Re: [ccp4bb] SAXS models and data

Yes, the SASBDB is the most commonly used repository. https://www.sasbdb.org Citation: https://onlinelibrary.wiley.com/doi/10.1002/pro.3731 -- Thomas D. Grant, Ph.D. Assistant Professor Depa

Re: [ccp4bb] SAXS models and data

Hi Gloria, I second David’s suggestion. SASBDB is where we deposited our data. Cheers, Chris -- Christopher L. Colbert, Ph.D. Pronouns: he/him/his Professor Department of Chemistry and Biochemistry NORTH DAKOTA STATE UNIVERSITY QBB 346 Dept 2710, P.O. Box 6050 Fargo, ND 58108-6050 phone: 701.23

Re: [ccp4bb] SAXS models and data

Hi Gloria, There are repositories of SAXS data. https://www.sasbdb.org/ For example. Hth, Dave Dr David C. Briggs CSci MRSB Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == about.me/david_briggs

[ccp4bb] SAXS models and data

Do we deposit these anywhere? To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB,

[ccp4bb] wwPDB Preprint Published on NextGen Archive

Dear all, A new paper describes how therecently-announced NextGen Archive provides centralized access to integrated annotations and enriched structural information for PDB data: *NextGen Archive: Centralising Access to In

[ccp4bb] Error in "Prepare and validate files for deposition" task"

Dear all, I am trying to deposit 2 structures to the PDBe, solved and refined in CCP4 (version 7), and checked in PRIVATEER as they have a lot of sugars in. To this end, I used "Prepare and validate files for deposition" task, as I had previously (and succesfully) done. However, and in spite

[ccp4bb] RCSB.org Office Hour -- February 5

Do you have questions about how to use RCSB.org? Interested in learning how to search for certain structures? Or want to explore annotations in 3D? Please join me, RCSB PDB's Scientific Support & Customer Lead, at a virtual office hour on February 5, 2024.  I would be glad to answer any RCSB.o

[ccp4bb] Technician Position available

Hi All, We have a technician position open with the possibility of transitioning to a PhD student in the lab. I appreciate your help in spreading the word. Technician Position in Structural and Chemical Biology of Neurodegenerative diseases. Position Description: Applicants are invited to appl

Re: [ccp4bb] Problem running CCP4I2 in CCP4 8 * SOLVED

Thanks, David! That did the trick. The script still finds a missing library (libjvm.so) in what appears to be Java Runtime Environment, but now CCP4I2 works, and probably also the Update feature on CCP4I. Best regards, Pedro On 30/01/2024 14:48, David J. Schuller wrote: Similar messa

[ccp4bb] Two 3-year post-doc positions in membrane protein cryo-EM

Dear all, two 3-year post-doc positions are open in our group at Lund University, Sweden, as part of the AMBER initiative. The projects focus on ion channel structural biology employing cryo-EM. Find out more and apply here: Position 1: lu.varbi.com/en/what:job/jobID:695312

Re: [ccp4bb] Problem running CCP4I2 in CCP4 8

Similar messages appear on the Known Issues page: https://www.ccp4.ac.uk/download/doc/known_issues_linux.html "Download find-missing-libs.sh and run it as a normal user (not root). The script will advise on what to do next." ==

Re: [ccp4bb] Problem running CCP4I2 in CCP4 8

Hi Arnaud, I have installed Fedora 38 from scratch and reinstalled CCP4 since the previous FC version was too old to update. I will try again after the next reboot. Thanks, Pedro On 30/01/2024 13:44, Arnaud Basle wrote: Hi Pedro, Can you reboot your machine and try again? I have see this

Re: [ccp4bb] Problem running CCP4I2 in CCP4 8

Hi Pedro, Can you reboot your machine and try again? I have see this error before on linux mint/ubuntu. Did you also updated the OS? Cheers, Arnaud On 30/01/2024 11:43, Pedro Matias wrote: > ⚠ External sender. Take care when opening links or attachments. Do not > provide your login details. >

Re: [ccp4bb] Problems updating CCP4 via CCP4i

Hi Christian, ccp4um fails with the same type of error message I get for CCP4I2: matias@ishtar % sudo /home/pxsoft/ccp4/ccp4-8.0/bin/ccp4um [sudo] password for matias: qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start be

Re: [ccp4bb] Problems updating CCP4 via CCP4i

Dear all, I have sometimes similar issues on my Ubuntu 22.04. Nevertheless, this command works well for me every time:  sudo /opt/ccp4/ccp4-8.0/bin/ccp4um i.e. calling the update manager using its full path and with admin permissions. Best wishes, Martin On Tue, 2024-01-30 at 13:01 +, David J.

Re: [ccp4bb] Problems updating CCP4 via CCP4i

Hi David, The OS is Fedora 38 - I don't have LD_LIBRARY_PATH defined in my system. Thanks, Pedro On 30/01/2024 13:01, David J. Schuller wrote: What is your operating system? I have encountered a problem on Scientific Linux 7 where ccp4um will not run correctly unless I clear out LD_LIBR

Re: [ccp4bb] Problems updating CCP4 via CCP4i

What is your operating system? I have encountered a problem on Scientific Linux 7 where ccp4um will not run correctly unless I clear out LD_LIBRARY_PATH first. This apparently happens because ccp4um requires certain libraries that ship with CCP4, and if the system libraries, which are a differe

Re: [ccp4bb] Problems updating CCP4 via CCP4i

Dear Pedro, you can start the graphical update manager from command line with ccp4um you can also run updates without the GUI using ccp4um -auto Hope this helps, Christian Am 30.01.24 um 12:40 schrieb Pedro Matias: Dear All, I am no longer able to update CCP4 via CCP4i When I click on "

[ccp4bb] Problem running CCP4I2 in CCP4 8

Dear All, After updating CCP4 to version 8, CCP4I2 stopped working with the following error message: Running CCP4i2 browser from: /home/pxsoft/ccp4/ccp4-8.0/lib/python3.7/site-packages/ccp4i2 Python 3.7.12 (default, Jan  6 2022, 21:30:12) [GCC 8.2.1 20180905 (Red Hat 8.2.1-3)] Qt version 5.1

[ccp4bb] Problems updating CCP4 via CCP4i

Dear All, I am no longer able to update CCP4 via CCP4i When I click on "Proceed" Instead of opening the update window, I get back to exactly this view. Is it possible to update CCP4 via the command line? I haven't tried using CCP4I2 because it doesn't work on my PC (separate e-mail). Than

[ccp4bb] CCPBioSim Talk - NAMD

Dear all, Our next online talk will be all about NAMD. The talk is at 15:00 UK time on 28 February 2024 given by David Hardy (NAMD developer). Information and the link for free registration is at https://www.ccpbiosim.ac.uk/namd2024. Best wishes, Sarah #