[ccp4bb] AlphaFold Protein Structure Database - releasing updated structures

2022-10-04 Thread Sameer Velankar
Dear All, We plan to release an updated set of AlphaFold structure predictions on AFDB in the coming weeks. This will update a subset of predictions affected by a temporary numerical bug (miscompilation). This temporary issue resulted in low accuracy predictions with correspondingly low pLDDT

Re: [ccp4bb] EDR (Sophos) and CCP4 compatibility

2022-10-04 Thread Andrew Purkiss
Hi Mark and Dave (who just beat me to it), Generally Sophos has been fine. However, I did get the following a couple of weeks ago which Sophos cleared up for me by deleting the relevant files. "Generic ML PUA detected at C:\CCP4-7-1\7.1\bin\check_cell_sg.exe" "Generic ML PUA detected at

Re: [ccp4bb] PAIREF, Anisotropy and STARANISO

2022-10-04 Thread Petr Kolenko
Dear Gerard, A great remark! Thank you for starting this thread separately. I think that you are absolutely right in many of the points. However, it also raises several questions. Here are my favourite ones: 1) If STARANISO generally suggests "the same" resolution as PAIREF, there are fewer

Re: [ccp4bb] EDR (Sophos) and CCP4 compatibility

2022-10-04 Thread David Briggs
Hi Mark, Our IT admin has mandated various AntiVirus software on OSX, including Sophos, and I have never encountered a problem installing and downloading CCP4, Phenix, Coot, Chimera , etc etc HTH, Dave Dr David C. Briggs CSci MRSB Principal Laboratory Research Scientist Signalling and

[ccp4bb] EDR (Sophos) and CCP4 compatibility

2022-10-04 Thread Mark J. van Raaij
Dear CCP4-ers, After a hacking scare, in our institution all computers connected to the internet will have to have EDR software installed for safety against hackers. We will get Sophos here, at least on OSX, to be installed directly by IT services, not by ourselves, from an admin account on

[ccp4bb] PAIREF, Anisotropy and STARANISO

2022-10-04 Thread Gerard Bricogne
Dear all, First of all, apologies for breaking the threads entitled "PAIREF - Warning - not enough free reflections in resolution bin" and "Anisotropy" by merging them into a new one, but it somehow felt rather against nature to keep them separate. Since the early days of the

[ccp4bb] HTCC5 announcement

2022-10-04 Thread Elspeth Garman
Dear Colleagues, The Croatian Association of Crystallographers is inviting you to the fifth edition of its advanced crystallography workshop "Hot Topics in Contemporary Crystallography" to be held in Dubrovnik, Apr. 16 - 21, 2023, and dedicated entirely to macromolecular crystallography.

Re: [ccp4bb] Anisotropy

2022-10-04 Thread vincent Chaptal
Hi Eleanor, well, anisotropy results in artifacts in maps, with different outputs depending on softwares and truncation or not. There is also the fact that the definition of anisotropy can vary. Membrane proteins are definitely affected by this pehnomenon, but a single value of anisotropy as