Dear Eike,
Yes, it helps a little.
Changing weights on switching refinement maps is inconvenient, but not a
point of failure.
Alternative conformations may need some assistance - pin an atom using
anchoring.
When Coot starts a refinement it tells you in the terminal about the bad
bonds and non-bonded contacts that it found in the model. Do you
perceive that to be wrong or missing interactions?
There are many ways to skin a covalent ligand complex. I use the
Acedrg-Coot interface (as described in my blog). Do you?
If you wish, you can calculate an average map, the tool for that can be
found in Calculate -> Map Tools -> Average Maps...
Perhaps it would be useful to have an alert "You're not looking at the
map into which you are trying to fit the model" - maybe the background
should go pink - or something.
I feel that you are annoyed but I still don't understand why. As Phil
used to like to say, the devil's in the details.
I see that previously I didn't answer your question. So let me correct
that now:
(i) You can turn on interactive contact dots ("Contact Dots On") using
Refinement Tools from Curlew. This is a validation tool however and
doesn't describe what is going on with the refinement energy inside
Coot's head. I have it turned on by default for myself, FWIW.
(ii) There is no way to turn on "Old Style" refinement in 0.9 - although
"proportional editing" in 0.9.1 will bring some of that non-refined
initial displacement of surrounding atoms [1]
(iii) 0.8.2 is the best release for the 0.8.x series. I did quite a bit
of work on 0.8.3 but I never released it. Most (not all) of the updates
have been folded into 0.9.x.
Paul.
[1] it was seeing that Tristan had added to ISOLDE something like the
tool I had intended that that actually made me write it for Coot [2] -
it is a useful technique when shoving around domains in cryo-EM.
[2] That and watching Blender tutorials.
On 04/09/2020 19:04, Schulz, Eike-Christian wrote:
Dear Paul,
thanks for your comprehensive response in spite of my rather general comment.
And thanks for listening! I hope you see this as constructive criticism and not
only as blunt complaining (a national tradition ;) ):
Instead of a screencast I'd like to give at least a few more details on the
trouble on my end.
The problems mainly arise when:
- switching maps e.g. from 2Fo-Fc to Fo-Fc, or omit maps (X-ray restraints ?)
- modelling alternative / low occupancy conformations
- modelling covalent ligand complexes (atom clashes ?)
- parts of the solution are in either of the maps (maybe map averaging would
help?)
--> which is practically all I am doing, and the result is often a model next
to but not inside of the density. I am a long-term practitioner of ctrl-drag, but
with little help in these cases.
With respect to sophisticated solution and the "method developers’ intention",
I would like to answer with some experience from our own serial crystallography method
development.
For even distribution of micro-crystal slurries, we developed a
custom-multichannel pipette adapter, went through different iterations, adapted
and improved the design added more features optimized parameters and it now
works nicely as intended. However, users rather like to use a single empty
pipette-tip and distribute a big puddle of slurry manually. Not half as pretty
as the solution I intended, but admittedly easier, faster cheaper. Thus, in the
end the user-perspective won over my intention.
With respect to pull-atoms restraints, I don't think more visibility is going
to help the case. The restraints themselves appear to be off (if that’s a
statement that helps in any way).
I hope this helps a little bit to narrow down the hard-to-describe problem.
Best,
Eike
-----Original Message-----
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of "Schreuder, Herman
/DE" <herman.schreu...@sanofi.com>
Reply to: "Schreuder, Herman /DE" <herman.schreu...@sanofi.com>
Date: Friday, 4. September 2020 at 15:02
To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8
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
>
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