Dear Paul, Sorry to re-open old thread (staycatation...) glad for you listening to the feedback - much appreciated.
> I think the situation has arisen because Coot users are bringing previous > experience of using RSR into their > use of 0.9. Because the movement of the non-dragged atoms in 0.8.x was > rather unsophisticated, many people > learnt (I discovered, rather late in the day) to "flick" the dragged atom > with a large and fast movement to > get over a local energy barrier. (Needless to say, I hadn't intended for This +1 (everyone using coot, that I know does it) > For myself, by using eigen-flip and jiggle fit beforehand and then by > combining pepflip, JED Flip and > backrub rotamer during RSR I often don't even need to pull on the atoms. By Do you mean in the new version: instead of simple "drag - large and fast movement to get over a local energy barrier" - you recommend to do this above multiple steps? Sadly, it would be a great decrease in usability. Best regards, Vero PS: I still have not used the new version. > adding in interactive contact > dots, I can see what it is that's causing Coot to not move the atom to where > I'm trying to drag it (the NBCs > have been re-paramaterized and up-weighted in the 0.9.x rewrite). I have, > from time to time in the past > year, used Coot 0.8.x and to me it now feels painfully crippled. RSR in Coot > 0.9.x is joyfully expeditious > and pleasingly animated. > > For now (which is to say, before Coot 0.9.1 is available) I suggest keeping > an eye out for unsatisfied atom > pull restraints, and using the "Clear Pull Restraints" at moments of > confusion. Also, use less flick and > more smoothness when dragging atoms. For example, a 180 degree rotation of > the ribose from the Coot tutorial > would be difficult, if not impossible using 0.8.x, but in 0.9.x one can pull > on the hydrogen atom of the O5' > to rotate it in a few seconds. I have added a (rather poor) video of me > doing just that to my channel (I > should make a better video). > > With all that said, I am still listening - I will add a change shortly that > will make the pull atom > restraints more obvious by making them fatter, pinker and more opaque. If > there are still problems and you > could somehow make a screencast available to me that illustrates the > problem, then I would be very > interested to view it. > > Regards, > > Paul. > > > On 04/09/2020 10:05, Schreuder, Herman /DE wrote: >> Dear Paul, >> >> Here I fully agree with Eike. With the real space refinement in the new >> coot the ligand often goes >> everywhere, except where it should go. Changing the Xray weight helps >> sometimes, but not always. In many >> cases I do not real-space refine and leave it to Buster to do the >> refinement. It would be very good if the >> old behavior could be reinstalled. >> >> Best regards, >> >> Herman >> >> *Von:*CCP4 bulletin board <[email protected]> *Im Auftrag von *Schulz, >> Eike-Christian >> *Gesendet:* Freitag, 4. September 2020 10:36 >> *An:* [email protected] >> *Betreff:* [EXTERNAL] [ccp4bb] Going back to Coot 0.8 >> >> *EXTERNAL : *Real sender is [email protected] >> <mailto:[email protected]> >> >> Dear Paul, >> >> I have been working with coot for over 10 years now with little reason to >> complain. >> >> However, in spite of trying for a few months now, I am not getting warm >> with coot 0.9. >> >> I like the new eye-candy, and the more organized menus. But fitting >> residues and ligands into ED, has never >> before been so difficult, and frankly it annoys me that previously simple >> tasks have become an effort. It >> seems as if coot and I see different minima and we always disagree where >> to put the residue. At the moment >> all my data are at convenient resolutions of 1.7Å or better, so there is >> little ambiguity on that side. >> >> I am using all default settings, but maybe there is something that needs >> to be changed? >> >> * Is there a way to go back to the old (0.8-style) fitting functions in >> coot 0.9? If so how? >> * If not, which of the last coot versions >> >> (https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/ >> >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www2.mrc-2Dlmb.cam.ac.uk_personal_pemsley_coot_binaries_release_&d=DwMGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=3AflakQZ5Fz_M9sPnssJL3oU4C-u25224gN5ljs5KwA&s=_vveOeCJ42OXDKFFrxFP_yaBEA0xSQBIGW2RWy8kmAk&e=>) >> would you recommend? >> >> With best regards, >> >> Eike >> >> ------------------------------------------------------------------------------------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=3AflakQZ5Fz_M9sPnssJL3oU4C-u25224gN5ljs5KwA&s=75WQhZGYOtd4zWRp-4QbaftNeHjcD7TdnUNJCeafm8o&e=> >> >> >> >> >> ------------------------------------------------------------------------------------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
