Hi Paul and Rob, Many thanks for your prompt reply.
One more question. Would you use the same settings for fitting RNA? (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) Best wishes, Sorbhi > On Oct 12, 2020, at 8:11 PM, Paul Emsley <[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/
