— The RNA segment that I am trying to fit is ~130 bp. — If I try to fit it without restraints, the RNA helix doesn't go into the density. When I drag or remove the restraints it collapses (base pairing, planarity is destroyed.) — Even if I reduce the map weight it has same issues. (I have tried different map weights, but I did not see much improvement) — This stretch of the map varies in resolution from ~4-6Å.
Best wishes, Sorbhi > On Oct 13, 2020, at 4:12 PM, Paul Emsley <[email protected]> wrote: > > > > On 13/10/2020 14:59, Sorbhi Rathore wrote: >> Hi Paul and Rob, >> >> Many thanks for your prompt reply. >> >> One more question. Would you use the same settings for fitting RNA? > > my thinking would be the same. > > > >> (I have tried the exact settings shown in your YouTube video tutorial. >> However, in the low resolution regions of the map it is extremely tricky to >> move the RNA chain, especially when there is a conformational change) > > Can you explain this in more detail? Why is it tricky? How many bp? If you > refined your fragment without GM restraints and without dragging on an atom, > what would happen? What happens when you reduce the map weight? Fitting RNA > with a conformational change is one of the things that Coot now does well (if > I may be so bold). > > > > Paul > > > > >> >> >>> On Oct 12, 2020, at 8:11 PM, Paul Emsley <[email protected] >>> <mailto:[email protected]>> wrote: >>> >>> >>> >>> On 12/10/2020 13:44, Sorbhi Rathore wrote: >>>> Dear all, >>>> >>>> Could anyone please suggest the best way to decide which German- McClure >>>> Alpha value to use during refinement (both at a higher resolution and >>>> lower resolution areas for a cryo-EM map)? >>>> I am using coot 0.9.1 pre EL(ccpem). >>>> >>> >>> A carefully-worded question. >>> >>> For cases, where the model doesn't initially fit the map: >>> >>> In 0.9, there was the danger or tearing the protein apart with too much >>> yank and too much alpha (low weight). That's why I used to be conservative >>> - using an alpha of 0.03 or so (occasionally 0.1 or 0.001). >>> >>> With proportional editing in 0.9.1, I find I yank less (instead, using >>> several micro yanks) and because the shift is distributed over a far larger >>> range and is ameliorated by distance from the yanked atom, I find that >>> protein either doesn't tear or usually re-anneals very pleasingly even >>> with a high alpha. >>> >>> Proportional editing radius is changed by Ctrl-middle-mouse scroll. >>> >>> For cases where the model more or less fits the map, I use 1 or (.3 or 10 >>> (if I want to practically turn them off without deleting them)) >>> >>> Paul. >>> >>> >>> >> ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
