Re: [ccp4bb] AW: Going back to Coot 0.8

[Robert Nicholls]

Hello Dirk,

Upon reviewing this thread I saw your comment:

> On 11 Sep 2020, at 08:41, Dirk Kostrewa  
> wrote:
> 
> I'm still convinced since the beginning of Coot, that an implementation of 
> hydrogen-bond potentials in the RSR would give a huge improvement and 
> probably renders the use of secondary structure restraints unnecessary.

Yes you can do this! If using CCP4 then you can generate h-bond restraints with 
prosmart (externally) and then read them into Coot. 

If wanting to use the command line then the simplest command would be: 
"prosmart -p1 [model filename] -h". The -h flag tells prosmart to generate 
backbone hydrogen bond restraints. There are lots of other keywords, e.g. to 
control sigmas etc. see prosmart --help for the full list. There are also 
interfaces to prosmart in the various CCP4 GUIs.

To get the correct menu in Coot, go to: Calculate -> Modules -> Restraints. 
This will cause a new "Restraints" menu to appear at the top. Then select "Read 
Refmac Extra Restraints..." and select the restraints file output by prosmart. 
Coot will display these restraints (although you can undisplay them), and Coot 
will use them in RSR. 

Best regards,
Rob




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Re: [ccp4bb] AW: Going back to Coot 0.8

[Dirk Kostrewa]

Hi Paul,

thanks - I've setup my own key bindings, already ;-)

Cheers,

Dirk.

On 11.09.20 12:34, Paul Emsley wrote:
Maybe because I've never attended a Coot course? And maybe because, 
I've even never searched for Coot tutorials because the usage of Coot 
was (almost) always very intuitive? I am open for any new developments 


OK "Pro Tip of the Day!" then...

Edit -> Settings -> Install Template Key Bindings  # you need only do 
this once.


(this is how I move around in Coot)

Fast navigation by residue: Ctrl-G {Type a number in the little box} 
Enter -> Coot jumps to that residue number


Fast navigation by blob: {Point at a blob with your mouse cursor} G -> 
Coot brings blob to screen centre




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--

***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: dirk.kostr...@lmu.de
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***



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Re: [ccp4bb] AW: Going back to Coot 0.8

[Paul Emsley]

Maybe because I've never attended a Coot course? And maybe because, 
I've even never searched for Coot tutorials because the usage of Coot was (almost) always very intuitive? I 
am open for any new developments 


OK "Pro Tip of the Day!" then...

Edit -> Settings -> Install Template Key Bindings  # you need only do this once.

(this is how I move around in Coot)

Fast navigation by residue: Ctrl-G {Type a number in the little box} Enter -> 
Coot jumps to that residue number

Fast navigation by blob: {Point at a blob with your mouse cursor} G -> Coot 
brings blob to screen centre



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

[Frank von Delft]

I believe Paul is trying to make the caffeine materialise directly in 
your bloodstreams.


He seems to have forgotten that people actually like harvesting and 
roasing the coffee beans and folding the paper cup - so even if he 
figured out how to simulate the burning sensation in your throat as the 
hot coffee goes down, it would still frustrate a significant section of 
people.


I suspect in the long term, we'll get comfortable with just the caffeine 
hit.






On 09/09/2020 21:27, Schulz, Eike-Christian wrote:

Hi Tim,

I don't think that metaphor is quite correct. To me it seems that no matter 
what button you pushed you got coffee. In my opinion intuitive software is a 
blessing and should not easily be disregarded.

But as I said before, I am happy to read into new stuff.

Also there seem to be mixed experiences here. Might this be map-resolution 
related ?

Best,

Eike



-Original Message-
From: CCP4 bulletin board  on behalf of Georg Zocher 

Reply to: Georg Zocher 
Date: Wednesday, 9. September 2020 at 22:17
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

 Dear Herman,

 Am 09.09.2020 um 17:46 schrieb Schreuder, Herman /DE:
 > The old real-space refinement was intuitive and easy to use and did 
exactly what the user expected, without having to consult the manual! The result 
might not have been perfect, but was good enough for subsequent Refmac, Buster, 
Phenix refinement.

 That fits perfectly to my user experience with RSR in coot 0.8.x. and
 also explains why at least a number of people having some issues with
 the new RSR.

 All the best,

 Georg

 

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Re: [ccp4bb] AW: Going back to Coot 0.8

[Dirk Kostrewa]

Dear Paul,

I'm using Coot since its first April 2000 version and see a lot of 
improvements since then - so, really many thanks for your development!


In version 0.9, I like the much improved interface (I didn't like the 
ever growing complex Extra menu), and from a recent practical course, 
the new RSR either works marvelously or just moves residues completely 
out of density with no visual close contacts (I didn't check the probe 
clashes in the course, though ...).


The Lennard-Jones type potential might be the cause for such a 
non-obvious "mis-behaviour" of the RSR. I remember XPLOR sometimes 
blowing up the refinement because of its use of LJ potentials for VdW 
contacts and some very close contacts in the starting model. I would be 
grateful if I could switch between Lennard-Jones and harmonic potential 
in the "R/RC" settings.


I'm still convinced since the beginning of Coot, that an implementation 
of hydrogen-bond potentials in the RSR would give a huge improvement and 
probably renders the use of secondary structure restraints unnecessary.


Although I'm always interested in new method development, I must admit, 
that I've also never heard of Eigen-flip, JED-flip, backrub or CURLEW. 
Maybe because I've never attended a Coot course? And maybe because, I've 
even never searched for Coot tutorials because the usage of Coot was 
(almost) always very intuitive? I am open for any new developments - so, 
I will have a look at the pointers that you gave below. I would also be 
grateful if you could give some pointers (which I've probably 
overlooked!) where Eigen-flip, JED-flip, backrub and CURLEW are explained.


Best regards,

Dirk.

On 10.09.20 17:59, Paul Emsley wrote:

I'm not against the old style of coffee, I just don't know why anyone
would want to drink it now that the new stuff is available. I am not
against choice, it just needs to be clear to me why it is necessary.

Having thought about this a bit, I think that there are two major
differences in the real space refinement in Coot since 0.8.9.

i) The non-bonded contacts were modelled with an harmonic
   approximation and now use Lennard-Jones. The harmonic code is still
   in the source files but is not in the execution path. With a
   judicious adjustment of a few if statements, it can be
   re-established.

   For now, you can adjust the LJ weights like this:
   set_refinement_lennard_jones_epsilon(0.005)

   That will soften up the NBC and may allow some interactions that
   are repelled using the default weights.

   Also (as I said) you can use the interactive contact dots to keep
   a visual track of atom overlaps.

ii) The rigid-body "rubber-sheet" proportional neighbour drag has
    gone. Initially I thought that it was unnecessary (and normally
    that's the case), but I see that it can be useful and is now in
    0.9.1-pre.

The introductory tutorials were written a long time ago and don't
mention key-bindings ("hot keys") or interface customisation. Perhaps
they should. Here is a more modern tutorial that mentions interface
customisation:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/tutorial/Coot-Cryo-EM-basics.html 


Now that I read it, I see that it needs to be updated - Curlew is now a
full member of the Coot GUI (found under "File").

You can see me tweaking the interface in a video I did for SBGrid (it
was only meant for SBGrid attendees really):
https://www.youtube.com/watch?v=hhB8qUBBnJQ
Although note that the interface has changed (improved?) since then -
I need to redo that video.

Here is the ligand fitting/ribose rotation that I mentioned the other 
day:

https://www.youtube.com/watch?v=HTNsBBXAc78
I need to redo that video too (it was a quicky I made for Frank), but
maybe better than nothing to illustrate the utility of the new style of
atom dragging.

The multi-threaded update to the refinement was tricky to write and
now it behaves pretty stably for me but there were quite an number of
brain-twisting timing/synchronisation issues that I needed to work
out. I admit that I get "Failed: Error No Progress" more frequently
than I did when I used 0.8.x. I wonder if that's what you're seeing. I
wonder if your hardware, your map and model, your mousing skills are
tickling a race condition that I don't see (which in the coffee
analogy would be "The light is on on this new machine you've given me,
I press the button, but nothing comes out"). But then again, no one
has mentioned a bug, merely an unfamiliar behaviour. So I don't know
if the software in your hands is working as intended and we are having
a discussion about model building workflows or, rather more
prosaically, what you're seeing is just a bug.

  I had said:
  many people learnt (I discovered, rather late in the day)...

What I meant by that was two things in particular: (i) not Ctrl
dragging (as we've discussed) and (ii) (it seemed to me) that people
were asking the RSR to do too much (i.e. starting too far from where
they wanted to end up). 

Re: [ccp4bb] AW: Going back to Coot 0.8

[Paul Emsley]

I'm not against the old style of coffee, I just don't know why anyone
would want to drink it now that the new stuff is available. I am not
against choice, it just needs to be clear to me why it is necessary.

Having thought about this a bit, I think that there are two major
differences in the real space refinement in Coot since 0.8.9.

i) The non-bonded contacts were modelled with an harmonic
   approximation and now use Lennard-Jones. The harmonic code is still
   in the source files but is not in the execution path. With a
   judicious adjustment of a few if statements, it can be
   re-established.

   For now, you can adjust the LJ weights like this:
   set_refinement_lennard_jones_epsilon(0.005)

   That will soften up the NBC and may allow some interactions that
   are repelled using the default weights.

   Also (as I said) you can use the interactive contact dots to keep
   a visual track of atom overlaps.

ii) The rigid-body "rubber-sheet" proportional neighbour drag has
    gone. Initially I thought that it was unnecessary (and normally
    that's the case), but I see that it can be useful and is now in
    0.9.1-pre.

The introductory tutorials were written a long time ago and don't
mention key-bindings ("hot keys") or interface customisation. Perhaps
they should. Here is a more modern tutorial that mentions interface
customisation:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/tutorial/Coot-Cryo-EM-basics.html
Now that I read it, I see that it needs to be updated - Curlew is now a
full member of the Coot GUI (found under "File").

You can see me tweaking the interface in a video I did for SBGrid (it
was only meant for SBGrid attendees really):
https://www.youtube.com/watch?v=hhB8qUBBnJQ
Although note that the interface has changed (improved?) since then -
I need to redo that video.

Here is the ligand fitting/ribose rotation that I mentioned the other day:
https://www.youtube.com/watch?v=HTNsBBXAc78
I need to redo that video too (it was a quicky I made for Frank), but
maybe better than nothing to illustrate the utility of the new style of
atom dragging.

The multi-threaded update to the refinement was tricky to write and
now it behaves pretty stably for me but there were quite an number of
brain-twisting timing/synchronisation issues that I needed to work
out. I admit that I get "Failed: Error No Progress" more frequently
than I did when I used 0.8.x. I wonder if that's what you're seeing. I
wonder if your hardware, your map and model, your mousing skills are
tickling a race condition that I don't see (which in the coffee
analogy would be "The light is on on this new machine you've given me,
I press the button, but nothing comes out"). But then again, no one
has mentioned a bug, merely an unfamiliar behaviour. So I don't know
if the software in your hands is working as intended and we are having
a discussion about model building workflows or, rather more
prosaically, what you're seeing is just a bug.

  I had said:
  many people learnt (I discovered, rather late in the day)...

What I meant by that was two things in particular: (i) not Ctrl
dragging (as we've discussed) and (ii) (it seemed to me) that people
were asking the RSR to do too much (i.e. starting too far from where
they wanted to end up). Quick Transformation (Ctrl Arrow keys), jiggle
fit and eigen-flip bring the residue or ligand close to the target
position before RSR is initiated.  These are meat and drink for the
Coot tutorials I teach at courses.

   Eike wrote:
   No special key-binding, no scripts - just out of the box, default
   settings, ...  Eigen-flip, jiggle-fit, pepflip, JED-flip, backrub,
   interactive contact dots, acedrg – sorry I’ve never heard of them.

Well if you add to that list pyrogen, lbg, flev, lidia, LO/Carb,
ligand validation, Curlew, the bespoke colour system, Geman-McClure,
RNA base and metal restraints you will be missing almost all of the
work that I've done on Coot since 2009... :-), :-( or maybe :-/

Relatedly:

   Often we are restrained in time and improving your toolbox in an
   unexpected manner is harder...

I recognise this and am trying to act on it - in the new (new) Coot - the
interface is quite a bit different, I am trying to use more familiar
idioms.

  Herman said:

   > The old real-space refinement was intuitive and easy to use and
 did exactly what the user expected, without having to consult the
 manual! The result might not have been perfect, but was good
 enough for subsequent Refmac, Buster, Phenix refinement.

I am glad you think so. I thought so too. But I also think that 0.9.x
is even better at doing that.

   Eike:
   I also make use of the stepped-refine procedure

I no longer use the "All Molecule" menu items and considered removing
them from the interface. There is a function (fill_partial_residues)
to cover what the "Fill Partial Residues" menu item does - and does
them all at once. The improvement in refinement means that the length
of the molten 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

[Robbie Joosten]

Indeed, and that is why testing new developments in courses is so important 
because there you get naïve users. Obviously, this has been very difficult this 
year. It is also exactly the reason why you do need to have developers at 
courses, not just power users. 

For those struggling to get used to Coot 0.9 there are few tips:
1) Drag atoms where you want them to go, not beyond where you want them. I.e. 
don't "overdrag" like you used to do in Coot.
2) Try to get close to the right answer first by rigid body movement. This is 
particularly useful for ligands.
3) Practice*. The C-termini in PDB entry 1ggx are nice to practice resisting to 
overdrag.

Cheers,
Robbie

* Ling Ling practices 40 hours a day!

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Tim
> Gruene
> Sent: Wednesday, September 9, 2020 23:01
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8
> 
> Hi Eike,
> 
> one of the points is that, only because you got used to a certain operation
> (over many years after someone showed it to you), does not mean it is
> intuitive. This could be judged by e.g. showing an ignorant user both
> methods and let the person judge which one is easier to use...
> 
> Cheers,
> Tim
> 
> On Wed, 9 Sep 2020 20:27:55
> + "Schulz, Eike-Christian"  wrote:
> 
> > Hi Tim,
> >
> > I don't think that metaphor is quite correct. To me it seems that no
> > matter what button you pushed you got coffee. In my opinion intuitive
> > software is a blessing and should not easily be disregarded.
> >
> > But as I said before, I am happy to read into new stuff.
> >
> > Also there seem to be mixed experiences here. Might this be
> > map-resolution related ?
> >
> > Best,
> >
> > Eike
> >
> >
> >
> > -Original Message-
> > From: CCP4 bulletin board  on behalf of Georg
> > Zocher  Reply to: Georg Zocher 
> > Date: Wednesday, 9. September 2020 at 22:17
> > To: "CCP4BB@JISCMAIL.AC.UK" 
> > Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot
> > 0.8
> >
> > Dear Herman,
> >
> > Am 09.09.2020 um 17:46 schrieb Schreuder, Herman /DE:
> > > The old real-space refinement was intuitive and easy to use and
> > > did exactly what the user expected, without having to consult
> > > the manual! The result might not have been perfect, but was
> > > good enough for subsequent Refmac, Buster, Phenix refinement.
> >
> > That fits perfectly to my user experience with RSR in coot 0.8.x.
> > and also explains why at least a number of people having some issues
> > with the new RSR.
> >
> > All the best,
> >
> > Georg
> >
> >
> >
> ###
> ###
> > ##
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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
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> >
> >
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> 
> 
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis Faculty of Chemistry
> University of Vienna
> 
> Phone: +43-1-4277-70202
> 
> GPG Key ID = A46BEE1A
> 
> ###
> #
> 
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

[Tim Gruene]

Hi Eike,

one of the points is that, only because you got used to a certain
operation (over many years after someone showed it to you), does not
mean it is intuitive. This could be judged by e.g. showing an ignorant
user both methods and let the person judge which one is easier to use...

Cheers,
Tim

On Wed, 9 Sep 2020 20:27:55
+ "Schulz, Eike-Christian"  wrote:

> Hi Tim, 
> 
> I don't think that metaphor is quite correct. To me it seems that no
> matter what button you pushed you got coffee. In my opinion intuitive
> software is a blessing and should not easily be disregarded. 
> 
> But as I said before, I am happy to read into new stuff. 
> 
> Also there seem to be mixed experiences here. Might this be
> map-resolution related ? 
> 
> Best, 
> 
> Eike
> 
> 
> 
> -Original Message-
> From: CCP4 bulletin board  on behalf of Georg
> Zocher  Reply to: Georg Zocher 
> Date: Wednesday, 9. September 2020 at 22:17
> To: "CCP4BB@JISCMAIL.AC.UK" 
> Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot
> 0.8
> 
> Dear Herman,
> 
> Am 09.09.2020 um 17:46 schrieb Schreuder, Herman /DE:
> > The old real-space refinement was intuitive and easy to use and
> > did exactly what the user expected, without having to consult
> > the manual! The result might not have been perfect, but was
> > good enough for subsequent Refmac, Buster, Phenix refinement.  
> 
> That fits perfectly to my user experience with RSR in coot 0.8.x.
> and also explains why at least a number of people having some issues
> with the new RSR.
> 
> All the best,
> 
> Georg
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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
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> 
> 
> 
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-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Description: OpenPGP digital signature

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

[Georg Zocher]

Dear Herman,

Am 09.09.2020 um 17:46 schrieb Schreuder, Herman /DE:

The old real-space refinement was intuitive and easy to use and did exactly 
what the user expected, without having to consult the manual! The result might 
not have been perfect, but was good enough for subsequent Refmac, Buster, 
Phenix refinement.


That fits perfectly to my user experience with RSR in coot 0.8.x. and 
also explains why at least a number of people having some issues with 
the new RSR.


All the best,

Georg



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Re: [ccp4bb] AW: Going back to Coot 0.8

[Georg Zocher]

Dear Tim,

I really like your example.


Has anyone of the disappointed users asked how to do it properly? Maybe
it is just as easy.


I think it's also up to me to do it properly and put more effort in it. 
Often we are restrained in time and improving your toolboox in an 
unexpected manner is harder to except than. But that's ok as this keeps 
one flexible. I hope, I will find the time soon and get used to it as 
much as whatever "the thing labelled as coffee" was;-)


Thank you all for your contributions,

Georg


Cheers,
Tim

On Wed, 9 Sep 2020 17:22:27 +0200
Georg Zocher  wrote:


Dear Paul,

people are complaining that they have issues fitting their model in
real space using coot 0.9.x. Personally, I very briefly used coot
other the last months but also have problems using RSR properly
because I'm used to do it the way it was over the last 10 years. This
might be due to my ignorance that I did not have a more closer look
into the new features of RSR in 0.9 release and how to use them. But
from the user site it's different to handle now.

I do not understand your Ferrari comparison (sorry) as I would not
buy one even if I would have more money than one can spend. But I
would take a cup of coffee as an example. If you always go to the
same dealer to get your coffee in the morning as you know you get a
very descent and excellent tasting cup of coffee that you fully enjoy
every morning than you really get used to it. It might be than a hard
time for you if your coffee dealer tells you: Sorry guys, I do have
now an optimized coffee that is much better, taste a lot better, is
fair produced,... It's just not the coffee you drunk over the last 10
years and I will not offer that one anymore. You might give the new
one a chance, you might find it as excellent as the dealer but you
might not. From my point of view it's the lack of choice that
personally I do not like so much, especially if there is no other
coffee dealer around...

Nevertheless, I'm aware and fully respect all the effort you put in
the development of coot and I'm really grateful that coot is
available.

All the best,
Georg



Am 08.09.20 um 17:44 schrieb Paul Emsley:

On 08/09/2020 16:25, Georg Zocher wrote:


we have the same experience in our lab.


What experience is that? I am still in the dark about you think is
now worse.

  

Personally, I did would not like to judge here, as so far, I did
not have had enough time to get into the new RSR of coot 0.9.x by
myself. But many colleagues did not like the new refinement module
maybe just as they are used to the method in all coot versions
before.


You have a Ferrari parked beside your house but you want to to take
the bus to work because that's what you've always done. Or maybe
the Ferrari is parked around the back and you don't know it's there?

  

I just thought if it wouldn't be an option to let the user decide
what kind of RSR implementation she/he would like to use and give
them the choice via an option in coot preferences?


That would be possible but not easy. Unlike much of the CCP4 suite,
Coot is Free Software. But, again... why would you want to take the
bus? Explain.


regards,


Paul.



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Re: [ccp4bb] AW: Going back to Coot 0.8

[Tim Gruene]

Dear Georg and others, 

if I followed the thread correctly, the coffee story should really go
like this:

for years you have been pushing the button of a machine
showing a cup with a black liquid inside. After ten years, the
manufacturer of the machine tells you:
"Sorry guy, it is not coffee what you have been drinking. If
you want to drink coffee, you should push the button down here, which
is labelled 'coffee'."
Because you drank the other liquid for years, you are very
disappointed by the taste of real coffee and keep on pushing the old
button that you got used to.

That's how I interpret Paul's statement 
"[...] many people learnt (I discovered, rather late in the day) [...]"

Has anyone of the disappointed users asked how to do it properly? Maybe
it is just as easy.

Cheers,
Tim

On Wed, 9 Sep 2020 17:22:27 +0200
Georg Zocher  wrote:

> Dear Paul,
> 
> people are complaining that they have issues fitting their model in
> real space using coot 0.9.x. Personally, I very briefly used coot
> other the last months but also have problems using RSR properly
> because I'm used to do it the way it was over the last 10 years. This
> might be due to my ignorance that I did not have a more closer look
> into the new features of RSR in 0.9 release and how to use them. But
> from the user site it's different to handle now.
> 
> I do not understand your Ferrari comparison (sorry) as I would not
> buy one even if I would have more money than one can spend. But I
> would take a cup of coffee as an example. If you always go to the
> same dealer to get your coffee in the morning as you know you get a
> very descent and excellent tasting cup of coffee that you fully enjoy
> every morning than you really get used to it. It might be than a hard
> time for you if your coffee dealer tells you: Sorry guys, I do have
> now an optimized coffee that is much better, taste a lot better, is
> fair produced,... It's just not the coffee you drunk over the last 10
> years and I will not offer that one anymore. You might give the new
> one a chance, you might find it as excellent as the dealer but you
> might not. From my point of view it's the lack of choice that
> personally I do not like so much, especially if there is no other
> coffee dealer around...
> 
> Nevertheless, I'm aware and fully respect all the effort you put in
> the development of coot and I'm really grateful that coot is
> available.
> 
> All the best,
> Georg
> 
> 
> 
> Am 08.09.20 um 17:44 schrieb Paul Emsley:
> > On 08/09/2020 16:25, Georg Zocher wrote:  
> >>
> >>
> >> we have the same experience in our lab.  
> >
> >
> > What experience is that? I am still in the dark about you think is
> > now worse.
> >
> >  
> >> Personally, I did would not like to judge here, as so far, I did
> >> not have had enough time to get into the new RSR of coot 0.9.x by
> >> myself. But many colleagues did not like the new refinement module
> >> maybe just as they are used to the method in all coot versions
> >> before.  
> >
> >
> > You have a Ferrari parked beside your house but you want to to take 
> > the bus to work because that's what you've always done. Or maybe
> > the Ferrari is parked around the back and you don't know it's there?
> >
> >  
> >>
> >> I just thought if it wouldn't be an option to let the user decide 
> >> what kind of RSR implementation she/he would like to use and give 
> >> them the choice via an option in coot preferences?  
> >
> >
> > That would be possible but not easy. Unlike much of the CCP4 suite, 
> > Coot is Free Software. But, again... why would you want to take the 
> > bus? Explain.
> >
> >
> > regards,
> >
> >
> > Paul.
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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=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/



-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

[Schreuder, Herman /DE]

Dear Paul,

I fully agree with Georg and the others. As I said in my first reaction, with 
the new coot, the inhibitor or side chain often does not end up a little wrong, 
but goes off completely in the wrong direction, which makes me wonder whether I 
had somehow selected the wrong map. It might also be that the default settings 
that had been distributed with coot are wrong. I will try to find an example 
that is non-confidential, but often the moment you want something to go wrong, 
everything works perfectly. 

The old real-space refinement was intuitive and easy to use and did exactly 
what the user expected, without having to consult the manual! The result might 
not have been perfect, but was good enough for subsequent Refmac, Buster, 
Phenix refinement.  

Best regards,
Herman


-Ursprüngliche Nachricht-
Von: CCP4 bulletin board  Im Auftrag von Georg Zocher
Gesendet: Mittwoch, 9. September 2020 17:22
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 Paul,

people are complaining that they have issues fitting their model in real space 
using coot 0.9.x. Personally, I very briefly used coot other the last months 
but also have problems using RSR properly because I'm used to do it the way it 
was over the last 10 years. This might be due to my ignorance that I did not 
have a more closer look into the new features of RSR in 0.9 release and how to 
use them. But from the user site it's different to handle now.

I do not understand your Ferrari comparison (sorry) as I would not buy one even 
if I would have more money than one can spend. But I would take a cup of coffee 
as an example. If you always go to the same dealer to get your coffee in the 
morning as you know you get a very descent and excellent tasting cup of coffee 
that you fully enjoy every morning than you really get used to it. It might be 
than a hard time for you if your coffee dealer tells you: Sorry guys, I do have 
now an optimized coffee that is much better, taste a lot better, is fair 
produced,... It's just not the coffee you drunk over the last 10 years and I 
will not offer that one anymore. You might give the new one a chance, you might 
find it as excellent as the dealer but you might not. From my point of view 
it's the lack of choice that personally I do not like so much, especially if 
there is no other coffee dealer around...

Nevertheless, I'm aware and fully respect all the effort you put in the 
development of coot and I'm really grateful that coot is available.

All the best,
Georg



Am 08.09.20 um 17:44 schrieb Paul Emsley:
> On 08/09/2020 16:25, Georg Zocher wrote:
>>
>>
>> we have the same experience in our lab.
>
>
> What experience is that? I am still in the dark about you think is now 
> worse.
>
>
>> Personally, I did would not like to judge here, as so far, I did not 
>> have had enough time to get into the new RSR of coot 0.9.x by myself.
>> But many colleagues did not like the new refinement module maybe just 
>> as they are used to the method in all coot versions before.
>
>
> You have a Ferrari parked beside your house but you want to to take 
> the bus to work because that's what you've always done. Or maybe the 
> Ferrari is parked around the back and you don't know it's there?
>
>
>>
>> I just thought if it wouldn't be an option to let the user decide 
>> what kind of RSR implementation she/he would like to use and give 
>> them the choice via an option in coot preferences?
>
>
> That would be possible but not easy. Unlike much of the CCP4 suite, 
> Coot is Free Software. But, again... why would you want to take the 
> bus? Explain.
>
>
> regards,
>
>
> Paul.
>
> ##
> ##
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
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> Gz-

Re: [ccp4bb] AW: Going back to Coot 0.8

[Georg Zocher]

Dear Paul,

people are complaining that they have issues fitting their model in real 
space using coot 0.9.x. Personally, I very briefly used coot other the 
last months but also have problems using RSR properly because I'm used 
to do it the way it was over the last 10 years. This might be due to my 
ignorance that I did not have a more closer look into the new features 
of RSR in 0.9 release and how to use them. But from the user site it's 
different to handle now.


I do not understand your Ferrari comparison (sorry) as I would not buy 
one even if I would have more money than one can spend. But I would take 
a cup of coffee as an example. If you always go to the same dealer to 
get your coffee in the morning as you know you get a very descent and 
excellent tasting cup of coffee that you fully enjoy every morning than 
you really get used to it. It might be than a hard time for you if your 
coffee dealer tells you: Sorry guys, I do have now an optimized coffee 
that is much better, taste a lot better, is fair produced,... It's just 
not the coffee you drunk over the last 10 years and I will not offer 
that one anymore. You might give the new one a chance, you might find it 
as excellent as the dealer but you might not. From my point of view it's 
the lack of choice that personally I do not like so much, especially if 
there is no other coffee dealer around...


Nevertheless, I'm aware and fully respect all the effort you put in the 
development of coot and I'm really grateful that coot is available.


All the best,
Georg



Am 08.09.20 um 17:44 schrieb Paul Emsley:

On 08/09/2020 16:25, Georg Zocher wrote:



we have the same experience in our lab.



What experience is that? I am still in the dark about you think is now 
worse.



Personally, I did would not like to judge here, as so far, I did not 
have had enough time to get into the new RSR of coot 0.9.x by myself. 
But many colleagues did not like the new refinement module maybe just 
as they are used to the method in all coot versions before.



You have a Ferrari parked beside your house but you want to to take 
the bus to work because that's what you've always done. Or maybe the 
Ferrari is parked around the back and you don't know it's there?





I just thought if it wouldn't be an option to let the user decide 
what kind of RSR implementation she/he would like to use and give 
them the choice via an option in coot preferences?



That would be possible but not easy. Unlike much of the CCP4 suite, 
Coot is Free Software. But, again... why would you want to take the 
bus? Explain.



regards,


Paul.



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Re: [ccp4bb] AW: Going back to Coot 0.8

[Schulz, Eike-Christian]

Dear Paul, 

sorry for the delay. 

I did not answer your previous questions in detail, because going back to coot 
0.8 did solve the problem for me, which kept me busy. But of course, to do sth. 
about the situation you need to understand a lot better what is going on. 

What I have is a “phenotype” (coot 0.9) that presents differently than the 
previous generation (coot 0.8) and since it’s not possible for me to revert any 
of the mutations its hard to pinpoint the cause of the problem. The most 
general description I can come up with: in coot 0.9 the model moves “funny” – 
different from coot 0.8. Some (new?) restraints seem to act on the atoms 
preventing them to stay where I put them. This "hidden-thinking" coot 0.9 
appears to apply confuses me. 

*I don’t think this description is a major improvement from before, maybe 
someone else (Georg?, Eleanor? Herman?) can give it a try?

However, I have a hunch that the root of our communication trouble is that the 
way you and I are using coot is very different. Therefore, I think it maybe 
best if (a) I told you how I use it most of the time and (b) provide you with a 
specific example (off-list). Maybe you can reproduce the trouble if you follow 
my procedure. 

Staying in the picture of your Ferrari/bus metaphor, I think I am probably 
walking to work:

I am predominantly using the real-space refine options, going through the 
structure bit by bit, putting the model where (I think) it belongs. I also make 
use of the stepped-refine procedure, but I know more than one colleague who 
considers that “cheating” already or do not know about that option at all. Of 
course, I am making use of the validation, measurement, map and model tools, 
but hardly of any automation (§). No special key-binding, no scripts - just out 
of the box, default settings, iterative cycles with refinement. That may not be 
what you have intended, but the people in my echo chamber just do the same. 

Eigen-flip, jiggle-fit, pepflip, JED-flip, backrub, interactive contact dots, 
acedrg – sorry I’ve never heard of them. 

You mentioned a blog and/or other coot info before. With coot 0.9 I tried 
finding more information but your coot-website and the included tutorials 
appear to be a bit older https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/. 

Is there a new source of info somewhere? - I am happy to look into it. 

Best, 

Eike


§ automatic building of alternate conformations for HR-structures would be 
really helpful though. 


-Original Message-
From: CCP4 bulletin board  on behalf of Paul Emsley 

Reply to: Paul Emsley 
Date: Tuesday, 8. September 2020 at 17:44
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] AW: Going back to Coot 0.8

On 08/09/2020 16:25, Georg Zocher wrote:
>
>
> we have the same experience in our lab.


What experience is that? I am still in the dark about you think is now 
worse.


> Personally, I did would not like to judge here, as so far, I did not 
> have had enough time to get into the new RSR of coot 0.9.x by myself. 
> But many colleagues did not like the new refinement module maybe just 
> as they are used to the method in all coot versions before.


You have a Ferrari parked beside your house but you want to to take the 
bus to work because that's what you've always done. Or maybe the Ferrari 
is parked around the back and you don't know it's there?


>
> I just thought if it wouldn't be an option to let the user decide what 
> kind of RSR implementation she/he would like to use and give them the 
> choice via an option in coot preferences?


That would be possible but not easy. Unlike much of the CCP4 suite, Coot 
is Free Software. But, again... why would you want to take the bus? Explain.


regards,


Paul.



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Re: [ccp4bb] AW: Going back to Coot 0.8

[Paul Emsley]

On 08/09/2020 16:25, Georg Zocher wrote:



we have the same experience in our lab.



What experience is that? I am still in the dark about you think is now 
worse.



Personally, I did would not like to judge here, as so far, I did not 
have had enough time to get into the new RSR of coot 0.9.x by myself. 
But many colleagues did not like the new refinement module maybe just 
as they are used to the method in all coot versions before.



You have a Ferrari parked beside your house but you want to to take the 
bus to work because that's what you've always done. Or maybe the Ferrari 
is parked around the back and you don't know it's there?





I just thought if it wouldn't be an option to let the user decide what 
kind of RSR implementation she/he would like to use and give them the 
choice via an option in coot preferences?



That would be possible but not easy. Unlike much of the CCP4 suite, Coot 
is Free Software. But, again... why would you want to take the bus? Explain.



regards,


Paul.



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Re: [ccp4bb] AW: Going back to Coot 0.8

[Georg Zocher]

Dear Paul,

we have the same experience in our lab. Personally, I did would not like 
to judge here, as so far, I did not have had enough time to get into the 
new RSR of coot 0.9.x by myself. But many colleagues did not like the 
new refinement module maybe just as they are used to the method in all 
coot versions before.


I just thought if it wouldn't be an option to let the user decide what 
kind of RSR implementation she/he would like to use and give them the 
choice via an option in coot preferences?


All the best,
Georg




Am 08.09.20 um 03:10 schrieb Paul Emsley:

Dear Eike,


This is not about me trying to convince you to change. I was pleased
with Coot 0.8.9.2 when I released it and I am pleased that you like it
too.  I was trying to express that *I* think that the refinement in
0.9.x is across the board better and I am not seeing the problems that
you see.

Instead, this is about me trying to find out what you (and others)
think is going wrong.  This is about turning your email into a useful
bug report.  What I've got now is "it does not work any more and I
don't like it" - and that is not helpful.

You mentioned that you had problem with a ligand complex. I tried to
investigate further by asking you if you were using Acedrg-Coot. You
didn't answer.

You suggest that atom clashes may be a problem. I tried to investigate
further by asking you if you noticed a problem with Coot's description
of non-bonded contacts. You didn't answer.

To be clear, these were not rhetorical questions, they were an attempt
to address the problems - or at least begin to do so.

What I need is an example of *what* is going wrong.  Just one example
would be a start.  It seems to me that if the problem is as pervasive
as you seem to think it is, then it shouldn't be difficult for you to
conjure up a problematic case.  This is the sort of thing that I want:

   This model is based on 1xyz from the PDB, except that I've adjusted
   the model to create a problem.  See the region of A501 - you can
   see that that model and the map do not correspond. It is hard for
   me to fix it in 0.9 because when I do X, Coot does Y, but in 0.8.9
   all I had to do was A, B and C.

It might be the case that Coot can trivially solve the problem, but
you don't know about it - and that might be because I have
insufficiently explained how to do it. Or made the means by which you
can do so too opaque. Or maybe you have to type something. At the
moment I have no clue.

Normally, I would have taken to private correspondence by now.  I
recognise that your primarily interest is the latest and greatest of
the 0.8 series, and you may think that this may not be worth your
effort, so if you don't do this perhaps some of the other frustrated
Coot users may do so? Hence the public continuation of our discussion.


Regards,


Paul.

On 07/09/2020 10:28, Schulz, Eike-Christian wrote:

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  on behalf of Paul 
Emsley 

Reply to: Paul Emsley 
Date: Saturday, 5. September 2020 at 02:05
To: "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,

Re: [ccp4bb] AW: Going back to Coot 0.8

[Paul Emsley]

Dear Eike,


This is not about me trying to convince you to change. I was pleased
with Coot 0.8.9.2 when I released it and I am pleased that you like it
too.  I was trying to express that *I* think that the refinement in
0.9.x is across the board better and I am not seeing the problems that
you see.

Instead, this is about me trying to find out what you (and others)
think is going wrong.  This is about turning your email into a useful
bug report.  What I've got now is "it does not work any more and I
don't like it" - and that is not helpful.

You mentioned that you had problem with a ligand complex. I tried to
investigate further by asking you if you were using Acedrg-Coot. You
didn't answer.

You suggest that atom clashes may be a problem. I tried to investigate
further by asking you if you noticed a problem with Coot's description
of non-bonded contacts. You didn't answer.

To be clear, these were not rhetorical questions, they were an attempt
to address the problems - or at least begin to do so.

What I need is an example of *what* is going wrong.  Just one example
would be a start.  It seems to me that if the problem is as pervasive
as you seem to think it is, then it shouldn't be difficult for you to
conjure up a problematic case.  This is the sort of thing that I want:

   This model is based on 1xyz from the PDB, except that I've adjusted
   the model to create a problem.  See the region of A501 - you can
   see that that model and the map do not correspond. It is hard for
   me to fix it in 0.9 because when I do X, Coot does Y, but in 0.8.9
   all I had to do was A, B and C.

It might be the case that Coot can trivially solve the problem, but
you don't know about it - and that might be because I have
insufficiently explained how to do it. Or made the means by which you
can do so too opaque. Or maybe you have to type something. At the
moment I have no clue.

Normally, I would have taken to private correspondence by now.  I
recognise that your primarily interest is the latest and greatest of
the 0.8 series, and you may think that this may not be worth your
effort, so if you don't do this perhaps some of the other frustrated
Coot users may do so? Hence the public continuation of our discussion.


Regards,


Paul.

On 07/09/2020 10:28, Schulz, Eike-Christian wrote:

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  on behalf of Paul Emsley 

Reply to: Paul Emsley 
Date: Saturday, 5. September 2020 at 02:05
To: "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 

Re: [ccp4bb] AW: Going back to Coot 0.8

[Schulz, Eike-Christian]

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  on behalf of Paul Emsley 

Reply to: Paul Emsley 
Date: Saturday, 5. September 2020 at 02:05
To: "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

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

[Paul Emsley]

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  on behalf of "Schreuder, Herman 
/DE" 
Reply to: "Schreuder, Herman /DE" 
Date: Friday, 4. September 2020 at 15:02
To: "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  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

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

[Schulz, Eike-Christian]

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  on behalf of "Schreuder, 
Herman /DE" 
Reply to: "Schreuder, Herman /DE" 
Date: Friday, 4. September 2020 at 15:02
To: "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  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 il

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

[Schreuder, Herman /DE]

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  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  *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_=DwIDaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM=5NsBSHjvi7V_A6kImjIckNzc50syFHFM

Re: [ccp4bb] AW: Going back to Coot 0.8

[Eleanor Dodson]

 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  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  *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  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 

Re: [ccp4bb] AW: Going back to Coot 0.8

[Paul Emsley]

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  *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 


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/

)
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=1 

[ccp4bb] AW: Going back to Coot 0.8

[Schreuder, Herman /DE]

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  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

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/)
 would you recommend?

With best regards,

Eike






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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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