Dear Users - yes , I had shared my frustrations with Paul, mostly caused I must say because COOT now worries (excessively I think) about atom clashes and wouldn't let me drag an ARG or HIS or GLU into the obvious density till I had deleted any rogue waters..
However there are real gains - Tandem Refine is great, the new menus are great , etc etc.. And as Paul says - learning new tricks is always a hassle, but worth it I guess (sigh..) Thanks Paul - remember LBC - life before COOT?? Eleanor 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. On Fri, 4 Sep 2020 at 12:57, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > Dear Frustrated Coot 0.9 Users, > > I'd like to let you know that you I have heard similar reports in the > recent past (including, as you can > see, from EJD). I have taken what I believe to be remedial action to > address the most pressing issue. > > 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 > that to happen, the approved way to > make such modifications was Ctrl-drag over-dragging.) Applying a large and > fast flick to the dragged atom in > 0.9 often leads to an undesired result. If one then misses that fact that > an atom pull restraint is still in > effect and goes on to drag on another atom, then confusion and frustration > ensues. > > 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 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 <CCP4BB@JISCMAIL.AC.UK> *Im Auftrag von > *Schulz, Eike-Christian > > *Gesendet:* Freitag, 4. September 2020 10:36 > > *An:* CCP4BB@JISCMAIL.AC.UK > > *Betreff:* [EXTERNAL] [ccp4bb] Going back to Coot 0.8 > > > > *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk <mailto: > owner-ccp...@jiscmail.ac.uk> > > > > 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/
