[ccp4bb] CCP4-BCA Protein Crystallography Summer School (1st – 6th Sept 2024) hosted by the John Innes Centre – deadline extended to 24th June

Hi All, The John Innes Centre in Norwich (UK) will be hosting this year’s CCP4-BCA Protein Crystallography Summer School. We will cover the range of techniques required for a protein structure solution from protein expression through to structure validation. We have a great line-up of tutors a

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

Hi All, The deadline for applications is rapidly approaching – please apply by 10th June. Dave - 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 appl

[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] Structural Biology Facility Manager vacancy at the John Innes Centre, Norwich UK

Dear All, We have a vacancy for a Structural Biology Facility Manager at the John Innes Centre. The John Innes Centre is an independent, international centre of excellence in plant and microbial sciences. We nurture a creative, curiosity-led approach to answering important questions in bioscie

[ccp4bb] Structural Biology Facility Manager vacancy at the John Innes Centre, Norwich UK

Dear All, We have a vacancy for a Structural Biology Facility Manager at the John Innes Centre. The John Innes Centre is an independent, international centre of excellence in plant and microbial sciences. We nurture a creative, curiosity-led approach to answering important questions in bioscie

Re: [ccp4bb] re-open the results from a previous DIALS User Interface session in CCP4 cloud?

Hi both, Thanks for the suggestions. I will see if I can find a workable solution based on what you say. Best wishes Dave --- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: ht

[ccp4bb] re-open the results from a previous DIALS User Interface session in CCP4 cloud?

Hi All, In CCP4i2 it is possible to re-open the results from a previous DUI session by cloning the job and selecting the "Continue from previous dials session" option from the drop-down. I'm trying to find a way to do this in CCP4 cloud for a tutorial - perhaps it's not possible? Any suggestio

Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]

. -Original Message- From: CCP4 bulletin board On Behalf Of Paul Emsley Sent: 09 August 2023 15:31 To: ccp4bb Subject: Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7] On 09/08/2023 10:54, David Lawson (JIC) wrote: > Hi Paul, > > Just wondering

Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]

Hi Paul, Just wondering where we are with this fix. Is it safe to apply the latest CCP4 updates? Many thanks Dave --- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.

Re: [ccp4bb] real space refinement broken in COOT 0.9.8.8 EL?

...@jic.ac.uk<mailto:david.law...@jic.ac.uk> From: Eugene Pichkur Sent: Monday, July 17, 2023 11:59 AM To: David Lawson (JIC) Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] real space refinement broken in COOT 0.9.8.8 EL? You don't often get email from eugene.pich...@gmail.com<mail

[ccp4bb] real space refinement broken in COOT 0.9.8.8 EL?

Hi All, Is it just me, but is real space refinement broken in COOT 0.9.8.8 EL? I am seeing this working through CCP4i2 (CCP4-8.0.012) and CCP4 cloud (v 1.7) on an M1 iMac (running Monterey 12.6.7). I am working on a protein-DNA complex and finding that often when I do real space refinement (wel

Re: [ccp4bb] Unidentified density

Hi Zeya, Did you cryoprotect with glycerol perhaps? Dave --- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk

[ccp4bb] Application deadline approaching - Virtual CCP4 Protein Crystallography Summer School 2021 (6th-10th September)

Dear colleagues, We are pleased to announce the Virtual CCP4 Protein Crystallography Summer School 2021 to be hosted by the John Innes Centre (Norwich, UK). The school will take place from Monday 6 September – Friday 10 September inclusive and is intended for students and researchers new to cry

[ccp4bb] Virtual CCP4 Protein Crystallography Summer School 2021 (6th-10th September) - applications open

Dear colleagues, We are pleased to announce the Virtual CCP4 Protein Crystallography Summer School 2021 to be hosted by the John Innes Centre (Norwich, UK). The school will take place from Monday 6 September – Friday 10 September inclusive and is intended for students and researchers new to cry

Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

: Eleanor Dodson Sent: 09 February 2021 13:33 To: David Lawson (JIC) Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file? Yes, I agree.. garish? Rob Nichols?? Can you email this to them directly? E On Tue, 9 Feb 2021 at 13:28, David Lawson (JIC

Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk From: Eleanor Dodson Sent: 09 February 2021 13:15 To: David Lawson (JIC) Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb

[ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

Hi All, By default, when you run REFMAC5 run through CCP4I2, it uses riding hydrogens during refinement. It then writes out a PDB file without the hydrogens and an MMCIF file that retains these hydrogens. In the latter, you end up with mostly hydrogens with unit occupancy and a few with zero oc

[ccp4bb] running the CCP4i2 export utility from the command line?

Hi All, I would like to run the CCP4i2 export utility from the command line (on a Mac) to produce a zip file from a project directory that can then be imported in the normal way using the CCP4i2 GUI. I assume this is possible? Thanks in advance Dave --- Prof. David

Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

r Aniso Developers, If this turns out to be because we are “missing something” i.e. there is an expectation on a property being present in the output files but it’s not there in our MTZ output, please let us know :-) Best wishes Graeme On 14 Jan 2020, at 09:06, David Lawson (JIC) mailto:david.

[ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

Dear ccp4bb I am trying to get the staraniso server to accept a scaled but unmerged mtz file from DIALS processing, but it reports an "Internal Server Error" after thinking about it for a while. Should this be possible? The file is 31 MB, so not huge. It works fine for a merged mtz from DIALS,

[ccp4bb] Warning - ccp4 update 7.0.069 breaks ccp4i2 on MacBook running Mojave (v 10.14.2)

Hi All, I installed the latest ccp4 update on my MacBook through the CCP4i2 update manager. After doing so, refmac appeared to be broken. I tried to restart the I2 GUI but it refused to even after a reboot. Eventually I got running again by uninstalling this update through the CCP4i update mana

Re: [ccp4bb] photograph of Enraf-Nonius FAST detector

Hi All, In a similar vein, does anyone have a photo of the eight cassette carousel (ideally in situ on a beamline) that was used to collect data on film at Daresbury? Many thanks, Dave --- Dr. David M. Lawson Department of Biological Chemistry, John Innes Centre,

[ccp4bb] Name that protein!

Hi All, Many thanks to those who responded. The general opinion is that it is some sort of pore/channel, possibly a voltage-gated potassium or sodium channel. Best wishes, Dave Hi All Apologies for the off-topic question. The attached image has been hang

[ccp4bb] Name that protein!

Hi All Apologies for the off-topic question. The attached image has been hanging on the wall at our institute for several years and nobody knows what it is or who generated it. If anyone recognises it, please let me know. Many thanks Dave Lawson --- Dr. David M.

Re: [ccp4bb] restraints for pseudo-amino acids within a peptide chain

603-450018 Email: david.law...@jic.ac.uk<mailto:david.law...@jic.ac.uk> From: Robbie Joosten [mailto:robbie_joos...@hotmail.com] On Behalf Of Robbie Joosten Sent: 27 September 2017 17:04 To: david lawson (JIC) ; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] restraints for pseudo-amino acids within

[ccp4bb] restraints for pseudo-amino acids within a peptide chain

Hi All, I am having issues with getting pseudo-amino acids to behave in refmac such that they correctly form peptide bonds with standard residues before and after them. The problem I have is that when naming atoms forming the peptide bonds, there are effectively two C-alpha atoms, as shown belo

[ccp4bb] SUMMARY: [ccp4bb] microsoft 3-button wheel mouse with OS X 10.5

the responses: -- Bill: ------ Hi David: david lawson (JIC) wrote: > Dear All, > > Sorry for the slightly off-topic subject. > > We have recently bought a few iMacs for crystallography. I'm not keen > on the supplied "mighty mouse" May I have them? >

[ccp4bb] microsoft 3-button wheel mouse with OS X 10.5

Dear All, Sorry for the slightly off-topic subject. We have recently bought a few iMacs for crystallography. I'm not keen on the supplied "mighty mouse" so I have switched to using a microsoft 3-button wheel mouse. I would like to configure it so that it behaves as it would with other unix system

[ccp4bb] Archiving onto DVD with RH linux

Dear ccp4BB, Sorry for the non-ccp4 post. I have been using a NEC DVD_RW ND-2500A drive to archive onto DVD-Rs (using 'mkisofs' and 'dvdrecord' commands) from our RH linux system. This has worked very well with 8x compatible DVD-R disks, but doesn't recognise the newer 16x disks that only seem t

Re: [ccp4bb] Popularity of Stereo graphics in crystallography

I haven't used stereo since the last millenium - I don't miss it. You don't really need it and it's not worth the expense/hassle to set up. In my opinion it's just something to impress visitors! Dave --- Dr. David M. Lawson Biological Chemistry Dept., John Innes C

[ccp4bb] SUMMARY: His-His H-bond

Dear All, As usual the bulletin board has been enormously helpful. To remind you here was my original post: We have solved a structure that has an intersubunit His-His H-bond (ND1---NE2). The protein most likely undergoes conformational changes that involve the making and breaking of H-bonds at t

[ccp4bb] His-His H-bond

Dear All, We have solved a structure that has an intersubunit His-His H-bond (ND1---NE2). The protein most likely undergoes conformational changes that involve the making and breaking of H-bonds at this interface. In all the protein structures I have previously studied I don't recall ever seeing s

[ccp4bb] INDEPENDENT RESEARCH FELLOWSHIPS CONFERENCE 4/5 June 2007, John Innes Centre UK

Dear All, Apologies for the non-CCP4 related post. Please can you bring the following ad to the attention of researchers who either hold, or wish to apply for Independent Research Fellowships. - INDEPENDENT RESEARCH FELLOWSHIPS CONFERENCE 4/5 June 2007 The John In