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
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