*Ahem* *ISOLDE
Tristan Croll Research Fellow Cambridge Institute for Medical Research University of Cambridge CB2 0XY > On 13 Jul 2017, at 08:02, Tristan Croll <[email protected]> wrote: > > This is more-or-less exactly the task I'm building ISODE for. It's early > days, still quite rough around the edges and by no means complete, but if you > have a machine with a decent GPU running a modern Linux distro, then it's > easily available as a plugin to ChimeraX after installing the latest daily > build from https://www.rbvi.ucsf.edu/chimerax/download.html. Think of it as > an interactive real-space refinement environment, and you won't be far off. > This video is getting a little dated now, but should give you some idea of > what it can do: > https://drive.google.com/open?id=0B6uMjfjuw4k8aUdyTEJWeEJ1UnM. I'm currently > working on a longer, narrated demo/tutorial video showing all the latest > features (interactive position/rotamer/secondary structure assignment, a very > fun tool for shifting stretches in register, ...). > > There are some caveats: > - It doesn't yet do any building (adding or removing of atoms/residues) > - It requires all residues to be complete including hydrogens > - Currently only protein, nucleic acid and metal ions are supported (although > the metal ions need more work to be properly useful) > > Let me know if it's of interest, and we can talk more offline. > > Cheers, > > Tristan > >> On 2017-07-13 00:17, Rhys Grinter wrote: >> Dear All, >> I'm currently in the process of refining a low(ish) resolution >> structure at 3.2 Ang, with a fair level of anisotropy. I processed the >> data through the anisotropy server >> (https://services.mbi.ucla.edu/anisoscale/ [1]), which elliptically >> truncated the data to 4.0, 3.8 and 3.2 Ang. This really improved the >> maps and allowed me to trace the majority of the chain and build most >> side chains. >> The R-factors are reasonable (0.29 work and 0.35 free respectively). >> but I'm having trouble with over fitting in refinement as I continue >> to refine. What parameters/restraints would the community generally >> use when refining this kind of structure? Additionally Refmac doesn't >> seem to read the structure factors from the anisotropy server output >> file properly, giving vastly inflated R values and strange looking >> maps. >> Cheers, >> Rhys >> -- >> Dr Rhys Grinter >> Sir Henry Wellcome Fellow >> Monash University >> +61 (0)3 9902 9213 >> +61 (0)403 896 767 >> Links: >> ------ >> [1] https://services.mbi.ucla.edu/anisoscale/
