. " and no, hopefully they don't mean that, since their example shows plenty of 2-letter and 3-letter atom names starting at column 14 in

Re: [ccp4bb] a dinosaur asks ... PDB format query

'CA' for carbon-alpha is a 2-letter atom name so applying the rule exactly as stated it should start in column 13; it states that only 1-letter atom names (C, N, O) go in column 14. This must be a case of poorly-written documentation; it must mean 'element symbol' not 'atom name' in those cases

Re: [ccp4bb] a dinosaur asks ... PDB format query

On 15/05/2024 18:45, Filipe Maia wrote: CAUTION: This email originated from outside of the LMB: *.-owner-ccp...@jiscmail.ac.uk-.* Do not click links or open attachments unless you recognize the sender and know the content is safe. If you think this is a phishing email, please forward it to

Re: [ccp4bb] a dinosaur asks ... PDB format query

It is, I think you would agree, unconventional to put a CA label for a main-chain carbon at positions 13 and 14 (I have never seen such a thing). But is it wrong ("Incorrect" - as Harry labels it)? In this case, putting "CHA" in positions 13-15 is unconventional (again, I have never seen such a

Re: [ccp4bb] a dinosaur asks ... PDB format query

Hi Robbie I’m not actually using PDB files of proteins - I’m using the PDB format files in PDBeChem, because at the moment I’m interested in doing stuff with ligands/substrates/etc. The charges I’ve seen so far seem to be not quite what I’d expect, but I’m prepared to work around that. Harry

Re: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC

On 13/05/2024 17:38, Otsile Mojanaga wrote: *From:*Otsile Mojanaga *Sent:* Monday, May 13, 2024 3:29 PM *To:* Paul Emsley *Subject:* RE: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC Dear Paul/All Thank you for the response. I am on Windows 11

Re: [ccp4bb] a dinosaur asks ... PDB format query

On 15/05/2024 11:28, Harry Powell wrote: Hi folks [...] I noticed this because I was encouraged to try Moorhen and found that a HEM (apparently written by this module) did not have the atoms connected with bonds in the display. Q: Is it necessary to check columns 77-78 if I really want to be

[ccp4bb] Attn: UK Based research groups - UK CryoEM community Meeting - 19th July @Royal Society

Dear all, On behalf of the UK cellular structural biology community, with support from Diamond and Instruct-ERI (UK centre), we would like to alert all UK based groups using or intending to use CryoEM as part of their research, the opportunity to attend a one-day community meeting together

Re: [ccp4bb] a dinosaur asks ... PDB format query

Hi Harry,It might be better now, but there used to positively charged aspartates in the PDB. You have a better chance taking charges out of the CCD for your atoms of interest. I'm not saying all charges in the CCD are correct, but they are much more reliable. If you find errors, please report them

Re: [ccp4bb] AW: [ccp4bb] a dinosaur asks ... PDB format query

> It sounds as though you need the power of the script. You can (from memory) > run pdbcur to drop the aniso lines and hydrogen atoms, which helps. Or from command-line: gemmi convert --anisou=no --remove-h in.pdb out.pdb > You could probably get it to delete everything except CA's too. this

Re: [ccp4bb] AW: [ccp4bb] a dinosaur asks ... PDB format query

Dear Jon, If I understand your question right, I would use Gemmi for this purpose: https://gemmi.readthedocs.io/en/latest/mol.html https://gemmi.readthedocs.io/en/latest/analysis.html It's not in GUI, it involves scripting in Python. It's a very powerful tool and capable of working with both

Re: [ccp4bb] a dinosaur asks ... PDB format query

For those wanting a text editor solution, there is the purpose built pdb-mode plugin for (x)emacs which works under most operating systems. The download location has moved around a bit, but a current version is available from https://github.com/mmagnus/emacs-pdb-mode/ with more details at

Re: [ccp4bb] a dinosaur asks ... PDB format query

Hi This is very, very useful and hits on the four-letter name problem that I am encountering - thank you. Saves me trying to produce a new design for a circular object with an axle… For the files that I am trying to use, columns 77-78 are present (actually, columns 79-80 are there so I can

Re: [ccp4bb] AW: [ccp4bb] a dinosaur asks ... PDB format query

You could probably get it to delete everything except CA's too. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail mobile Original Message On 15 May 2024, 13:22, Jon Cooper wrote: > It sounds as though you need the power of the script. You can (from

Re: [ccp4bb] AW: [ccp4bb] a dinosaur asks ... PDB format query

It sounds as though you need the power of the script. You can (from memory) run pdbcur to drop the aniso lines and hydrogen atoms, which helps. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail mobile Original Message On 15 May 2024, 13:11, Hughes,

[ccp4bb] AW: [ccp4bb] a dinosaur asks ... PDB format query

hello CCP4 people, rather off-topic: is there a purpose-written windows editor for PDF files? with interleaved anisotropy lines, missing column delimiters etc., simply extracting the B-factors for Ca atoms is hard work using a standard character editor. would anyone think of working with DNA

Re: [ccp4bb] a dinosaur asks ... PDB format query

It would also be good to check the monomer library (expanded with any user-supplied dictionaries). Cases where an element in columns 77-78 exists and it does not agree with the component definition should probably be flagged up. Cheers, Paul On Wed, 15 May 2024 at 12:39, Marcin Wojdyr wrote: >

Re: [ccp4bb] a dinosaur asks ... PDB format query

> > > • Alignment of one-letter atom name such as C starts at column 14, while > > two-letter atom name such as FE starts at column 13. > > indicating a rule does exist. There are programs that don't read/write the element from columns 77-78, so this rule still matters, but using it is less

Re: [ccp4bb] a dinosaur asks ... PDB format query

Hi Harry,Deducing the element from the atom name has always been unreliable so since PDB version 3 you have to get it from columns 77-78. There is no implied element in the atom name anymore.HTH,RobbieOn 15 May 2024 12:28, Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:Hi folks

Re: [ccp4bb] a dinosaur asks ... PDB format query

Sorry - just read that > • Alignment of one-letter atom name such as C starts at column 14, while > two-letter atom name such as FE starts at column 13. indicating a rule does exist. Harry > On 15 May 2024, at 11:54, Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >

Re: [ccp4bb] a dinosaur asks ... PDB format query

Hi Ezra Thanks for this. In other words, would it be true to say that there are no actual rules about what appears in columns 13-16 because “it's a rose by any other name”? Harry > On 15 May 2024, at 11:38, Ezra Peisach wrote: > > If you take a look at >

Re: [ccp4bb] a dinosaur asks ... PDB format query

If you take a look at https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM you will see the following: 77 - 78    LString(2)    element  Element symbol, right-justified. Going by atom name will get you in trouble.  As you stated calcium vs Calpha.  The

[ccp4bb] a dinosaur asks ... PDB format query

Hi folks I’m sure that this has been answered many times before (I’m sure that when I was young I even read it here…), and I *know* that we should all be using mmCIF, but I’m using PDB format files generated by a popular Python module and I wanted to check the output against a definitive

[ccp4bb] CCPBioSim Industry Talks - 29 May and 19 June

Hi all, I want to remind you about our next industry talk by Brannon Batson a hardware design engineer at D. E. Shaw Research. The talk "Using specialized hardware pipelines to massively accelerate molecular dynamics simulations in Anton 3" is online Wednesday 29 May 2024, 15:00 UK time. Free

[ccp4bb] Second NYC Integrative Structural Biology symposium (NYC-ISB24) - Oct 9-11, 2024 - NYC, USA

Dear all, General registration is now open for NYC-ISB24: http://nyc-isb24.eventbrite.com This 3-day event will be held October 9-11, 2024 at CUNY ASRC and NYSBC, and is focused on integrative

[ccp4bb] Postdoc position Sweden

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Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

I agree with Harry, I suspect that embarrassment has no definition/ meaning in the context of Nature. From: CCP4 bulletin board on behalf of Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> Sent: Tuesday, May 14, 2024 6:28 PM To:

Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

Hi Marco, An alternative would be to scrap the SeMet crystals and collect anomalous data on native crystals at I23, Diamond Light Source. We are optimised for S-SAD and could likely help you with your phasing. Happy to talk off-list if you'd like to come and do an experiment (I am a beamline

Re: [ccp4bb] AlphaFold3 Transparency and Reproducibility

Do Nature do embarrassment? H > On 14 May 2024, at 10:54, Frank von Delft > wrote: > > What we really need is a tweet from Nature, declaring their embarrassment at > having been suckered into becoming DeepMind's advertising arm. > > > On

Re: [ccp4bb] AlphaFold3 Transparency and Reproducibility

What we really need is a tweet from Nature, declaring their embarrassment at having been suckered into becoming DeepMind's advertising arm. On 14/05/2024 01:56, Paul Adams wrote: The letter may have had (or helped have) an impact already: On X today from Pushmeet Kohli @ DeepMind "We love

Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

Hi With this in mind, I have found the easiest way to generate AlphaFold models (for those not in the DB) is actually in CCP4 Cloud-remote - makes MR using AF models a real doddle. See the Tutorials (in particular on MR) available with CCP4 Cloud. Harry > On 14 May 2024, at 09:20, Randy

Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

Dear Marco, You don’t mention here or in the earlier thread whether you tried AlphaFold models and, if you did, how you prepared them for MR. I’m happy to hear of any case where we still need experimental phasing methods to solve new protein structures, but we’ve seen very few examples where

[ccp4bb] PDRA in serial crystallography at Diamond Light Source

Hi all, We have a PDRA position open at Diamond to help us develop new methods for time-resolved crystallography. You will work closely with a number of groups at Diamond and beyond to improve approaches for both SSX and SFX. For further info and to apply see

Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips

Hi Marco, A few suggestions that I like to follow for MAD experiments: Before everything, check you have at least about 1 SeMet per 100 residues Then before crystallisation check by MassSpec that SeMet is properly incorporated in your protein After crystallisation collect first on the peak

Re: [ccp4bb] AlphaFold3 Transparency and Reproducibility

The letter may have had (or helped have) an impact already: On X today from Pushmeet Kohli @ DeepMind "We love the excitement & results from the community on AlphaFold 3 and are doubling the AF Server daily job limit to 20. Happy to also share that we're working on releasing the AF3 model

[ccp4bb] RES: [ccp4bb] What could these crystals be?

It seems to me that your drop has dried. By the pic, I would not say these are crystals Best Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São

[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

[ccp4bb] Tenure-track Assistant Professor position - Artificial Intelligence / Machine Learning

I would like to attract your attention to the following position that opens up at The University of Texas Medical Branch (UTMB). Cheers. Matt ​___ Assistant

[ccp4bb] Early Career Diffraction Methods Seminar 2024 - reduced student fees and student grants available!

Dear CCP4BB, A friendly reminder that Early Career Diffraction Methods Seminar 2024 is on the horizon! Taking place July 21-22, 2024 at The Harnack Haus, Berlin, this meeting is designed for early-career scientists to present and explore the latest advancements in diffraction methods, and

Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

If it does what it claims – incredibly impressive. The issue we have is there is no way to verify or validate the claims it is making. The letter is a call and start of a conversation about how the ever-changing landscape of communication and publication of science should be. -Stephanie

Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

It definitely is impressive but it also has clear limitations On 13 May 2024, at 15:22, Sylvia Fanucchi wrote:  You don't often get email from d0c4e77ae410-dmarc-requ...@jiscmail.ac.uk. Learn why this is

Re: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC

From: Otsile Mojanaga Sent: Monday, May 13, 2024 3:29 PM To: Paul Emsley Subject: RE: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC Dear Paul/All Thank you for the response. I am on Windows 11 and I tried looking around Coot to see where I could

Re: [ccp4bb] What could these crystals be?

Hello, what is in the purification buffer? Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail mobile Original Message On 13 May 2024, 15:15, 张慧欣 wrote: > Hi all > We have been trying with no success to crystalize a protein. Recently we got > these

[ccp4bb] CCP4-BCA Protein Crystallography Summer School (1st – 6th Sept 2024) hosted by the John Innes Centre

Hi All, The John Innes Centre in Norwich (UK) will be hosting this year’s CCP4-BCA Protein Crystallography Summer School. Please follow this link for more details and to apply: https://www.jic.ac.uk/event/ccp4-bca-protein-crystallography-summer-school-2024/ Best wishes Dave

[ccp4bb] Scientific Coordinator post - grade 8 Oxford University

Please forward If you know anyone who might be interested in a drug discovery senior scientific coordinator post ... We are seeking to appoint a Programme Manager/Scientific Coordinator at the University of Oxford's Centre for Medicines Discovery (CMD). The CMD was established in 2020 with the

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 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: [ccp4bb]

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] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC

On 13/05/2024 13:03, Otsile Mojanaga wrote: Dear All I have been using coot as part of my normal workflow but since last week I have been having issues with Coot after I built my own PC which contains the following Hardware: CPU - AMD Ryzen 9 5950X 16-Core Processor - 16 Cores, 32 Threads

[ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC

Dear All I have been using coot as part of my normal workflow but since last week I have been having issues with Coot after I built my own PC which contains the following Hardware: CPU - AMD Ryzen 9 5950X 16-Core Processor - 16 Cores, 32 Threads RAM - 64 GB GPU - AMD Radeon RX 6600 XT -

Re: [ccp4bb] coot - how to define a keyboard shortcut for "update NCS ghosts with local match" ?

On 13/05/2024 11:23, Laurent Maveyraud wrote: Hello, I like the function "update NCS ghosts with local match" found in the calculate/NCT tools menu. It's really helpful when NCS is not really strict. However, I find it clumsy that you have to go in a submenu to get it, so I would like to

Re: [ccp4bb] Postdoctoral position at the Sussex Drug Discovery Centre

Dear ccp4bb community, There are just a few days left to apply for this position - deadline 17th of May. Many thanks We have a postdoctoral position available to join the Drug Discovery team at the Sussex Drug

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] coot - how to define a keyboard shortcut for "update NCS ghosts with local match" ?

Hello, I like the function "update NCS ghosts with local match" found in the calculate/NCT tools menu. It's really helpful when NCS is not really strict. However, I find it clumsy that you have to go in a submenu to get it, so I would like to define a keyboard shortcut... this would be much

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

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Re: [ccp4bb] ccp4i2 stopped working (no startup) - advice?

Renato and Stuart McNicholls wrote exactly the right thing: deleting this file resolved the issue. Thank you very much! -Original Message- From: CCP4 bulletin board On Behalf Of Renato Weiße Sent: 08 May 2024 16:44 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] ccp4i2 stopped working

[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] Post-doctoral position protein-nucleic acid complexes Granneman lab

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[ccp4bb] Free CryoEM Webinar - May 30th, 2024, 12pm (Eastern)

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[ccp4bb] Issue with PanDDA inspect step - Need Assistance

Dear CCP4 Bulletin Board Community, I am currently working with PanDDA 2.0 and CCP4 8.0 and have encountered an issue during the inspect step of the process. I've been following the tutorial available on Bitbucket, and after some initial adjustments, I was able to progress through the

Re: [ccp4bb] Ubuntu and Coot

And yet another quick update- I rebooted the machine again and now the ccp4 version of Coot is working, but the standalone version is not (and the Phenix version continues to work). Just thought I would throw this out there for others... cheers, tom From: CCP4

Re: [ccp4bb] Ubuntu and Coot

Just an update- I tested using Coot through the Phenix package and that seems to work (version 1.21-5207-000 and version 0.9.8.93 of Coot). Maybe a version issue? Or Phenix just comes with libraries that ccp4 doesn't? Not sure yet. cheers, tom From: CCP4 bulletin

[ccp4bb] CryoEM Research Assistant position at MSKCC

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Re: [ccp4bb] [EXTERNAL]Re: [ccp4bb] Modeling Disulfide Bond Occupancies

Thank you so much From: Eleanor Dodson Date: Monday, May 6, 2024 at 3:30 PM To: Liliana Margent Cc: CCP4BB@jiscmail.ac.uk Subject: [EXTERNAL]Re: [ccp4bb] Modeling Disulfide Bond Occupancies ***ATTENTION: This email came from an external source. Do not open attachments or click on links from

[ccp4bb] 3 cryo-EM facility positions at Scottish Centre for Macromolecular Imaging, Glasgow, UK

On behalf of Dr James Streetley. Please pass all enquiries to him. Dear colleagues, The Scottish Centre for Macromolecular Imaging (SCMI) is Scotland’s national cryo-EM facility, based at the University of Glasgow. Using our JEOL CRYO

Re: [ccp4bb] ccp4i2 stopped working (no startup) - advice?

Hi Andrea, concerning Log #1: there is a log file /home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml, which is probably empty. If it is, then deleting it should resolve the error. I have seen this problem from time to time on students laptops, but could not figure out, for

[ccp4bb] ccp4i2 stopped working (no startup) - advice?

Dear all, My ccp4i2 installation stopped working - it does not start up properly anymore (see Log #1 below for the output). I started ccp4i which brought up the update manager and ran outstanding updates. This did not fix the issue. I also sourced the source file manually, just to make sure.

Re: [ccp4bb] Ubuntu and Coot

Dear Tom, I am using basically the same setup (Linux Mint 21.3 Xfce based on Ubuntu 22.04, CCP4 8.0.019 including Coot 0.9.8.93). Everything works well on my computer. I did not have any issues with Coot even in CCP4 8.0.017. I am sorry I don't know the reason of the error... Cheers, Martin

[ccp4bb] Ubuntu and Coot

Hello All, I'm not sure if this is specific to me or whether I missed the fix, but I'm currently running Ubuntu 22.04.1 and updated to the latest ccp4 version 8.0.019 and Coot crashes. I tested to see whether it was just the ccp4 version by downloading coot separately into my bin directory

[ccp4bb] Register Now for a May 14 Webinar on Understanding PDB Validation: Which experimental structures should I rely on?

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[ccp4bb] Postdoctoral position - Ion Channels

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Re: [ccp4bb] Multiple ligand simultaneous docking

Haddock certainly has support for this HADDOCK Web Server science.uu.nl [favicon.ico] But I have not run it myself… regards

[ccp4bb] Reminder: EMBO SAXS/SANS practical course

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Re: [ccp4bb] Modeling Disulfide Bond Occupancies

Do not know what the resolution is here, try an anisotropic refinement of the Cys side chains first to see if this solves your problem. __ Dr. math. et dis. nat. Jeroen R. Mesters University of Lübeck https://orcid.org/-0001-8532-6699 Am 06.05.2024 um 21:48 schrieb Eleanor Dodson

Re: [ccp4bb] Modeling Disulfide Bond Occupancies

In the CCP4 program refmac5, you specify occupancy groups and then specify how to refine them.  The setup, afaik, is not automatic. Documentation for how to do it is here: http://www.ysbl.york.ac.uk/refmac/data/refmac_keywords.html#Occupancy You may also find this link helpful?

Re: [ccp4bb] Modeling Disulfide Bond Occupancies

But are there two conformations of the disulphide? or one disulphide and one broken link? Eleaor On Mon, 6 May 2024 at 20:42, Dr. Kevin M Jude wrote: > I have done this in shelxl or phenix refinement, you can define occupancy > groups (or free variables in shelxl) so that 472A and 384A are one

Re: [ccp4bb] Modeling Disulfide Bond Occupancies

I have done this in shelxl or phenix refinement, you can define occupancy groups (or free variables in shelxl) so that 472A and 384A are one group, 472B and 384B are another. Pretty sure there is a similar solution in refmac. Though also if the 384A rotamer doesn’t clash with the 472B rotamer,

Re: [ccp4bb] Modeling Disulfide Bond Occupancies

Well - I turn off occupancy refinement once there is a sort of consensus.. Disulphides often break after long exposures and you see the positive and negative blobs clearly. I must admit I usually just set 0.5 as occ , fix the surviving disulphide link and let the B values suggest a better ratio

[ccp4bb] Modeling Disulfide Bond Occupancies

Greetings everyone, I'm currently in the process of modeling a disulfide bond in two structures. However, when I attempt to model single occupancy for the cysteines involved in the bond, negative density blobs emerge within the disulfide bond. This suggests the possibility of alternate

[ccp4bb] 4-year PhD position in structural biology at Lund University

Dear all, I have a 4-year PhD position in structural biology available in my research group at Lund University. More details can be found at the link below. Please spread the announcement to any suitable candidates you know. Last application date is 20th May! /Derek

[ccp4bb] Multiple ligand simultaneous docking

Greetings! I am learning the concept of multiple ligand simultaneous docking and would like to know if there is any standard protocol for the same. Thanking you in advance, With regards, Thripthi Shenoy. To unsubscribe

[ccp4bb] Barcelona Integrative Structural Biology Symposium

Dear all, The Spanish *Network of Integrative Structural Biology (ISBIN)* is pleased to announce the symposium on the integrative use of NMR, cryo-electron microscopy, macromolecular crystallography (static and time-resolved), small-angle X-ray scattering and computation in Barcelona and at the

Re: [ccp4bb] update manager

My mistake, that was on my Fedora 40 host, not my Alma 9 host. Installing libxcrypt-compat fixed the problem. === All Things Serve the Beam ===

Re: [ccp4bb] update manager

ccp4um does not work for me. # ccp4um /usr/local/xtal/ccp4_master/ccp4-8.0/libexec/python3.7: error while loading shared libraries: libcrypt.so.1: cannot open shared object file: No such file or directory --- I recently updated from Scientific Linux 7 to Alma 9. I don't know if this is part

[ccp4bb] update manager

Dear all, update manager on ccp4 8.0.017 doesn´t run (two new updates available). Did anyone else have this problem? Stefan To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] PDB validation - oligosacchides

Hi Natalie, comp_id needs to be a valid CCD ID, in this case 'GLC'. Not sure why/how the invalid value 'GLC-b-D' was generated. Let us know if you need further assistance, Deborah On 03/05/2024 22:25, Natalie Losada wrote: I am validating a structure with two sucrose molecules. I am

[ccp4bb] Post-doc position in protein crystallography and drug discovery at the City of Hope

Dear All, I have a post-doctoral position in protein crystallography and drug discovery is available in my laboratory at the City of Hope Medical Center in Los Angeles, California. The project is an NIH funded collaborative effort, coupling cell biology, chemistry and structural biology for

Re: [ccp4bb] PDB validation - oligosacchides

Natalie If you send me the model file off-list I can help. BTW, there is a Phenix specific BB that can help with all things Phenix. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235

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