Re: [ccp4bb] CCP4 Cloud structure determination help

i Kabasakal *Sent:* 10 February 2025 11:40 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] CCP4 Cloud structure determination help Hi Marco, I would try MR with the N-terminal domain only separately, or the domains that fit well in one single chain, and the N-terminal domain other chain and

Re: [ccp4bb] CCP4 Cloud structure determination help

Burak Veli Kabasakal Sent: 10 February 2025 11:40 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4 Cloud structure determination help Hi Marco, I would try MR with the N-terminal domain only separately, or the domains that fit well in one single chain, and the N-terminal domain other chain

Re: [ccp4bb] CCP4 Cloud structure determination help

Hi Marco, I would try MR with the N-terminal domain only separately, or the domains that fit well in one single chain, and the N-terminal domain other chain and try to find these two in the map with MR. Good luck, Burak Marco Bravo , 10 Şub 2025 Pz

Re: [ccp4bb] CCP4 Cloud structure determination help

Hi Marco, Did you try putting the MR solution into ModelCraft for automated building? You say that the N-terminal domain does not fit the map, but does it look like this region is resolved, i.e. could you build it interactively in Coot? If you have good maps then I would expect automated model-bui

[ccp4bb] CCP4 Cloud structure determination help

Hello all, I am currently trying ccp4 cloud for structure solution of a 4 domain protein, 543 amino acids monomeric protein. I split the aplhaphold model into 4 domains, and prepared a single chain ensemble with the 4 domains . I see a good fit for two of the C-terminal large domain that appear

[ccp4bb] CCP4 cloud refinement after manual model building

Hello all, I am trying to run another round of refmac5 on ccp4 cloud with my model that i adjusted and did some manual model building. I got the MTZ and coordinates downloded after ccp4 cloud did the automatic simple MR workflow where it did MR and refined the model, added waters, and gave the p

Re: [ccp4bb] CCP4 installer on Sequoia

be added or removed using ccp4sm supplied with CCP4 and located in ccp4-9/bin. Best regards, Ville From: CCP4 bulletin board on behalf of Patrick Loll Sent: Wednesday, November 27, 2024 20:54 To: ccp4bb Subject: [ccp4bb] CCP4 installer on Sequoia Hi all, I’m

[ccp4bb] CCP4 installer on Sequoia

Hi all, I’m encountering problems installing CCP4 9.0 on a brand-new MacBook Pro (M4 chip, OS 15.1.1). Specifically, when I try to launch the Package Manager (cntrl-click-open, ccp4sm-uni), the icon does that brief “zoom out” thing, but then nothing else happens. I’ve worked my way down from

Re: [ccp4bb] CCP4 v9 installation issue

Dear all The issue with the CCP4 setup manager should be fixed now. If you still see a warning about write permissions, you can hopefully ignore that. Let us know if the problem persists. This error seemed to occur on some Linux distros, but not on all. All the best Ville CCP4 team #

Re: [ccp4bb] CCP4 v9 installation issue

l.edu From: CCP4 bulletin board on behalf of Oliver H. Weiergräber Sent: Thursday, September 12, 2024 4:20 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] CCP4 v9 installation issue Dear community, I am running into an unexpected problem while trying to install CCP4 v9 on a

[ccp4bb] CCP4 v9 installation issue

Dear community, I am running into an unexpected problem while trying to install CCP4 v9 on a RHEL8 workstation. The installer (run as root) complains about missing write permission for the target directory (a subdirectory of /usr/local), which is simply not true. Both standard Unix permissions

[ccp4bb] CCP4 series 9 update 003

Dear All 003 is available for installation. It includes update to coot 1 (linux and osx), ccp4cloud, ccp4i2, servalcat and Arcimboldo (linux and osx). Also included are fixes for mosflm issues on windows. Enjoy Charles (CCP4 Core Team) Ps – various CCP4 team members will be in Padova at the

Re: [ccp4bb] CCP4 database transfer to new computer

Never mind. I figured it out. From: CCP4 bulletin board On Behalf Of Poland, Brad Sent: Thursday, August 8, 2024 2:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] [ccp4bb] CCP4 database transfer to new computer Hi all. Does anyone know how to transfer my current CCP4 database to a new

[ccp4bb] CCP4 database transfer to new computer

Hi all. Does anyone know how to transfer my current CCP4 database to a new computer? I'm using the gen 1 GUI. Thank you, Brad Brad Poland, PhD Structural Biology Lead Corteva Agriscience 7200 NW 62nd Ave Johnston, IA 50131

Re: [ccp4bb] CCP4 Cloud Server Structure Prediction Task Unavailable

Dear Harry, Thank you for your email and the information regarding the CCP4 Cloud server. It was really helpful. On Wed, Jun 26, 2024 at 2:36 PM Harry Powell < 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi > > You probably need to try again later... > > It looks to me as if the CCP4

Re: [ccp4bb] CCP4 Cloud Server Structure Prediction Task Unavailable

Hi You probably need to try again later... It looks to me as if the CCP4 Cloud server (for “remote”) is down for some reason - I just tried to run it and I get a pop-up that says “CCP4 Cloud Maintenance”, that includes the text “failed to connect”. I think that the “structure prediction” task

[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

Re: [ccp4bb] ccp4 monomer library atom name change

Dear Charis, Please see: https://www.wwpdb.org/news/news?year=2023#654a801dd78e004e766a96bd Because wwPDB has changed these atoms names, the monomer library was updated accordingly. More than 800 monomers were affected. We have added the old atom names in _chem_comp_atom.alt_atom_id to help progr

[ccp4bb] ccp4 monomer library atom name change

Dear colleagues, We have recently discovered a change in the monomer library and specifically a change in the atom names of PYR.cif. The atom names of this monomer were changed between ccp4 version 8.0.016 and version 8.0.018. We were wondering if this change was on purpose and if these new ato

[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] Fw: [ccp4bb] CCP4 Study Weekend 2024 - In-person registration CLOSES TODAY - 4TH DECEMBER!

ccp4bb Subject: Re: [ccp4bb] CCP4 Study Weekend 2024 - In-person registration CLOSES MONDAY 4TH DECEMBER! In-person registration for the CCP4 Study Weekend 2024 closes on Monday 4th December (this coming Monday). Virtual registration will still be available after this date. Register now if you w

Re: [ccp4bb] CCP4 Study Weekend 2024 - In-person registration CLOSES MONDAY 4TH DECEMBER!

pm, Friday 10:30am to 3.30pm. Please note that I only work part-time ** From: McIntyre, Karen (STFC,RAL,SC) Sent: Thursday, November 23, 2023 12:21 PM To: 'ccp4bb' ; CCP4 WG1 ; CCP4 WG2 ; 'cc...@jiscmail.ac.uk' ; 'c...@jiscmail.ac.uk' ; 'pheni...@phenix-onlin

Re: [ccp4bb] CCP4 Study Weekend 2024 - In-person Early bird registration including standard student bursary CLOSES TODAY!

n.mcint...@stfc.ac.uk> Zoom phone: 01235 44 5790 [cid:image001.png@01DA1E07.81C310E0] **Hours of work: Monday to Thursday: 8.30am to 1.30pm, Friday 10:30am to 3.30pm. Please note that I only work part-time ** From: McIntyre, Karen (STFC,RAL,SC) Sent: Tuesday, November 21, 2023 10:34 AM To: '

Re: [ccp4bb] CCP4 Study Weekend 2024 - Early bird registration including standard student bursary deadline EXTENDED TO FRIDAY 24TH NOVEMBER!

L,SC) Sent: Friday, November 17, 2023 12:05 PM To: 'ccp4bb' ; CCP4 WG1 ; CCP4 WG2 ; 'cc...@jiscmail.ac.uk' ; 'c...@jiscmail.ac.uk' ; 'pheni...@phenix-online.org' ; 'pdbe-api-us...@ebi.ac.uk' Subject: CCP4 Study Weekend 2024 - Early bird registr

[ccp4bb] CCP4 Study Weekend 2024 - Early bird registration including standard student bursary deadline ends this SUNDAY!

Dear all, Registration is open for the 2024 CCP4 study weekend entitled "Decision making in MX - how to be a productive structural biologist". Important Key Dates: * Early bird registration final date: 19 November 2023; * We have assisted places available for students registering during early bi

Re: [ccp4bb] CCP4 Study Weekend 2024 - Early bird registration including standard student bursary deadline coming soon!

Dear all, Registration is open for the 2024 CCP4 study weekend entitled "Decision making in MX - how to be a productive structural biologist". Important Key Dates: * Early bird registration final date: 19 November 2023; * We have assisted places available for students registering during early bi

Re: [ccp4bb] CCP4 Study Weekend 2024 - Early bird registration including standard student bursary deadline coming soon!

Dear all, Registration is open for the 2024 CCP4 study weekend entitled "Decision making in MX - how to be a productive structural biologist". This year we are focusing on decision-making in macromolecular crystallography: when to use what automated tool, how to interpret the output and when yo

[ccp4bb] CCP4 Study Weekend 2024 - Early bird registration including standard student bursary deadline coming soon!

Dear all, Registration is open for the 2024 CCP4 study weekend entitled "Decision making in MX - how to be a productive structural biologist". This year we are focusing on decision-making in macromolecular crystallography: when to use what automated tool, how to interpret the output and when yo

[ccp4bb] CCP4 Summer School 2023: extra places available

Dear all, There are now extra places available at the CCP4 Summer School being held in York from the 19th to the 25th August 2023. The school programme has been designed to not only cover practical and theoretical macromolecular X-

[ccp4bb] CCP4 NORTHERN PROTEIN STRUCTURE MEETING 2023

Dear All, The 2023 CCP4 Northern Protein Structure Workshop will be held at the University of Nottingham on the 26-27th October. Registration is FREE and this year we have a limited number of travel bursaries available so please encourage your research students and early career post-doctoral re

[ccp4bb] CCP4 Summer School 2023: deadline approaching!

Dear CCP4bb subscribers, As you may know, the CCP4 Summer School is returning to York after a 4-year hiatus – this is a continuation of the excellent work done by our colleagues at St. Andrews pre-2019. We've got an exciting programme prepared for the students, including lectures not just on macr

[ccp4bb] CCP4 Cloud workshop IGBMC, Illkirch, France

WORKSHOP CCP4 Cloud for structure solution Tuesday 26 September 2023 Auditorium, IGBMC Maria Fando and Eugene Krissinel CCP4, UKRI-STFC, Rutherford Appleton Laboratory, Didcot, United Kingdom The workshop will begin with a lecture overview of the development of structural solution pro

[ccp4bb] ccp4 on cluster

Dear all, I need to install CCP4 on my disk in cluster computer. The OS is CentOS Linux 7. Please instruct me for this. Thank you in advance. Best regards, Rafiga To unsubscribe from the CCP4BB list, click the following

[ccp4bb] ccp4 update 009

Dear All A little late, but update to 8.0 009 is now available. Brief description: ccp4cloud -update to 1.7.010 https://cloud.ccp4.ac.uk/manuals/html-userguide/jscofe_version_log.html ccp4i2 - update to v2.0. https://ccp4i2.gitlab.io/rstdocs/updatelog/index.html cbuccaneerNN - new model bui

Re: [ccp4bb] CCP4 8.0.008 Python2 <-> 3 problem

Hi Michael, I recently installed panDDAs on an older Linux system. It still runs Centos 7, which was nice since I've run into compatibility issues with python3/python 2.7 on a newer Mac. Here are the basic steps that I've had to follow: --Install cpp4 7.0 and download the updates to get to the ri

Re: [ccp4bb] CCP4 8.0.008 Python2 <-> 3 problem

Hi Michael New version coming on Friday. Should fix the issues. You will be able to upgrade using ccp4um Sorry for the issues Charles From: CCP4 bulletin board on behalf of Michael Weyand Date: Thursday, 16 February 2023 at 07:30 To: ccp4bb Subject: [ccp4bb] CCP4 8.0.008 Python2 <-

[ccp4bb] CCP4 8.0.008 Python2 <-> 3 problem

Dear colleagues, First, I don't want to flood ccp4bb with all the concrete program error code(s). Therefore a more general description. I can give more details if needed. To the board or by direct mails to the real experts. I would like to use the Panndda/PanDEMIC

[ccp4bb] CCP4 Study Weekend 2023 Survey

If you attended this year's CCP4 Study Weekend either virtually or in-person and haven't already given us feedback, please do so before the survey closes on 31st Jan 2023. You will have received a link to the survey via e-mail. Your responses help us make the SW better! Thanks to all you have

[ccp4bb] CCP4 Cloud news

Dear All, In response to your feedback and requests, we have significantly increased default CPU quota for all CCP4 Cloud accounts and introduced automatic top-up of cloud storage. You should see your new quotas at next login, along with a notification e-mail from the system. Please notify CCP4

Re: [ccp4bb] CCP4 Study Weekend 2023 - In-person registration closes Monday 5th December 2022

35 44 5790 [cid:image001.png@01D9057C.D74D9610] **Please note that I only work mornings until 1.30pm** From: McIntyre, Karen (STFC,RAL,SC) Sent: 15 November 2022 10:59 To: CCP4 WG1 ; CCP4 WG2 ; ccp4bb ; cc...@jiscmail.ac.uk Subject: FW: [ccp4bb] CCP4 Study Weekend 2023 - Early bird registration extend

[ccp4bb] FW: [ccp4bb] CCP4 Study Weekend 2023 - Early bird registration extended to 20th November

n board On Behalf Of Warren, Anna (DLSLtd,RAL,LSCI) Sent: 09 November 2022 08:57 To: ccp4bb Subject: [ccp4bb] CCP4 Study Weekend 2023 - Early bird registration ends 13th November This year the CCP4 Study Weekend will be held as a hybrid event from the 4th - 6th January at the East Midla

[ccp4bb] CCP4 Study Weekend 2023 - Early bird registration ends 13th November

This year the CCP4 Study Weekend will be held as a hybrid event from the 4th - 6th January at the East Midlands Conference Centre, Nottingham, UK, with an exciting programme confirmed below. Early bird registration is open until 13th November, more details of which can be found here: https://cc

Re: [ccp4bb] ccp4 installation problem

Hi Robert, On Fri, Sep 16, 2022 at 4:11 PM Kay Diederichs wrote: > Your real problem seems to be the Qt installation; I think that the error > message > qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though > it was found. > This application failed to start because no Qt

Re: [ccp4bb] ccp4 installation problem

Hi Kay Thanks again and for more insight and feedback on the Qt installation. Reply in blue text below. Take care, Rob -Original Message- From: Kay Diederichs Sent: Friday, September 16, 2022 4:11 PM To: CCP4BB@JISCMAIL.AC.UK; Robert Gampe Subject: Re: ccp4 installation problem

Re: [ccp4bb] ccp4 installation problem

Hi Robert, you are welcome. It seems that you own (rgampe.rgampe) the directory /software/ccp4-8.0 . You should revert the ownerships in /software/ccp4-8.0 from root.root with sudo chown -R rgampe.rgampe /software/ccp4-8.0 so that in the future you don't need sudo for updates. Your real probl

Re: [ccp4bb] ccp4 installation problem

Hi Robert, hmm, more ideas: a) check if CCP4 directory is writable, and who the owner is: mount | grep software sudo touch /software/ccp4-8.0/deleteme ls -ld /software/ccp4-8.0 ls -l /software/ccp4-8.0/deleteme sudo rm /software/ccp4-8.0/deleteme b) try sudo su ccp4um c) try sudo -i ccp4um

Re: [ccp4bb] ccp4 installation problem

Hi Robert, two points - a) before you tried to update, did you source /where/ever/ccp4/bin/ccp4.setup-sh ? The above applies to bash; for (t)csh you need to source /where/ever/ccp4/bin/ccp4.setup-csh That sets the PATH environment variable such that you don't always have to specify the absolut

Re: [ccp4bb] ccp4 installation problem

Hi Robert, Concerning PROBLEM 1: have you tried sudo ccp4um or sudo ccp4i ? HTH, Kay P.S. didn't find Andrey Lebedev's reply on August 30 that you refer to On Fri, 16 Sep 2022 14:11:34 +, Robert Gampe wrote: >Hello Marcin Pedro and the CCP4 community, > > > >PROBLEM 1: I have the same st

Re: [ccp4bb] ccp4 installation problem

Hi Marcin, If you are not logged on as root I think you need to run the installer with sudo Hope this helps, Pedro Matias Em 06/09/2022 13:33, Marcin Jaciuk escreveu: Dear All, After upgrading to newest Ubuntu 22.04 I am trying to install ccp4 via Package Manager with /opt directory as in

[ccp4bb] ccp4 installation problem

Dear All, After upgrading to newest Ubuntu 22.04 I am trying to install ccp4 via Package Manager with /opt directory as installation destination. When installer asks me for super user password (which I am) it rejects it, see below: AUTHENTICATING FOR org.freedesktop.policykit.exec === Auth

[ccp4bb] CCP4/CCP-EM workshop at ECM33

Dear All There will be a CCP4/CCP-EM workshop on the two days prior to the ECM33 meeting at Soleil. Details and registration are at https://www.ecm33.fr/ccp4andccpemworkshops Accommodation will be provided at the Soleil guest house during the workshop (individual’s responsibility to pay, bu

[ccp4bb] CCP4/CCP-EM workshop at ECM33

Dear All Following on for the CSD workshop e-mail there will be a joint CCP4/CCP-EM event at ECM33 https://www.ecm33.fr/copie-de-mechanical-properties Date : 21 & 22 August 2022 Venue : Synchrotron SOLEIL Organizer : Charles BALLARD Descrip

[ccp4bb] CCP4 error in job missing

While Running CCP4 7.0. All the jobs get cleared from the main window and project. How will I get back all the job lists? Thanks in advance for suggestions. SMITA To unsubscribe from the CCP4BB list, click the following li

[ccp4bb] CCP4 Study Weekend 2022 - registration still open - places still available for in person event

Dear all, Registration is open for the 2022 CCP4 study weekend https://cvent.me/YPqVd0 The topic this year is "Current trends in macromolecular model refinement and validation". This year the meeting will be a hybrid meeting from 5th - 7th January 2022 with the in-person event held at East Mid

[ccp4bb] CCP4 Study Weekend 2022

Dear all, Registration is open for the 2022 CCP4 study weekend https://cvent.me/YPqVd0 The topic this year is "Current trends in macromolecular model refinement and validation". This year the meeting will be a hybrid meeting from 5th - 7th January 2022 with the in-person event held at East Mid

[ccp4bb] CCP4 Cloud down -- resolved

Dear All, CCP4 Cloud is now back to fully operational state after recent hardware failure. The failure did not affect user data and projects. Please report any malfunction to CCP4 team. Many thanks for using CCP4 Cloud, Eugene Krissinel This email and any attachments are intended solely for t

[ccp4bb] CCP4 Cloud outage

Dear All, CCP4 Cloud was taken down abruptly due to hardware malfunction, which we try to rectify. All user and project data should be safe but unavailable at the moment. Once the problem is resolved, we will inform you with separate posting. Apologies for the inconvenience, Eugene Krissinel.

[ccp4bb] ccp4.ac.uk offline

Dear All we are currently off line. The water cooling is undergoing maintenance where our servers sit. We had hoped to continue to run downloads,etc, but it looks like the front-end machine has gone down. Planned return to normal is 9 am GMT, this is if the front-end shutdown was a planned e

[ccp4bb] CCP4 Online at risk

Dear ccp4bb, Just to let you know that the CCP4 Online service (https://ccp4online.ccp4.ac.uk) is currently 'at risk'. If you notice that you fail to connect to the server, refreshing your browser is usually enough to get things working again. This is due a recent firewall upgrade. It should g

Re: [ccp4bb] CCP4 tutorials (files)

On Thu, Jul 30, 2020 at 02:18:58PM +, Winter, Graeme (DLSLtd,RAL,LSCI) wrote: > http://legacy.ccp4.ac.uk/docs.php > > -> tutorials > > Looks like there’s something very broken with the style sheets or something > but the information does appear to be available > > The links to tar files of

Re: [ccp4bb] CCP4 tutorials (files)

Hi Rafael, CCP4 ships with lots of tutorial data. If you launch CCP4i2, then there is a Help/Tutorials menu which will introduce those techniques through CCP4i2, and help you identify file locations if you want to have a crack at command line structure determination. Best wishes Martin On 30

Re: [ccp4bb] CCP4 tutorials (files)

Hello, it should be possible to get the example data, at least for SAD, thru the i2 interface. It worked last week... Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Original Message On 30 Jul 2020, 15:10, Rafael Marques wrote: > Hello folks. > > During the quarantine I a

Re: [ccp4bb] CCP4 tutorials (files)

Hi Rafael, http://legacy.ccp4.ac.uk/docs.php -> tutorials Looks like there’s something very broken with the style sheets or something but the information does appear to be available The links to tar files of data appear to work Best wishes Graeme On 30 Jul 2020, at 15:10, Rafael Marques mai

[ccp4bb] CCP4 tutorials (files)

Hello folks. During the quarantine I am trying to use some softwares on CCP4 that I have never used before and also to learn how to solve structures differently than the usual MR (for me). However, the ccp4 tutorial website is down and error 404 is everywhere. Does anybody know a link where I c

Re: [ccp4bb] CCP4-7.1 Crash in CentOS 8.1

Hi Could you send a screenshot of the run in debug mode? Generally the 'Floating point exception/error' comes up when an unexpected infinity or undefined number comes up, for example, while executing x/y where x=int but y=0. You can do that by editing your ccp4i bash/csh file in /home/user/softw

Re: [ccp4bb] CCP4 source code

Thank you for making the 7.1 source available ! For those interested, http://www.ccp4.ac.uk/download/index.php#os=src Thierry From: CCP4 bulletin board On Behalf Of Fischmann, Thierry Sent: Monday, May 4, 2020 3:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] CCP4 source code EXTERNAL

Re: [ccp4bb] CCP4 source code

Dear Thierry, Check here: http://devtools.fg.oisin.rc-harwell.ac.uk/nightly/7.0/ccp4-src-7.0/ "Checkout" folder seems to contain the source code. пн, 4 мая 2020 г. в 21:26, Fischmann, Thierry < 22f7fda0a875-dmarc-requ...@jiscmail.ac.uk>: > Hello, > > > > This question is addressed to the CCP4

[ccp4bb] CCP4 source code

Hello, This question is addressed to the CCP4 staff, but the answer may be of general interest: Do you have a projection for when the 7.1 source code will be available? Is there a way to access the source code for 7.0 in the mean time? Of course it is understood that the source code availabili

Re: [ccp4bb] ccp4 and ccpEM on same workstation?

https://www.jiscmail.ac.uk/CCPEM > > Best wishes, > Colin > > -- > Dr. Colin Palmer > CCP-EM | www.ccpem.ac.uk | @ccp_em > > Research Complex at Harwell > STFC Rutherford Appleton Laboratory > Didcot OX11 0FA, UK > +44 1235 567864 > > > > > From: CCP4

Re: [ccp4bb] ccp4 and ccpEM on same workstation?

wishes, Colin -- Dr. Colin Palmer CCP-EM | www.ccpem.ac.uk | @ccp_em Research Complex at Harwell STFC Rutherford Appleton Laboratory Didcot OX11 0FA, UK +44 1235 567864 From: CCP4 bulletin board On Behalf Of Sam Tang Sent: 30 April 2020 12:31 To: ccp4bb Subject: [ccp4bb] ccp4 and ccpEM on same

[ccp4bb] ccp4 and ccpEM on same workstation?

Hi, I'm going to install ccpEM on a same fedora 30 workstation that already has ccp4 will they touch on my pre-existing Coot and Refmac setup? Maybe I'm just worrying too much..? Cheers Sam To unsubscribe from th

Re: [ccp4bb] CCP4 7.1 problems

I met a similar problem when I ran the "Geometry analysis" in coot-0.9. Coot crashed with the following words. I had to roll back to ccp4-7.0. My system is CentOS 7. make_df_restraints_indices() 508 --- terminate called afte

Re: [ccp4bb] {Disarmed} Re: [ccp4bb] CCP4 7.1 problems

0)1865 275392 University of Oxford Oxford UK, OX1 3QU From: CCP4 bulletin board On Behalf Of Robert S Phillips Sent: 24 April 2020 14:01 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] CCP4 7.1 problems I installed CCP4 7.1 yesterday, and I have problems. On an Ubuntu 18.04 LTS system, I g

Re: [ccp4bb] CCP4 7.1 problems

f Oxford Oxford UK, OX1 3QU From: CCP4 bulletin board On Behalf Of Robert S Phillips Sent: 24 April 2020 14:01 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] CCP4 7.1 problems I installed CCP4 7.1 yesterday, and I have problems. On an Ubuntu 18.04 LTS system, I get the following: rob@rob-SA76R4:~$ cc

Re: [ccp4bb] CCP4 7.1 problems

On 24/04/2020 14:01, Robert S Phillips wrote: I installed CCP4 7.1 yesterday, and I have problems.  On an Ubuntu 18.04 LTS system, I get the following: Similarly, with COOT: rob@rob-SA76R4:~$ coot INFO:: Reading coordinate file: /home/rob/CCP4/ccp4-7.1/share/coot/standard-residues.pdb INFO:

[ccp4bb] CCP4 7.1 problems

I installed CCP4 7.1 yesterday, and I have problems. On an Ubuntu 18.04 LTS system, I get the following: rob@rob-SA76R4:~$ ccp4i2 Running CCP4i2 browser from: /home/rob/CCP4/ccp4-7.1/share/ccp4i2 Python 2.7.16 (default, Apr 22 2020, 09:15:14) [GCC 4.9.1 20140922 (Red Hat 4.9.1-10)] Qt version 4.

Re: [ccp4bb] CCP4 7.1 released

Not yet all. It is a significant project, but one that is very much underway. -- David On Thu, 23 Apr 2020 at 18:55, David Schuller wrote: > Coincidentally, Python 2 had its final release just a few days ago. I > trust python components of CCP4 are all now using Python 3. > > https://www.thereg

Re: [ccp4bb] CCP4 7.1 released

Coincidentally, Python 2 had its final release just a few days ago. I trust python components of CCP4 are all now using Python 3. https://www.theregister.co.uk/2020/04/21/the_final_python_2_release/ - === All Things Serve the B

[ccp4bb] CCP4 7.1 released

Dear CCP4 Users, The CCP4 Core Group is very pleased to announce the release of the latest version of the CCP4 Software Suite. Version 7.1 (Skipton) is now available from the CCP4 download website . The release is available for all MS Windows, Linux and Mac OSX

[ccp4bb] CCP4 Study Weekend live stream link

For those wanting to watch the CCP4 Study Weekend 2020 via the live stream the link is below: Please click the link below to join the webinar: https://ukri.zoom.us/j/195886424 On the CCP4 website people will be connected to the conference both days, 8th and 9th January Regards Karen McIntyre

[ccp4bb] CCP4 wiki server is down?

Dear CCP4 developers, ccp4wiki.org is throwing an exception: *Fatal error*: Uncaught TypeError: Argument 1 passed to wfReportException() must be an instance of Exception, instance of Error given, called in /home/ccp4wiki/public_html/wiki/includes/Exception.php on line 205 and defined in /home/ccp4

Re: [ccp4bb] CCP4 Study Weekend 2020: 2 places have become available

.png@01D5C23A.62E627C0] **Please note that I only work mornings until 1.30pm** From: McIntyre, Karen (STFC,RAL,SC) Sent: 12 November 2019 09:04 To: 'cc...@jiscmail.ac.uk' ; ccp4bb ; CCP4 WG2 Subject: [ccp4bb] CCP4 Study Weekend 2020: early bird period closes this Sunday!! Importance:

[ccp4bb] CCP4 Study Weekend - Diamond MX User meeting

Happy New Year! We would like to point you to the programme of the Diamond MX User Meeting at the CCP4 Study Weekend: http://www.cvent.com/events/ccp4-study-weekend-2020/agenda-001c74f5ecfa4987af3e908c7a9d7d60.aspx And we also thank all the speakers who sacrifice part of their holidays prepari

[ccp4bb] CCP4 Crystallographic School in South Africa 2020

Dear CCP4bb community, We are pleased to announce the CCP4 Crystallographic School in South Africa, to be held from 31 March — 08 April 2020 at the University of Cape Town, South Africa. The workshop will cover all aspects of protein structure solution by X-ray crystallography, including the fund

Re: [ccp4bb] CCP4 update manager command line options?

Dear Christoph, Unfortunately there is no command line option to install any earlier version; Windows installer provides only latest CCP4 version. All the best, Oleg Kovalevskiy and Andrey Lebedev -- Dr Oleg Kovalevskiy CCP4 team Science and Technology Facilities Council Rutherford Appleton L

[ccp4bb] CCP4 update manager command line options?

Hi, In context of an unattended installation/update of CCP4 for Windows 7/10  in a computer pool environment, is it possible to install CCP4 (from scratch) via update manager (ccp4um) command line option to an earlier version than the latest (e.g. 7.0.072 instead of 7.0.078)? If yes, what wou

Re: [ccp4bb] CCP4 Study Weekend 2020: less than 20 places left!!

] **Please note that I only work mornings until 1.30pm** From: McIntyre, Karen (STFC,RAL,SC) Sent: 12 November 2019 09:04 To: 'cc...@jiscmail.ac.uk' ; ccp4bb ; CCP4 WG2 Subject: [ccp4bb] CCP4 Study Weekend 2020: early bird period closes this Sunday!! Importance: High Only 5 more

[ccp4bb] CCP4 Study Weekend 2020: early bird period closes this Sunday!!

.ac.uk>>; CCP4 WG2 mailto:ccp4...@listserv.stfc.ac.uk>>; 'cc...@jiscmail.ac.uk' mailto:cc...@jiscmail.ac.uk>> Subject: FW: [ccp4bb] CCP4 Study Weekend 2020: early bird period closes on Sunday 17th November!!! Importance: High Just a reminder that the early bird period fo

[ccp4bb] CCP4 on MacOS Catalina

Dear CCP4 Users CCP4 Setup Manager and Update Manager are now functional on MacOS Catalina in both user and administrative mode. The corrected version of Setup Manager is now available from usual location, CCP4 Downloads . Technical details. Previo

[ccp4bb] FW: [ccp4bb] CCP4 Study Weekend 2020: early bird period closes on Sunday 17th November!!!

Subject: [ccp4bb] CCP4 Study Weekend 2020: registration now open! Dear colleagues, We are pleased to announce that the next CCP4 Study Weekend in its 2020 edition will be devoted to the single most synergic task in structural biology: model building. Aside from covering the latest advances in both

Re: [ccp4bb] CCP4 Computational Scientist

Dear all, Here's a reminder that CCP4 is looking for a computational scientist to investigate corrections for electron diffraction data. Job details are below. Best wishes -- David On Mon, 23 Sep 2019 at 13:20, Eugene Krissinel wrote: > Dear All, > > CCP4 is looking for computational scienti

[ccp4bb] CCP4 Computational Scientist

Dear All, CCP4 is looking for computational scientist to work on a research project in Electron Diffraction. The Project is funded by BBSRC UK, and will be conducted in CCP4 Core Group based in Rutherford Appleton Laboratory, UK. For full job details and direct links to online application portal,

Re: [ccp4bb] CCP4 Study Weekend 2020: registration now open!

Of course we want everyone to register immediately, but if you insist on seeing the programme first, please go to http://www.cvent.com/events/ccp4-study-weekend-2020/event-summary-001c74f5ecfa4987af3e908c7a9d7d60.aspx?fqp=true Cheers, Jon, Robbie and Alan On Wed, 11 Sep 2019 at 10:15, Jon Agirre

[ccp4bb] CCP4 Study Weekend 2020: registration now open!

Dear colleagues, We are pleased to announce that the next CCP4 Study Weekend in its 2020 edition will be devoted to the single most synergic task in structural biology: model building. Aside from covering the latest advances in both automated and manual procedures, the meeting will offer sessions

[ccp4bb] CCP4 Job Advert Beamline Scientist [SEC=UNCLASSIFIED]

Dear Colleagues, The Australian Synchrotron (Melbourne, Australia) is currently seeking to recruit a beamline scientist to join the existing MX team. The Australian Synchrotron currently operates 2 MX beamlines with a broad user base covering both Chemical and Protein Crystallography. As such

[ccp4bb] CCP4 Workshop at ECM-32

Dear All, Please take a notice of a 1-day CCP4 Workshop, which will be run as part of ECM-32 meeting in Vienna on 17th of August 2019. Full information may be found here: https://ecm2019.org/satellites/ccp4-structure-solution/ Please register if you are interested. Everybody is invited. Kind re

[ccp4bb] CCP4-7.0 Update 70 including ARP/wARP-8.0 patch 1

Dear CCP4 Users We would like to announce CCP4-7.0 update No 70 that includes the following. *ARP/wARP: patch 1 for version 8.0* Notes from Victor Lamzin, EMBL-Hamburg, Germany News in ARP/wARP 8.0 patch 1: Protein model building: – Large structures up to 50,000 residues can now be handled;

[ccp4bb] CCP4 Study Weekend: late addition and last chance to register - Registration extended to midnight Wednesday 12th December (today)!

ntil 1.30pm** -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Randy Read Sent: 07 December 2018 09:02 To: ccp4bb Subject: [ccp4bb] CCP4 Study Weekend: late addition and last chance to register The CCP4 Study Weekend on "Integrated, rational

Re: [ccp4bb] CCP4 Study Weekend: late addition and last chance to register - Registration extended to midnight Wednesday 12th December (tomorrow)!

: 07 December 2018 09:02 To: ccp4bb Subject: [ccp4bb] CCP4 Study Weekend: late addition and last chance to register The CCP4 Study Weekend on "Integrated, rational molecular replacement" will be held at the East Midlands Conferenced Centre in Nottingham, from 8th to 10th January 2019. T

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