Re: [ccp4bb] how to speed up polishing

Hi Takanori, We have changed now to 8 Mpi x 10 threads and things became a lot faster. So far seems like no particular problems with disk I/O. Thanks a lot for your help! Best Leonid On 15.11.24 13:20, Takanori Nakane wrote: [EXTERNAL EMAIL - USE CAUTION when clicking links or attachments]

Re: [ccp4bb] Registration now open for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models

Registration is still open for CCP4 Study Weekend 2025. In-person registration will close on 6th December 2024. Virtual registration will close on 9th January 2025. Regards Karen McIntyre CCP4 Project Administrator CCP4 ED&I Champion UKRI-STFC Rutherford Appleton Laboratory Harwell Campus Didc

Re: [ccp4bb] PDBe access issue

Maybe there are sporadic issues with the EBI website generally. I’ve also been having issues with continuous integration tests failing more than usual e.g. https://github.com/jamesmkrieger/ProDy/actions/runs/11855631938/job/33040243324. Best wishes James On 15 Nov 2024, at 08:22, Guillaume Gaul

Re: [ccp4bb] how to speed up polishing

Hi, I checked the node running the job and there seem to be no memory issue but out of 2 MPi X 30 threads apparently only two threads are running at 100% CPU usage and the rest at about 5% each. This is typical inefficiency when you have too many threads per MPI process. Each thread handles

Re: [ccp4bb] how to speed up polishing

Dear Takanori, Thank you very much for tips. I checked the node running the job and there seem to be no memory issue but out of 2 MPi X 30 threads apparently only two threads are running at 100% CPU usage and the rest at about 5% each. Our file system is based on ZFS and we use --sbs option.

Re: [ccp4bb] acedrg error in gui, command line only cif no pdb output

PS: CIF can be converted to PDB easily using (for instance) gemmi: $ gemmi convert OEX.cif OEX.pdb All available options can be listed using: $ gemmi convert -h Be aware that an output PDB file will have issues for 5-letter-code monomers as the PDB format can accommodate only monomer codes up to

Re: [ccp4bb] PDBe access issue

Thanks to all who have answered. It was probably an issue with my network settings Now I can reach the website. Best Xavier > Le 15 nov. 2024 à 08:22, Guillaume Gaullier a > écrit : > > It works here, I entered an accession code and it took me to the entry page. > > Guillaume > >> On 15 Nov