Dear Paul,
Thanks for the detailed response. The reason for me being a bit
annoyed is really simple: basic model building did work well in coot
0.8.x and (for me and others) it does not work anymore in coot 0.9.
Because I like coot (and because most computer problems are usually
30cm in front of the screen) I have tried to get used to it for a few
month, but on the weekend I have switched back to coot 0.8 * –>
problem(s) solved, what a relief.
I realize that I have not been particularly helpful in bug-fixing,
but the changes appear to be rather comprehensive and thus I can only
comment on the user experience. This is (naturally) a subjective
experience but what I hear from my colleagues tells me that I am not
alone with my frustration.
Try to look at it from my point of view:
- the previous version of coot does what I want,
- I see few advantages of the new version,
- the basic functionality (that I am used to) appears to be gone
in the new version.
Since I am not convinced - why should I switch ?
Best regards,
Eike
* thanks to Bill Scott for the pre-compiled mac-binaries
http://scottlab.ucsc.edu/xtal/wiki/index.php/Stand-Alone_Coot
-----Original Message-----
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Paul
Emsley <pems...@mrc-lmb.cam.ac.uk>
Reply to: Paul Emsley <pems...@mrc-lmb.cam.ac.uk>
Date: Saturday, 5. September 2020 at 02:05
To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] AW: Going back to
Coot 0.8
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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