Dear Paul, Thank you for your explanation. I will try to adapt my way of working to the new coot. Best, Herman
-----Ursprüngliche Nachricht----- Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Paul Emsley Gesendet: Freitag, 4. September 2020 13:58 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8 EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk 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://urldefense.proofpoint.com/v2/url?u=https-3A__www2.mrc-2Dlmb.cam.ac.uk_personal_pemsley_coot_binaries_release_&d=DwIDaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM&s=5NsBSHjvi7V_A6kImjIckNzc50syFHFMZyXcv7xVvNA&e= > > <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://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.u > k_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIDaQ&c=Dbf9zos > wcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8o > HzZyRHMQu1AQ&m=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM&s=eaYXeWi77 > kgDfJvtGBGRhDVnuYKmGhyagkOCVMZI02I&e= > <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=Dbf9zo > swcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8 > oHzZyRHMQu1AQ&m=3AflakQZ5Fz_M9sPnssJL3oU4C-u25224gN5ljs5KwA&s=75WQhZGY > Otd4zWRp-4QbaftNeHjcD7TdnUNJCeafm8o&e=> > > > > ---------------------------------------------------------------------- > -------------------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.u > k_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIDaQ&c=Dbf9zos > wcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8o > HzZyRHMQu1AQ&m=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM&s=eaYXeWi77 > kgDfJvtGBGRhDVnuYKmGhyagkOCVMZI02I&e= > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIDaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM&s=eaYXeWi77kgDfJvtGBGRhDVnuYKmGhyagkOCVMZI02I&e= This message was issued to members of https://urldefense.proofpoint.com/v2/url?u=http-3A__www.jiscmail.ac.uk_CCP4BB&d=DwIDaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM&s=WObQ0_zD2AkvVrmTBHIt0liSCRENbmeKP7NQJQfORwg&e=, a mailing list hosted by https://urldefense.proofpoint.com/v2/url?u=http-3A__www.jiscmail.ac.uk&d=DwIDaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM&s=MrY51xu69NDzoho1ql-Qe0SkcNY8eTjK5OyjAsr5os4&e=, terms & conditions are available at https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_policyandsecurity_&d=DwIDaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM&s=5tczq6xBwaqHxiS03OK4nvGKnbHGHUF6V61owlsnfNg&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 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/
