[ccp4bb] Instruct-NL Workshop on Wednesday April 25, 2012, in Leiden, the Netherlands

Dear Colleague, INSTRUCT-NL organize a one-day Instruct Workshop which will be on Wednesday April 25, 2012, in Leiden, the Netherlands, with as theme Developments in Structural Biology: Instruct meets industry The program can be found at

Re: [ccp4bb] Refmac executables - win vs linux in RHEL VM

On Sat, Apr 07, 2012 at 08:42:47AM -0700, Bernhard Rupp (Hofkristallrat a.D.) wrote: Something the developers might be interested in: The Refmac_5.6.0117 32-bit windows binaries run native on a win64 3-4x slower than those from the linux distribution run Thanks for benchmarking. If

[ccp4bb] Disorder or poor phases?

Hi all, Assume that the diffraction resolution is low (say 3.0A or worse) and the model (a high resolution homologue, from 2A xray data is available) was docked into experimental phases (say 4A or worse) and extended to the 3.0A data using refinement (the high resolution model as a source of

Re: [ccp4bb] Disorder or poor phases?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Francis, the phases calculated from the model affect the whole unit cell hence it is more likely this is real(-space, local) disorder rather than poor phases. Regards, Tim P.S.: The author should not look at an 2fofc-map but a sigma-A-weighted

Re: [ccp4bb] Disorder or poor phases?

Dale Thank you for the case study. I will certainly remember it when I next see: I don't see density for these atoms therefore they must be disordered. You do mention though, that when you were able to assign the sequence to the beta sheets, that the loop regions became clear. I consider

Re: [ccp4bb] Disorder or poor phases?

Dear Dale, There is perhaps a third factor in the progress you were able to make, namely the improvement in the refinement programs. Your first results were probably obtained with a least-squares-based program, while the more recent would have come from maximum-likelihood-based ones. The

Re: [ccp4bb] Disorder or poor phases?

Dear Gerard, No, the updated model (4BCL) was published in 1993 (although apparently not deposited until 1998 - What was wrong with me?) Both were refined with that classic least-squares program TNT. I hope there was some improvement in the software between 1986 and 1993, and I always tried

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Re: [ccp4bb] Disorder or poor phases?

Hi Dale, my experience is that high-B regions may become visible in maps only late in refinement. So my answer to the original poster would be - both global reciprocal-space (phase quality) and local real-space (high mobility) features contribute to a region not appearing ordered in the map.