Re: [ccp4bb] Coot 1.* in CCP4 9

[David J. Schuller]

Thanks for the guidance.

If I replace two occurrences of  "Coot" with "coot-1" in .../coot_py3/bin/coot
it works.


===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
 schul...@cornell.edu

From: Paul Emsley 
Sent: Wednesday, August 28, 2024 6:32 PM
To: David J. Schuller ; CCP4BB@JISCMAIL.AC.UK 

Subject: Re: [ccp4bb] Coot 1.* in CCP4 9



Hello David,


One need not change anything. Just run it from where it is (for now probably 
best not to override the path while other programs expect coot to be coot 0.9.x)


.../ccp4-9/coot_py3/bin/coot


Paul.



On 8/28/24 22:05, David J. Schuller wrote:
Thank you for the response.

My installation claims to be up-to-date, so any modifications have not yet been 
released.

I looked in the .../ccp4-9/bin/coot file and changed coot_py2 to coot_py3.
When next I try to execute I get:
""
$ coot
/nfs/chess/sw/macchess/ccp4_master/ccp4-9/coot_py3/bin/coot: line 196: 
/nfs/chess/sw/macchess/ccp4_master/ccp4-9/coot_py3/libexec/Coot: No such file 
or directory
Coot crashed.
""


===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
 
schul...@cornell.edu<mailto:schul...@cornell.edu>

From: Paul Emsley <mailto:pems...@mrc-lmb.cam.ac.uk>
Sent: Wednesday, August 28, 2024 4:54 PM
To: David J. Schuller <mailto:schul...@cornell.edu>; 
CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Coot 1.* in CCP4 9



On 8/28/24 21:53, David J. Schuller wrote:
I installed CCP4 9 on Alma 9 Linux. I requested installation of both 
Coot-0.9.8.95 and Coot-1.1.08.

How do I execute the latter?



It's in the coot_py3 directory after installation.

I believe that Charles has recently made a binary update to 1.1.10.


Paul.




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Re: [ccp4bb] Coot 1.* in CCP4 9

[Paul Emsley]

Hello David,


One need not change anything. Just run it from where it is (for now 
probably best not to override the path while other programs expect coot 
to be coot 0.9.x)



.../ccp4-9/coot_py3/bin/coot


Paul.



On 8/28/24 22:05, David J. Schuller wrote:

Thank you for the response.

My installation claims to be up-to-date, so any modifications have not 
yet been released.


I looked in the .../ccp4-9/bin/coot file and changed coot/_py2 to 
coot/_py3.

When next I try to execute I get:
""
$ coot
/nfs/chess/sw/macchess/ccp4_master/ccp4-9/coot_py3/bin/coot: line 196: 
/nfs/chess/sw/macchess/ccp4_master/ccp4-9/coot_py3/libexec/Coot: No 
such file or directory

Coot crashed.
""


===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
schul...@cornell.edu

*From:* Paul Emsley 
*Sent:* Wednesday, August 28, 2024 4:54 PM
*To:* David J. Schuller ; CCP4BB@JISCMAIL.AC.UK 


*Subject:* Re: [ccp4bb] Coot 1.* in CCP4 9


On 8/28/24 21:53, David J. Schuller wrote:
I installed CCP4 9 on Alma 9 Linux. I requested installation of both 
Coot-0.9.8.95 and Coot-1.1.08.


How do I execute the latter?



It's in the coot_py3 directory after installation.

I believe that Charles has recently made a binary update to 1.1.10.


Paul.





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






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Re: [ccp4bb] Coot 1.* in CCP4 9

[David J. Schuller]

Thank you for the response.

My installation claims to be up-to-date, so any modifications have not yet been 
released.

I looked in the .../ccp4-9/bin/coot file and changed coot_py2 to coot_py3.
When next I try to execute I get:
""
$ coot
/nfs/chess/sw/macchess/ccp4_master/ccp4-9/coot_py3/bin/coot: line 196: 
/nfs/chess/sw/macchess/ccp4_master/ccp4-9/coot_py3/libexec/Coot: No such file 
or directory
Coot crashed.
""


===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
 schul...@cornell.edu

From: Paul Emsley 
Sent: Wednesday, August 28, 2024 4:54 PM
To: David J. Schuller ; CCP4BB@JISCMAIL.AC.UK 

Subject: Re: [ccp4bb] Coot 1.* in CCP4 9



On 8/28/24 21:53, David J. Schuller wrote:
I installed CCP4 9 on Alma 9 Linux. I requested installation of both 
Coot-0.9.8.95 and Coot-1.1.08.

How do I execute the latter?



It's in the coot_py3 directory after installation.

I believe that Charles has recently made a binary update to 1.1.10.


Paul.




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Re: [ccp4bb] Coot 1.* in CCP4 9

[Paul Emsley]

On 8/28/24 21:53, David J. Schuller wrote:
I installed CCP4 9 on Alma 9 Linux. I requested installation of both 
Coot-0.9.8.95 and Coot-1.1.08.


How do I execute the latter?



It's in the coot_py3 directory after installation.

I believe that Charles has recently made a binary update to 1.1.10.


Paul.




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[ccp4bb] Coot 1.* in CCP4 9

[David J. Schuller]

I installed CCP4 9 on Alma 9 Linux. I requested installation of both 
Coot-0.9.8.95 and Coot-1.1.08.

How do I execute the latter?


===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
 schul...@cornell.edu



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[ccp4bb] Coot keybinding [was Re: [ccp4bb] libcheck]

[Paul Emsley]

On 15/08/2024 17:14, Petr Pachl wrote:

[And now this part]



Also two off topic questions regarding coot-1 and coot. I tried to
transfer some of my keybindings and settings to coot-1 "language".


The language is Python (well, one of them is).

Unfortunately, there is not a good web resource for the Python API. (I 
should see to that). The current API documentation is based on the C++ 
API. I hope it is not too difficult to translate.



However as I understand not all things are supported.

That's right. I dropped some things in the move.

  Like adding a icon  for example of "split-water" into the main icon menu...

OK, that's a good example for a blog post. (I should write it.)


And to old coot... is it possible to add keybinding for "tandem
refine"?


H? T? It depends on what is n in "tandem."


  I find it very useful.


Yes, me too. I will add some auto-accept functions for Coot 1.


Paul.



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Re: [ccp4bb] COOT 1.1 and Symmetry

[Paul Emsley]

On 12/07/2024 13:12, Karol Woloszyn wrote:

Hello,

I’m a COOT 1.1.09 user on Fedora 40 as well as MacOS, working on DNA model 
refinement.

I’ve noticed since updating to 1.1.09, the cell and symmetry master switch no 
longer brings up any symmetry molecules. I remember in older versions (I was 
last most active on COOT 0.9.8) there was also a symmetry by molecule tab that 
is now missing as well.

Am I missing a setting or is there another workaround this?



Try this:


$ export SYMINFO /somewhere/ccp4/ccp4-9/coot_py3/share/coot/data/syminfo.lib


before starting coot



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Re: [ccp4bb] COOT 1.1 and Symmetry

[Paul Emsley]

On 12/07/2024 13:12, Karol Woloszyn wrote:


Hello,


Hello Karol,


I’m a COOT 1.1.09 user

exciting.

  on Fedora 40 as well as MacOS,

a rare breed.

  working on DNA model refinement.

OK...


I’ve noticed since updating to 1.1.09, the cell and symmetry master switch no 
longer brings up any symmetry molecules.
I don't see this myself. It could be that the symmetry is rendered as 
very thin lines - depending on your GTK version and driver settings.

  I remember in older versions (I was last most active on COOT 0.9.8) there was 
also a symmetry by molecule tab that is now missing as well.
Yes. It was too esoteric and intricately written with old-style GTK to 
be deemed necessary for 1 and 1.1. It will come back at some stage.

Am I missing a setting or is there another workaround this?


We need to first be sure the problem is not merely thin symmetry.

From a fresh start, Calculate -> Load Tutorial Model and Data then 
delete the maps, Then flip on the Symmetry Master switch. You should see 
a few greyish symmetry bonds appear, more if you increase the radius to 
30 or so.



Paul.



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[ccp4bb] COOT 1.1 and Symmetry

[Karol Woloszyn]

Hello,

I’m a COOT 1.1.09 user on Fedora 40 as well as MacOS, working on DNA model 
refinement. 

I’ve noticed since updating to 1.1.09, the cell and symmetry master switch no 
longer brings up any symmetry molecules. I remember in older versions (I was 
last most active on COOT 0.9.8) there was also a symmetry by molecule tab that 
is now missing as well. 

Am I missing a setting or is there another workaround this?

Thank you,
Karol


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Re: [ccp4bb] Coot 1.1 General Tools

[Simon Vecchioni]

Lucrezia,

Thanks for your help!

1) This works very well -- thanks for pointing me in the right direction.

2) Thanks

3) When I do this, no anchor appears. There's a "no intermediate atoms"
error, with a 0x0 matrix of fixed atoms. Maybe it's a DNA refinement error?

Cheers

On Mon, Jun 3, 2024 at 1:15 PM lucrezia catapano 
wrote:

> Dear Simon,
>
> 1. The new clipping keybindings are ‘1’ and ‘2’ for clipping front and ‘3’
> and ‘4’ for clipping back (like in Moorhen as well). You can find them in
> ‘About’- ’Shortcuts' (page 2 to be precise).
> 2. We need to fix this (about a week)
> 3. You center on an atom, then click on ‘Fixed atom’ on the right vertical
> toolbar, then ‘Fix atom’, and an ‘anchor’ marker will appear. Then it
> should work.
>
> Regards
> Lucrezia
>
>
> Lucrezia Catapano
> Postdoctoral Scientist, Murshudov Group
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue,
> Cambridge CB2 0QH, UK.
> lucre...@mrc-lmb.cam.ac.uk
>
>
>
> On 3 Jun 2024, at 17:14, Simon Vecchioni  wrote:
>
> CAUTION: This email originated from outside of the LMB:
> *.-owner-ccp...@jiscmail.ac.uk-.*
> Do not click links or open attachments unless you recognize the sender and
> know the content is safe.
> If you think this is a phishing email, please forward it to
> phish...@mrc-lmb.cam.ac.uk
>
>
> --
> Paul and CCP4 Community,
>
> Emailing the larger listserv because some of these might be useful to all.
> Thanks for the updates to the latest build.
>
> 1) In Coot 1.1.08, the graphics are fantastic! I've been struggling to
> clip the view for figure building. In old Coot, there was a "d" and "f"
> keyset that would toggle the fill/depth. Now there are other commands tied
> to "d" and nearby keys. Is there a menu that contains this feature, or a
> way to edit key bindings? I've experimented with the graphics menus but
> don't know the name of the feature I'm looking for.
>
> 2) Saving symmetry coordinates used to be a click operation, but now the
> interface has moved away from click selection. I haven't successfully been
> able to save a symmetry state--is there a good way to do this now?
>
> 3) Fix/Unfix atom also ran on click--I can go to a particular atom using
> the GUI, but I haven't been successful in fixing that atom for refinement.
>
> Thanks for your advice and assistance,
> Simon
>
> --
> Simon Vecchioni [he/his]
> Postdoctoral Researcher
> NYU Chemistry
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
>
>
>



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Re: [ccp4bb] Coot 1.1 General Tools

[lucrezia catapano]

Dear Simon,

1. The new clipping keybindings are ‘1’ and ‘2’ for clipping front and ‘3’ and 
‘4’ for clipping back (like in Moorhen as well). You can find them in ‘About’- 
’Shortcuts' (page 2 to be precise).
2. We need to fix this (about a week)
3. You center on an atom, then click on ‘Fixed atom’ on the right vertical 
toolbar, then ‘Fix atom’, and an ‘anchor’ marker will appear. Then it should 
work.

Regards
Lucrezia


Lucrezia Catapano
Postdoctoral Scientist, Murshudov Group
MRC Laboratory of Molecular Biology
Francis Crick Avenue,
Cambridge CB2 0QH, UK.
lucre...@mrc-lmb.cam.ac.uk



> On 3 Jun 2024, at 17:14, Simon Vecchioni  wrote:
> 
> CAUTION: This email originated from outside of the LMB:
> .-owner-ccp...@jiscmail.ac.uk-.
> Do not click links or open attachments unless you recognize the sender and 
> know the content is safe.
> If you think this is a phishing email, please forward it to 
> phish...@mrc-lmb.cam.ac.uk
> 
> --
> 
> Paul and CCP4 Community,
> 
> Emailing the larger listserv because some of these might be useful to all. 
> Thanks for the updates to the latest build.
> 
> 1) In Coot 1.1.08, the graphics are fantastic! I've been struggling to clip 
> the view for figure building. In old Coot, there was a "d" and "f" keyset 
> that would toggle the fill/depth. Now there are other commands tied to "d" 
> and nearby keys. Is there a menu that contains this feature, or a way to edit 
> key bindings? I've experimented with the graphics menus but don't know the 
> name of the feature I'm looking for.
> 
> 2) Saving symmetry coordinates used to be a click operation, but now the 
> interface has moved away from click selection. I haven't successfully been 
> able to save a symmetry state--is there a good way to do this now? 
> 
> 3) Fix/Unfix atom also ran on click--I can go to a particular atom using the 
> GUI, but I haven't been successful in fixing that atom for refinement.
> 
> Thanks for your advice and assistance,
> Simon
> 
> --
> Simon Vecchioni [he/his]
> Postdoctoral Researcher
> NYU Chemistry
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 




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[ccp4bb] Coot 1.1 General Tools

[Simon Vecchioni]

Paul and CCP4 Community,

Emailing the larger listserv because some of these might be useful to all.
Thanks for the updates to the latest build.

1) In Coot 1.1.08, the graphics are fantastic! I've been struggling to clip
the view for figure building. In old Coot, there was a "d" and "f" keyset
that would toggle the fill/depth. Now there are other commands tied to "d"
and nearby keys. Is there a menu that contains this feature, or a way to
edit key bindings? I've experimented with the graphics menus but don't know
the name of the feature I'm looking for.

2) Saving symmetry coordinates used to be a click operation, but now the
interface has moved away from click selection. I haven't successfully been
able to save a symmetry state--is there a good way to do this now?

3) Fix/Unfix atom also ran on click--I can go to a particular atom using
the GUI, but I haven't been successful in fixing that atom for refinement.

Thanks for your advice and assistance,
Simon

-- 
Simon Vecchioni [he/his]
Postdoctoral Researcher
NYU Chemistry



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Re: [ccp4bb] coot - how to define a keyboard shortcut for "update NCS ghosts with local match" ?

[Paul Emsley]

On 13/05/2024 11:23, Laurent Maveyraud wrote:

Hello,
I like the function "update NCS ghosts with local match" found in the 
calculate/NCT tools menu. It's really helpful when NCS is not really 
strict. However, I find it clumsy that you have to go in a submenu to 
get it, so I would like to define a keyboard shortcut... this would be 
much faster.


Which function should I use to  do that ?

(add_key_binding "Update ghosts" "a" (unknown function)



(add-key-binding "Update NCS Ghosts" "a" update-ncs-ghosts-by-local-sphere)

P.



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[ccp4bb] coot - how to define a keyboard shortcut for "update NCS ghosts with local match" ?

[Laurent Maveyraud]

Hello,
I like the function "update NCS ghosts with local match" found in the 
calculate/NCT tools menu. It's really helpful when NCS is not really 
strict. However, I find it clumsy that you have to go in a submenu to 
get it, so I would like to define a keyboard shortcut... this would be 
much faster.


Which function should I use to  do that ?

(add_key_binding "Update ghosts" "a" (unknown function)

thanks a lot !

Laurent

--
logo-ipbs


 Laurent Maveyraud


   Professor of Biophysics | University of Toulouse

Doctoral School Biology - Health - Biotechnologies

+33 5 61 17 54 35 | +33 6 46 04 21 11 | laurent.maveyr...@ipbs.fr 



UMR5089 | CNRS - UT3 | 205 Route de Narbonne BP 64182 - 31077 Toulouse 
Cedex 4


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@IpbsToulouse 

ipbs.cnrs 

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Re: [ccp4bb] COOT 1.1 and DNA mutation

[Paul Emsley]

On 26/04/2024 02:44, Paul Emsley wrote:



On 25/04/2024 16:07, Simon Vecchioni wrote:



Paul,

Many thanks for fixing the [simple mutate] button for DNA in 
v1.1.08--works like a charm!


I would ask about two other DNA features--
1) The [add terminal residue] button seems unresponsive for DNA,


I see what you mean. From the terminal output it seems to want to try 
to add a residue via a peptide bond.


I have made a note of this bug.


and is often quite useful;


OK.

This has been fixed and is in the HEAD of main (I will be busy with 
other things for the next few weeks so there won't be a release soon).


You will probably need some local refinement/regularization to anneal 
the phosphodiester link.



Paul.



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Re: [ccp4bb] COOT 1.1 and DNA mutation

[Paul Emsley]

On 25/04/2024 16:07, Simon Vecchioni wrote:



--

Paul,

Many thanks for fixing the [simple mutate] button for DNA in 
v1.1.08--works like a charm!


I would ask about two other DNA features--
1) The [add terminal residue] button seems unresponsive for DNA,


I see what you mean. From the terminal output it seems to want to try to 
add a residue via a peptide bond.


I have made a note of this bug.


and is often quite useful;


OK.

2) There was a button chain in v0.8.9 to add base pair restraints, 
Calculate--Modules--Restraints, and then Restraints--DNA-Bform. Is 
this still present but moved? I haven't been able to dig this one out.


That code didn't make the transition. The whole module needs to be 
reworked, I see now.


OK, well I will do that.

My intention was that base pairing restraints should be applied 
automatically now. While RSR (Sphere, say) is active, give an atom in a 
DG a little tug in the opposite direction to the DC - if the DC follows 
then the base pair restraints are being applied (it would seem to me).


Paul



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Re: [ccp4bb] COOT 1.1 and DNA mutation

[Simon Vecchioni]

Paul,

Many thanks for fixing the [simple mutate] button for DNA in v1.1.08--works
like a charm!

I would ask about two other DNA features--

1) The [add terminal residue] button seems unresponsive for DNA, and is
often quite useful;
2) There was a button chain in v0.8.9 to add base pair restraints,
Calculate--Modules--Restraints, and then Restraints--DNA-Bform. Is this
still present but moved? I haven't been able to dig this one out.

Thanks again for your support,
Simon

On Thu, Apr 4, 2024 at 2:48 PM Simon Vecchioni  wrote:

> Paul,
>
> That's fantastic and swift. Many thanks for your help, and for making COOT
> the go-to for DNA slice and dice.
>
> Cheers
> Simon Vecchioni
> NYU Chemistry
>
>
> On Thu, Apr 4, 2024, 5:43 AM Paul Emsley 
> wrote:
>
>>
>> On 04/04/2024 02:27, Simon Vecchioni wrote:
>> >
>> >
>> > Dear CCP4 Wizards,
>> Hello Simon.
>> >
>> > I've upgraded to COOT v1.1.07 from 0.9.6, and am working on DNA model
>> > refinement.
>> exciting.
>> >
>> > The current setup does not seem to let me sequence mutate (simple
>> > mutate or mutate residue range), as it's hard coded to an amino acid
>> > drop down menu. Edit-->Replace residue with three letter code (for DNA
>> > "DC", "DA", etc.) also does not seem to swap residues.
>>
>> I see what you mean. The first is an oversight, the second is a bug.
>>
>> The first of these will be easy to fix, I think the second not so easy
>> as it involves the Python gui interface. However, I can give it a bash
>> and it should be available on Monday if you are using the HEAD build.
>>
>> >
>> > Am I missing a setting or button click/centering/toggle? Is there a
>> > workaround for this short of reverting to an older version where these
>> > features were well oiled?
>> >
>> Not until next week - or somewhat longer than that probably if you are
>> only using releases.
>>
>> Paul.
>>
>>
>>



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Re: [ccp4bb] COOT 1.1 and DNA mutation

[Simon Vecchioni]

Paul,

That's fantastic and swift. Many thanks for your help, and for making COOT
the go-to for DNA slice and dice.

Cheers
Simon Vecchioni
NYU Chemistry


On Thu, Apr 4, 2024, 5:43 AM Paul Emsley  wrote:

>
> On 04/04/2024 02:27, Simon Vecchioni wrote:
> >
> >
> > Dear CCP4 Wizards,
> Hello Simon.
> >
> > I've upgraded to COOT v1.1.07 from 0.9.6, and am working on DNA model
> > refinement.
> exciting.
> >
> > The current setup does not seem to let me sequence mutate (simple
> > mutate or mutate residue range), as it's hard coded to an amino acid
> > drop down menu. Edit-->Replace residue with three letter code (for DNA
> > "DC", "DA", etc.) also does not seem to swap residues.
>
> I see what you mean. The first is an oversight, the second is a bug.
>
> The first of these will be easy to fix, I think the second not so easy
> as it involves the Python gui interface. However, I can give it a bash
> and it should be available on Monday if you are using the HEAD build.
>
> >
> > Am I missing a setting or button click/centering/toggle? Is there a
> > workaround for this short of reverting to an older version where these
> > features were well oiled?
> >
> Not until next week - or somewhat longer than that probably if you are
> only using releases.
>
> Paul.
>
>
>



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Re: [ccp4bb] COOT 1.1 and DNA mutation

[Paul Emsley]

On 04/04/2024 02:27, Simon Vecchioni wrote:



Dear CCP4 Wizards,

Hello Simon.


I've upgraded to COOT v1.1.07 from 0.9.6, and am working on DNA model 
refinement.

exciting.


The current setup does not seem to let me sequence mutate (simple 
mutate or mutate residue range), as it's hard coded to an amino acid 
drop down menu. Edit-->Replace residue with three letter code (for DNA 
"DC", "DA", etc.) also does not seem to swap residues.


I see what you mean. The first is an oversight, the second is a bug.

The first of these will be easy to fix, I think the second not so easy 
as it involves the Python gui interface. However, I can give it a bash 
and it should be available on Monday if you are using the HEAD build.




Am I missing a setting or button click/centering/toggle? Is there a 
workaround for this short of reverting to an older version where these 
features were well oiled?


Not until next week - or somewhat longer than that probably if you are 
only using releases.


Paul.



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[ccp4bb] COOT 1.1 and DNA mutation

[Simon Vecchioni]

Dear CCP4 Wizards,

I've upgraded to COOT v1.1.07 from 0.9.6, and am working on DNA model
refinement.

The current setup does not seem to let me sequence mutate (simple mutate or
mutate residue range), as it's hard coded to an amino acid drop down menu.
Edit-->Replace residue with three letter code (for DNA "DC", "DA", etc.)
also does not seem to swap residues.

Am I missing a setting or button click/centering/toggle? Is there a
workaround for this short of reverting to an older version where these
features were well oiled?

Many thanks for your help,
Simon



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Re: [ccp4bb] Coot function - closest symmetry atom?

[Paul Emsley]

On 18/03/2024 10:26, Petr Pachl wrote:

--


Does anybody know if there is a function (or procedure) how to get info
about closest symmetry atom? For picking coot is performing something
like "Model atom pick (if failed) -> Symmetry atom pick", then it
returns to console and atom info at the bottom of the screen the found
atom. But can that be obtained in a function? My idea is to have a
shortcut "go to original atom based on symmetry related one".


Your second question is easier to answer than the first one - because it 
has been coded up already (in 2009). It's called "undo-symmetry-view" 
and all you need to do is bind it to a key. In fact, it's already bound 
to a key (Shift-V) if you have installed the key-bindings.


Paul.



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[ccp4bb] Coot function - closest symmetry atom?

[Petr Pachl]

Hi all.
Does anybody know if there is a function (or procedure) how to get info
about closest symmetry atom? For picking coot is performing something
like "Model atom pick (if failed) -> Symmetry atom pick", then it
returns to console and atom info at the bottom of the screen the found
atom. But can that be obtained in a function? My idea is to have a
shortcut "go to original atom based on symmetry related one".

Thanks a lot,
Petr

-- 
Petr Pachl PhD.
Structural Biology
Institute of Organic Chemistry and Biochemistry
Czech Academy of Sciences
Flemingovo n. 2
166 10 Prague 6
Czech Republic

office: + 420 220 183 210



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Re: [ccp4bb] Coot SSM Superpose Problem

[Eleanor Dodson]

Isnt this what you want? output of CCP4I2 fitting buccaneer to the other..


On Fri, 16 Feb 2024 at 09:46, zx2...@connect.hku.hk 
wrote:

> Dear all,
>
> Following the advice provided by Paul and Yi Min, the "*Symm Shift
> Reference Chain Here*" function has proven successful!
>
> I am deeply grateful for your guidance.
>
> Best regards,
> Xin
> --
> *From:* zx2...@connect.hku.hk 
> *Sent:* 16 February 2024 17:26
> *To:* Paul Emsley 
> *Subject:* Re: [ccp4bb] Coot SSM Superpose Problem
>
> Dear Paul,
>
> I apologize for the confusion in my previous description. To clarify,
> there are actually 4 copies within a single ASU.
>
> Following your suggestion, I tried the "Symm Shift Reference Chain Here" ,
> and it worked successfully. I greatly appreciate your assistance.
>
> Thank you so much!
>
> Best regards,
> Xin
> --
> *From:* Paul Emsley 
> *Sent:* 16 February 2024 11:06
> *To:* zx2...@connect.hku.hk ; CCP4BB@JISCMAIL.AC.UK
> 
> *Subject:* Re: [ccp4bb] Coot SSM Superpose Problem
>
>
>
> On 16/02/2024 01:45, zx2...@connect.hku.hk wrote:
>
> Dear all,
>
> Hello Xin,
>
>
> I encountered an issue while attempting to calculate the RMSD between two
> PDB files (each containing 4 ASUs)
>
> do they really though?
>
>
> using the SSM Superpose tool in Coot. Unfortunately, the tool was unable
> to superpose all ASUs accurately.
>
>
> That's because you have mismatched bundles. It seem to me that you need
> some "Symm Shift Reference Chain Here" action.
>
>
> Paul.
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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 ###
 ###
 ###
 ### CCP4 8.0.017: csymmatchversion 0.3 : 13/07/09##
 ###
 User: eleanor  Run date: 16/ 2/2024 Run time: 10:43:46 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 
235-242.
 as well as any specific reference in the program write-up.



pdbin   
/Users/eleanor/CCP4I2_PROJECTS/jim-24948v162/CCP4_JOBS/job_308/XYZIN_QUERY-coordinates.pdb
pdbin-ref   
/Users/eleanor/CCP4I2_PROJECTS/jim-24948v162/CCP4_JOBS/job_308/XYZIN_TARGET-coordinates.pdb
origin-hand
pdbout  
/Users/eleanor/CCP4I2_PROJECTS/jim-24948v162/CCP4_JOBS/job_309/309_jim-24948v162_xyzout_csymmatch.pdb

Reference molecule:
  Spacegroup: P 1 21 1
  Unit cell:  Cell (52.932,160.535,95.563,90, 95.91,90)
Moving molecule:
  Spacegroup: P 1 21 1
  Unit cell:  Cell ( 52.96,160.61, 95.61,90, 95.92,90)


 Change of hand  : NO
 Change of origin: uvw = (   0.5,  0.25, 0)

Chain: C1-  43 will be transformed as follows:
  Symmetry operator: x, y, z
  Lattice shift: uvw = ( 0, 0, 0)
  with normalised score:  0.557587
Chain: C   45- 100 will be transformed as follows:
  Symmetry operator: x, y, z
  Lattice shift: uvw = ( 0, 0, 0)
  with normalised score:  0.498482
Chain: C  102- 363 will be transformed as follows:
  Symmetry operator: x, y, z
  Lattice shift: uvw = ( 0, 0, 0)
  with normalised score:  0.610847
Chain: A5-  44 will be transformed as follows:
  Symmetry operator: -x, y+1/2, -z
  Lattice shift: uvw = ( 1,-1, 0)
  with normalised score:  0.593516
Chain: A   48-  96 will be transformed as follows:
  Symmetry operator: -x, y+1/2, -z
  Lattice shift: uvw = ( 1,-1, 0)
  with normalised score:  0.55637
Chain: A  100- 361 will be transformed as follows:
  Symmetry operator: -x, y+1/2, -z
  Lattice shift: uvw = ( 1,-1, 0)
  with normalised score:  0.622536
Chain: D1-  43 will be transformed as follows:
  Symmetry operator: x, y, z
  Lattice shift: uvw = ( 0, 0,-1)
  with normalised score:  0.615694
Chain: D   45-  46 will be transformed as follows:
  Symmetry operator: x, y, z
  Lattice shift: uvw = ( 0, 0,-1

Re: [ccp4bb] Coot SSM Superpose Problem

[zx2...@connect.hku.hk]

Dear all,

Following the advice provided by Paul and Yi Min, the "Symm Shift Reference 
Chain Here" function has proven successful!

I am deeply grateful for your guidance.

Best regards,
Xin

From: zx2...@connect.hku.hk 
Sent: 16 February 2024 17:26
To: Paul Emsley 
Subject: Re: [ccp4bb] Coot SSM Superpose Problem

Dear Paul,

I apologize for the confusion in my previous description. To clarify, there are 
actually 4 copies within a single ASU.

Following your suggestion, I tried the "Symm Shift Reference Chain Here" , and 
it worked successfully. I greatly appreciate your assistance.

Thank you so much!

Best regards,
Xin

From: Paul Emsley 
Sent: 16 February 2024 11:06
To: zx2...@connect.hku.hk ; CCP4BB@JISCMAIL.AC.UK 

Subject: Re: [ccp4bb] Coot SSM Superpose Problem



On 16/02/2024 01:45, zx2...@connect.hku.hk<mailto:zx2...@connect.hku.hk> wrote:
Dear all,
Hello Xin,

I encountered an issue while attempting to calculate the RMSD between two PDB 
files (each containing 4 ASUs)

do they really though?


using the SSM Superpose tool in Coot. Unfortunately, the tool was unable to 
superpose all ASUs accurately.


That's because you have mismatched bundles. It seem to me that you need some 
"Symm Shift Reference Chain Here" action.


Paul.




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Re: [ccp4bb] Coot SSM Superpose Problem

[Paul Emsley]

On 16/02/2024 01:45, zx2...@connect.hku.hk wrote:

Dear all,

Hello Xin,


I encountered an issue while attempting to calculate the RMSD between 
two PDB files (each containing 4 ASUs)


do they really though?


using the SSM Superpose tool in Coot. Unfortunately, the tool was 
unable to superpose all ASUs accurately.



That's because you have mismatched bundles. It seem to me that you need 
some "Symm Shift Reference Chain Here" action.



Paul.




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Re: [ccp4bb] Coot query

[Tom Peat]

Just in case something like this happens to someone else:
I am running the Gnome display server and I did another restart and I can now 
run Coot.
The magic of rebooting...
cheers, tom

From: Paul Emsley 
Sent: Friday, July 7, 2023 2:09 AM
To: Tom Peat ; CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Coot query



On 06/07/2023 08:51, Tom Peat wrote:
Hello All,

I just had a very strange experience- I rebooted my linux machine (Ubuntu jammy 
7.81.0) and tried to start up Coot and received the following error message:


It is my understanding that jammy jellyfish, by default, uses Wayland as the 
display server. It seems to me then that running an X11-based application will 
have to go via XWayland, and who knows what goodies that could bring. So my 
suggestion to you is to try rebooting and using an X11-based display manager.


I will note here that a person such as yourself Tom could compile the gtk4 
branch of Coot, which can now run on Wayland directly.


Paul.




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Re: [ccp4bb] Coot query

[Paul Emsley]

On 06/07/2023 08:51, Tom Peat wrote:

Hello All,

I just had a very strange experience- I rebooted my linux machine 
(Ubuntu jammy 7.81.0) and tried to start up Coot and received the 
following error message:



It is my understanding that jammy jellyfish, by default, uses Wayland as 
the display server. It seems to me then that running an X11-based 
application will have to go via XWayland, and who knows what goodies 
that could bring. So my suggestion to you is to try rebooting and using 
an X11-based display manager.



I will note here that a person such as yourself Tom could compile the 
gtk4 branch of Coot, which can now run on Wayland directly.



Paul.




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[ccp4bb] Coot query

[Tom Peat]

Hello All,

I just had a very strange experience- I rebooted my linux machine (Ubuntu jammy 
7.81.0) and tried to start up Coot and received the following error message:

The program 'coot-bin' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadValue (integer parameter out of range for operation)'.
  (Details: serial 351 error_code 2 request_code 152 minor_code 3)
  (Note to programmers: normally, X errors are reported asynchronously;
   that is, you will receive the error a while after causing it.
   To debug your program, run it with the --sync command line
   option to change this behavior. You can then get a meaningful
   backtrace from your debugger if you break on the gdk_x_error() function.)
. -- Coot crashed - trying to diagnose -
ldd -r on guile gives:
  linux-vdso.so.1 (0x7ffd6d0b9000)
  libguile.so.17 => 
/opt/xtal/ccp4-8.0/coot_py2/libexec/../lib/libguile.so.17 (0x7fd11380)
  libgmp.so.10 => /opt/xtal/ccp4-8.0/coot_py2/libexec/../lib/libgmp.so.10 
(0x7fd11340)
  libcrypt.so.1 => /lib/x86_64-linux-gnu/libcrypt.so.1 (0x7fd113c6b000)
  libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7fd113b84000)
  libltdl.so.7 => /opt/xtal/ccp4-8.0/coot_py2/libexec/../lib/libltdl.so.7 
(0x7fd11300)
  libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 
(0x7fd113b7d000)
  libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7fd112c0)
  /lib64/ld-linux-x86-64.so.2 (0x7fd113cbc000)
  libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x7fd113b78000)
Guile 1.8.8
Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 
2008 Free Software Foundation
Guile may be distributed under the terms of the GNU General Public Licence;
certain other uses are permitted as well.  For details, see the file
`COPYING', which is included in the Guile distribution.I
There is no warranty, to the extent permitted by law.
catching the crash log:
Gtk-Message: Failed to load module "gail"
Gtk-Message: Failed to load module "atk-bridge"
Gtk-Message: Failed to load module "canberra-gtk-module"
coot-exe: "/opt/xtal/ccp4-8.0/coot_py2/libexec/coot-bin"
/usr/bin/ls
-rwxr-xr-x 1 tom tom 9256240 Jun 21 12:54 
/opt/xtal/ccp4-8.0/coot_py2/libexec/coot-bin
coot-version:
/opt/xtal/ccp4-8.0/coot_py2/libexec/coot-bin
Builder_info: CCP4, Oxfordshire

I tried this both as command line (coot xxx.pdb) and through the CCP4i window 
and I get the same error message. I also tried with more than one coordinate 
file (in different directories).
I find this strange as I was just finishing up some structures with Coot/ 
Refmac (everything working fine) and had turned off my machine to take a break 
for a day, so things were working very recently. I don't remember doing any 
major updates either...
Has anyone else seen this behaviour?
cheers, tom



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Re: [ccp4bb] Coot run in terminal not opening mtz

[Mahmoud RIZK]

Hi Evgenii,
quick workaround is to add "--auto" before the mtz path
like this:

   $coot --pdb  --auto 

Best,
Mahmoud

On 19/06/2023 15:07, Evgenii Osipov wrote:

Dear CCP4BB,

I used to run coot from terminal using $coot  map mtz>


However this way is no longer working after I updated CCP4 to 8.0  
with Coot 0.9.8.7


In similar way, dimple script run-coot.py doens't work as intended — 
it will just open Coot but won't load structures and maps.


Coordinates/maps still could be loaded from Coot menu.

There are no errors/warnings when Coot is starting from the terminal.

What can cause such behaviour and how to fix it?

--
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O&N2



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[ccp4bb] Coot run in terminal not opening mtz

[Evgenii Osipov]

Dear CCP4BB,

I used to run coot from terminal using $coot  

However this way is no longer working after I updated CCP4 to 8.0  with
Coot 0.9.8.7

In similar way, dimple script run-coot.py doens't work as intended — it
will just open Coot but won't load structures and maps.

Coordinates/maps still could be loaded from Coot menu.

There are no errors/warnings when Coot is starting from the terminal.

What can cause such behaviour and how to fix it?

-- 
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O&N2



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[ccp4bb] COOT: Rotate/Translate Fragment tool

[Andrew Gulick]

When using the COOT (0.9.8.5 EL) on a Mac, the behavior appears to have changed 
for manually rotating a fragment (Rotate/Translate Zone/Chain Molecule tool)

When activated, the pop-up window allows me to use the sliders to rotate or 
translate. That works as advertised.

However, I used to be able to hold down the Control key (on Mac OS) and then 
use the LeftMouse to make the same minor adjustments to the rotation and 
translation. On current version, if I do that, it appears that rather than the 
center of rotation being the last atom chosen, the center of rotation is 
somewhere else (it is not the center of mass of the fragment). Thus, using 
Control-Mouse causes the fragment to fly off as it is rotating around some 
distant origin rather than the molecule itself.

Edit > Settings > Rotate Translate Zone Mode > provides two options (about 
fragment center and about second clicked atom) and neither seems to help.

Again, this tool works fine using the slider bars. Additionally, Control – 
LeftMouse ON an atom to move an atom works fine. It is just the Control – 
LeftMouse NOT ON an atom in an effort to rotate the entire fragment that is 
problematic.

Is there a setting to return this to operational.

Thanks for any suggestions.
Andy





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[ccp4bb] Coot Delete Item on MacOS Ventura

[Paul Emsley]

Last week I was using 13.2 and could reproduce the snap iconification on 
delete item.


This morning I updated to 13.3 and the iconification problem is no more 
- so the update fixed it. Apple didn't mention XQuartz or Coot in the 
release notes (fwiw).



Paul.



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Re: [ccp4bb] COOT crash in ccp4i2 - Error in wrapper coot_rebuild 0.0

[Harry Powell]

I hadn’t noticed until just now, but this also happens on Linux machines at 
SLAC - 

> Distributor ID:   Debian
> Description:  Debian GNU/Linux 10 (buster)
> Release:  10
> Codename: buster

:-(

Harry


> On 29 Mar 2023, at 15:02, Joseph Cockburn  wrote:
> 
> Dear BB,
> Quite a few of my students are having problems when they use COOT through 
> CCP4i2. COOT crashes, and throws the following error:
>  
> “- ERROR - Ccoot_rebuild:56 Error in wrapper coot_rebuild 0.0:: External 
> process exited”
>  
> (see attached screenshot).
> These are undergrad students who have installed the latest version of CCP4i2 
> onto their own machines. They are working through a tutorial on molecular 
> replacement, model rebuilding and refinement. They get this error when they 
> run COOT after REFMAC. This fault has occurred on both mac and windows 
> machines.
> Does anyone know how to fix this?
> Kind regards,
> Joe
>  
>  
> --
> Dr Joseph J B Cockburn DPhil
> Program Leader, Biochemistry and Medical Biochemistry
> Group Leader and Lecturer in X-ray Crystallography
> The Astbury Centre for Structural and Molecular Biology
> School of Molecular and Cellular Biology
> Faculty of Biological Sciences
> University of Leeds
> Leeds LS2 9JT
> UK
> +44 (0)113 3430758
>  
> Sometimes I need to send emails in the evenings or at weekends, but I don’t 
> expect a reply outside of your normal working hours.
>  
> 
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> 



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Re: [ccp4bb] Coot crashes when delete side chain

[Chris Langendorf]

Hi Jinhua,

Following on from Mike's great tip, if you do forget to tick the "Keep
Delete Active" dialog box and your coot window crashes, you can recover
your old session.  After coot crashes, open a new coot window and go to
"File" then "Save Coordinates", a new dialogue box pops up asking to
"Select Filename", click on that and your old (crashed) session will open
back up in a new window, the side chain will also be deleted! You can now
close the superfluous new coot session. I don't know why this works, just
glad that it does :)

Chris

On Wed, 8 Mar 2023 at 09:47, Michael Gorman <
9a16aac7520c-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi Jinhua,
> A temporary fix to the problem I have seen is to tick the 'Keep Delete
> Active' dialog box. Strange, but I'm sure Paul will come up with a fix soon.
> HTH
> Mike
>
> On Wednesday, 8 March 2023, 09:11:08 am AEDT, Wu, Jinhua <
> jinhua...@fccc.edu> wrote:
>
>
> Hi all,
>
>
>
> I recently upgraded my iMac to a 6-Core Intel i5 running Ventura 13.2.1. I
> installed Coot 0.9.8.7 together with CCP4. Now every time when I select
> delete sidechain (or sidechain zone) and click on the residue, Coot
> crashes. Does anyone have the same problem or know the solution to this
> issue?
>
>
>
> Thanks,
>
> Jinhua
>
> --
>
> This electronic message is intended to be for the use of the named
> recipient, and may contain information that is confidential or privileged.
> This communication may contain protected health information (PHI) that is
> legally protected from inappropriate disclosure by the Privacy Standards of
> the Health Insurance Portability and Accountability Act (HIPAA) and
> relevant Pennsylvania Laws. You can direct questions concerning PHI or
> HIPAA to the Corporate Compliance and Privacy Officer at (215) 707-5605. If
> you are not the intended recipient, please note that any dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this message in error, you should notify the sender
> immediately by telephone or by return e-mail and delete and destroy all
> copies of this message.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Coot crashes when delete side chain

[Wu, Jinhua]

Thanks Nick, Michael, Engin and others for sharing the insight. Indeed it did 
not crash but was only hidden. I can restore the window and keep it there by 
clicking the “keep delete active” box. So far it works fine.

Thanks,
Jinhua

From: Nicholas Clark 
Date: Tuesday, March 7, 2023 at 7:21 PM
To: Wu, Jinhua 
Cc: ccp4bb@jiscmail.ac.uk 
Subject: Re: [ccp4bb] Coot crashes when delete side chain
EXTERNAL sender! Do you TRUST this email? If you are unsure, send the email to 
InfoSec for review by using the Report Phish button.


Jinhua,

As Michael stated, ticking "keep delete active" will prevent the window from 
closing. Additionally, if you accidentally forget to do this, Coot does not 
actually crash. The window gets "hidden" or "minimized". If you right click on 
the XQuartz icon, you will see the window at the top of the menu as "Coot 
[Version]". Clicking it will restore the window to the viewscreen. It took me a 
while to realize this so figured I'd share.

Best,

Nick Clark

On Tue, Mar 7, 2023 at 5:11 PM Wu, Jinhua 
mailto:jinhua...@fccc.edu>> wrote:
Hi all,

I recently upgraded my iMac to a 6-Core Intel i5 running Ventura 13.2.1. I 
installed Coot 0.9.8.7 together with CCP4. Now every time when I select delete 
sidechain (or sidechain zone) and click on the residue, Coot crashes. Does 
anyone have the same problem or know the solution to this issue?

Thanks,
Jinhua



This electronic message is intended to be for the use of the named recipient, 
and may contain information that is confidential or privileged. This 
communication may contain protected health information (PHI) that is legally 
protected from inappropriate disclosure by the Privacy Standards of the Health 
Insurance Portability and Accountability Act (HIPAA) and relevant Pennsylvania 
Laws. You can direct questions concerning PHI or HIPAA to the Corporate 
Compliance and Privacy Officer at (215) 707-5605. If you are not the intended 
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communication is strictly prohibited. If you have received this message in 
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--
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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Re: [ccp4bb] Coot crashes when delete side chain

[Alice Dawson (Staff)]

You can also use the Command key plus the tilda ~ to toggle through the active 
windows of a current application (so you need to still be in XQuartz). I’ve 
found this to be the quickest way to get back to the main Coot window.

Alice

--

Alice Dawson
Structural Biologist
Division of Biological Chemistry and Drug Discovery
University of Dundee
Dow Street
Dundee DD1 5EH



From: CCP4 bulletin board  on behalf of Nicholas Clark 

Date: Wednesday, 8 March 2023 at 00:21
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Coot crashes when delete side chain

CAUTION: This email originated from outside the University of Dundee. Do not 
click links or open attachments unless you recognise the sender's email address 
and know the content is safe.
Jinhua,

As Michael stated, ticking "keep delete active" will prevent the window from 
closing. Additionally, if you accidentally forget to do this, Coot does not 
actually crash. The window gets "hidden" or "minimized". If you right click on 
the XQuartz icon, you will see the window at the top of the menu as "Coot 
[Version]". Clicking it will restore the window to the viewscreen. It took me a 
while to realize this so figured I'd share.

Best,

Nick Clark

On Tue, Mar 7, 2023 at 5:11 PM Wu, Jinhua 
mailto:jinhua...@fccc.edu>> wrote:
Hi all,

I recently upgraded my iMac to a 6-Core Intel i5 running Ventura 13.2.1. I 
installed Coot 0.9.8.7 together with CCP4. Now every time when I select delete 
sidechain (or sidechain zone) and click on the residue, Coot crashes. Does 
anyone have the same problem or know the solution to this issue?

Thanks,
Jinhua



This electronic message is intended to be for the use of the named recipient, 
and may contain information that is confidential or privileged. This 
communication may contain protected health information (PHI) that is legally 
protected from inappropriate disclosure by the Privacy Standards of the Health 
Insurance Portability and Accountability Act (HIPAA) and relevant Pennsylvania 
Laws. You can direct questions concerning PHI or HIPAA to the Corporate 
Compliance and Privacy Officer at (215) 707-5605. If you are not the intended 
recipient, please note that any dissemination, distribution or copying of this 
communication is strictly prohibited. If you have received this message in 
error, you should notify the sender immediately by telephone or by return 
e-mail and delete and destroy all copies of this message.



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--
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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Re: [ccp4bb] Coot crashes when delete side chain

[Nicholas Clark]

Jinhua,

As Michael stated, ticking "keep delete active" will prevent the window
from closing. Additionally, if you accidentally forget to do this, Coot
does not actually crash. The window gets "hidden" or "minimized". If you
right click on the XQuartz icon, you will see the window at the top of the
menu as "Coot [Version]". Clicking it will restore the window to the
viewscreen. It took me a while to realize this so figured I'd share.

Best,

Nick Clark

On Tue, Mar 7, 2023 at 5:11 PM Wu, Jinhua  wrote:

> Hi all,
>
>
>
> I recently upgraded my iMac to a 6-Core Intel i5 running Ventura 13.2.1. I
> installed Coot 0.9.8.7 together with CCP4. Now every time when I select
> delete sidechain (or sidechain zone) and click on the residue, Coot
> crashes. Does anyone have the same problem or know the solution to this
> issue?
>
>
>
> Thanks,
>
> Jinhua
>
> --
>
> This electronic message is intended to be for the use of the named
> recipient, and may contain information that is confidential or privileged.
> This communication may contain protected health information (PHI) that is
> legally protected from inappropriate disclosure by the Privacy Standards of
> the Health Insurance Portability and Accountability Act (HIPAA) and
> relevant Pennsylvania Laws. You can direct questions concerning PHI or
> HIPAA to the Corporate Compliance and Privacy Officer at (215) 707-5605. If
> you are not the intended recipient, please note that any dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this message in error, you should notify the sender
> immediately by telephone or by return e-mail and delete and destroy all
> copies of this message.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
>


-- 
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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Re: [ccp4bb] Coot crashes when delete side chain

[Michael Gorman]

 Hi Jinhua,A temporary fix to the problem I have seen is to tick the 'Keep 
Delete Active' dialog box. Strange, but I'm sure Paul will come up with a fix 
soon.HTHMike
On Wednesday, 8 March 2023, 09:11:08 am AEDT, Wu, Jinhua 
 wrote:  
 
  
Hi all,

  
 
I recently upgraded my iMac to a 6-Core Intel i5 running Ventura 13.2.1. I 
installed Coot 0.9.8.7 together with CCP4. Now every time when I select delete 
sidechain (or sidechain zone) and click on the residue, Coot crashes. Does 
anyone have the same problem or know the solution to this issue? 

  
 
Thanks,

Jinhua


This electronic message is intended to be for the use of the named recipient, 
and may contain information that is confidential or privileged. This 
communication may contain protected health information (PHI) that is legally 
protected from inappropriate disclosure by the Privacy Standards of the Health 
Insurance Portability and Accountability Act (HIPAA) and relevant Pennsylvania 
Laws. You can direct questions concerning PHI or HIPAA to the Corporate 
Compliance and Privacy Officer at (215) 707-5605. If you are not the intended 
recipient, please note that any dissemination, distribution or copying of this 
communication is strictly prohibited. If you have received this message in 
error, you should notify the sender immediately by telephone or by return 
e-mail and delete and destroy all copies of this message.


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[ccp4bb] Coot crashes when delete side chain

[Wu, Jinhua]

Hi all,

I recently upgraded my iMac to a 6-Core Intel i5 running Ventura 13.2.1. I 
installed Coot 0.9.8.7 together with CCP4. Now every time when I select delete 
sidechain (or sidechain zone) and click on the residue, Coot crashes. Does 
anyone have the same problem or know the solution to this issue?

Thanks,
Jinhua



This electronic message is intended to be for the use of the named recipient, 
and may contain information that is confidential or privileged. This 
communication may contain protected health information (PHI) that is legally 
protected from inappropriate disclosure by the Privacy Standards of the Health 
Insurance Portability and Accountability Act (HIPAA) and relevant Pennsylvania 
Laws. You can direct questions concerning PHI or HIPAA to the Corporate 
Compliance and Privacy Officer at (215) 707-5605. If you are not the intended 
recipient, please note that any dissemination, distribution or copying of this 
communication is strictly prohibited. If you have received this message in 
error, you should notify the sender immediately by telephone or by return 
e-mail and delete and destroy all copies of this message.



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Re: [ccp4bb] Coot (& phenix) on Ventura

[Charles Ballard - STFC UKRI]

Hi Pat

There may well be issues with the latest xquartz (2.8.3+) as the  libcairo 
compatibility version has changed to 1 from being 11 thousand odd.   This means 
that anything built against an older installation will fail.   The  workaround 
is to use an older xquartz, such as 2.8.0.

That pretty well summarises my knowledge, hopefully others will fill in the 
gaps.

Charles

From: CCP4 bulletin board  on behalf of Patrick Loll 

Date: Thursday, 16 February 2023 at 13:27
To: ccp4bb 
Subject: [ccp4bb] Coot (& phenix) on Ventura
Hi everyone,

I’ve been putting off upgrading to Mac OS 13 Ventura, but my computer is 
getting more and more pushy in its demands for a new OS.

Hence I ask, What’s the current status of coot running on Ventura? I’m aware of 
the issues that have been discussed in this forum, but that thread seems to 
have been quiet for a while. Are people able to get their work done under OS 
13? And have people encountered problems with any other structural biology 
programs?

Cheers,

Pat

---
Patrick J. Loll, Ph. D.  (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102  USA

(215) 762-7706
pjl...@gmail.com<mailto:pjl...@gmail.com>
pj...@drexel.edu<mailto:pj...@drexel.edu>



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[ccp4bb] Coot (& phenix) on Ventura

[Patrick Loll]

Hi everyone,

I’ve been putting off upgrading to Mac OS 13 Ventura, but my computer is 
getting more and more pushy in its demands for a new OS.

Hence I ask, What’s the current status of coot running on Ventura? I’m aware of 
the issues that have been discussed in this forum, but that thread seems to 
have been quiet for a while. Are people able to get their work done under OS 
13? And have people encountered problems with any other structural biology 
programs?

Cheers,

Pat


---
Patrick J. Loll, Ph. D.  (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102  USA

(215) 762-7706
pjl...@gmail.com 
pj...@drexel.edu


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Re: [ccp4bb] COOT 1.0 not showing content on MacOS

[Lucrezia Catapano MRC-LMB]

Hi Cheng,

this a problem related to gtk+3 installation. There is a workaround to 
solve the issue. You need to install a previous version of gtk+3. All 
the instructions are here:

https://github.com/pemsley/coot/issues/33#issuecomment-1374409909

Bw,
Lucrezia

On 2023-01-25 15:53, Cheng Zhang wrote:

Hi all,

I recently reinstalled the new Coot on my Mac (BigSur 11.7) following
the instructions of Dr. Scott. However, after I ran it, the Xwindow
didn't show anything. I also didn't see errors in the command lines.
Any suggestions on how to fix this? The X11 is up to date.

Best,

Cheng

--

-
Cheng Zhang

-

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Re: [ccp4bb] Coot issue

[Elsa Garcin]

Hello all,

We had a recent discussion on this recently when I encountered similar issues. 
The workaround suggested by Todd Green worked perfectly for me:

Here is the summary below:

Todd Green suggested installing CCP4 (see message below) with COOT.
It worked for me. There are still some issues (sometimes coot will quit 
unexpectedly; Graphic window will get minimized when using “delete” button if 
you do not keep “delete active”. I am sure I have not yet found all the 
possible issues with it, but it works. Just make sure you save often so you do 
not lose your work too many times.


Original message from Todd Green:

> I installed XQuartz (also Xcode < not sure if necessary for the coot 
> installation) then installed CCP4 with Coot and it worked. Though there are a 
> lot of nuances associated with security setting in the new OS (that I hadn't 
> encountered before). For the ccp4 installation, you have to follow the 
> instructions in the gui window, start cancel start install << that effect to get it to fire thru. I felt it a little clunky, but that is 
> the OS fault. Also that was on a brand new MacBook.

Cheers

Elsa
---
Elsa Garcin
Professor @ AMU, Adjunct Associate Professor @ UMBC
Laboratoire Information Génomique et Structurale (IGS)
Aix-Marseille Université - Campus Luminy, IGS, 163 av. de Luminy, case 901, 
13009 Marseille
email: gar...@igs.cnrs-mrs.fr
Twitter: @amu_eg
---







> On 25 Jan 2023, at 21:47, Nicholas Clark  wrote:
> 
> Mirek,
> 
> Yes, this is a known issue (I read about it previously either here or on the 
> Coot webpage, I can't recall which). 
> 
> The only "workaround" is to check the "keep delete active" box before you 
> begin deleting. It took me a bit to realize this, so I'll share: The window 
> is still open and can be accessed by right clicking on the XQuartz app in the 
> menu bar and selecting the coot window. 
> 
> Best,
> 
> Nick Clark
> 
> On Wed, Jan 25, 2023 at 3:40 PM Cygler, Miroslaw  > wrote:
>> Hi,
>> I just upgrade my Mac to Ventura v13.2 from v12.6.3 and run into issue with 
>> Coot. When I use the delete command it causes the main Coot window 
>> disappearing while other Coot windows stay open. Has anyone had this issue? 
>> Is there a way around it? No such problem on v12.6.3.
>> Best,
>> 
>> 
>> Mirek
>> 
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 
>> 
> 
> -- 
> Nicholas D. Clark (He/Him)
> PhD Candidate
> Malkowski Lab
> University at Buffalo
> Department of Structural Biology
> Jacob's School of Medicine & Biomedical Sciences
> 955 Main Street, RM 5130
> Buffalo, NY 14203
> 
> Cell: 716-830-1908
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 



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Re: [ccp4bb] Coot issue

[Nicholas Clark]

Mirek,

Yes, this is a known issue (I read about it previously either here or on
the Coot webpage, I can't recall which).

The only "workaround" is to check the "keep delete active" box before you
begin deleting. It took me a bit to realize this, so I'll share: The window
is still open and can be accessed by right clicking on the XQuartz app in
the menu bar and selecting the coot window.

Best,

Nick Clark

On Wed, Jan 25, 2023 at 3:40 PM Cygler, Miroslaw 
wrote:

> Hi,
> I just upgrade my Mac to Ventura v13.2 from v12.6.3 and run into issue
> with Coot. When I use the delete command it causes the main Coot window
> disappearing while other Coot windows stay open. Has anyone had this issue?
> Is there a way around it? No such problem on v12.6.3.
> Best,
>
> Mirek
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
>


-- 
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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[ccp4bb] Coot issue

[Cygler, Miroslaw]

Hi,
I just upgrade my Mac to Ventura v13.2 from v12.6.3 and run into issue with 
Coot. When I use the delete command it causes the main Coot window disappearing 
while other Coot windows stay open. Has anyone had this issue? Is there a way 
around it? No such problem on v12.6.3.
Best,

Mirek







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Re: [ccp4bb] Coot on MacOS Ventura

[wangsa tirta Ismaya]

Hi Elsa,
I'm still on high sierra but just updated quartz to the latest version.
Coot also suddenly stopped when I clicked the duck icon on the dock, but I
still can run it using command in the terminal (after going to the coot
folder).
Best regards,
wangsa

On Sat, 31 Dec 2022 at 00:15, Elsa Garcin  wrote:

> Hello all,
> Is it possible to run coot on MacOS Ventura and xquartz version 2.8.4?
> I tried installing coot with homebrew (instructions from Scottlab
> webpage), but was not successful.
> Has anyone figured out how to install it so it runs properly? If so, could
> you please share how you did it?
> Thank you.
> Cheers
> E.
>
> 
>
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> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
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>


-- 

Wangsa Tirta Ismaya
Jakarta, Indonesia



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Re: [ccp4bb] Coot on MacOS Ventura

[Tang, Jiazhi]

Dear Elsa and paul,

Have you solved this problem? Coot and iMosflm used to run on my Mac. However, 
after I updated my MacOS to the most recent version, both Coot and iMosflm 
stopped to work. Could you please let me know if you have solved the MacOS 
problem?

Thanks for your help!

Regards,
Jiazhi


Dr. Jiazhi Tang

School of Pharmacy

University College London

29-39 Brunswick Square

London WC1N 1AX

From: Paul Emsley<mailto:pems...@mrc-lmb.cam.ac.uk>
Sent: 30 December 2022 17:28
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Coot on MacOS Ventura

Hello Elsa,

On 30/12/2022 17:13, Elsa Garcin wrote:
> Is it possible to run coot on MacOS Ventura and xquartz version 2.8.4?
I believe so, but people have reported minimizing window when they try
to do so.
> I tried installing coot with homebrew (instructions from Scottlab webpage),

This is a quite different beast.

>   but was not successful.
I have been trying to work out what has gone wrong and how to fix it.
Still trying.
> Has anyone figured out how to install it so it runs properly? If so, could 
> you please share how you did it?

Mac OSX is not my most frequently-used platoform. I will keep bashing
away at it.

The situation is under discussion in issue 33 on the github page.

Paul.



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Re: [ccp4bb] Coot on MacOS Ventura

[Paul Emsley]

Hello Elsa,

On 30/12/2022 17:13, Elsa Garcin wrote:

Is it possible to run coot on MacOS Ventura and xquartz version 2.8.4?
I believe so, but people have reported minimizing window when they try 
to do so.

I tried installing coot with homebrew (instructions from Scottlab webpage),


This is a quite different beast.


  but was not successful.
I have been trying to work out what has gone wrong and how to fix it. 
Still trying.

Has anyone figured out how to install it so it runs properly? If so, could you 
please share how you did it?


Mac OSX is not my most frequently-used platoform. I will keep bashing 
away at it.


The situation is under discussion in issue 33 on the github page.

Paul.



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[ccp4bb] Coot on MacOS Ventura

[Elsa Garcin]

Hello all,
Is it possible to run coot on MacOS Ventura and xquartz version 2.8.4?
I tried installing coot with homebrew (instructions from Scottlab webpage), but 
was not successful.
Has anyone figured out how to install it so it runs properly? If so, could you 
please share how you did it?
Thank you.
Cheers
E.



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[ccp4bb] COOT on MacOS Ventura

[Maria Fando - STFC UKRI]

Dear MacOS Ventura users,


If you have issues with deleting residues/molecules/etc in COOT. Please try to 
open the delete dialogue, check the box "Keep dialogue active", delete what is 
needed and the close dialogue manually.
There may be other issues with the new macOS, the general recipe is to avoid 
automatically closing dialogues.


Best regards,
Maria Fando

CCP4 Core team
UKRI Science and Technology Facilities Council
Rutherford Appleton Laboratory
Harwell Campus
Didcot, Oxfordshire
OX11 0QX
UK


This email and any attachments are intended solely for the use of the named 
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copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
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Re: [ccp4bb] Coot installation issue

[Paul Emsley]

Coot is not (yet) an official part of brewsci, so the goocanvas update 
bonked coot.


This morning I uninstalled my coot and rebuilt it with YoshitakaMo's 
coot.rb. The second time it worked (i.e. build and installed just fine).


You can see from the patch

https://github.com/brewsci/homebrew-bio/commit/9f57646721018f584dffe700fccbfcb44105304e

that there are a couple of environment variables in the wrapper script. 
They didn't work for me, so I set them on the terminal (and that worked).


They were discovered (if that's the right verb - "ferreted out" or 
"unearthed" maybe?) by Charles Ballard's diligent reading of the 
Inkscape mailing list. For me they increased the fps by 70-100% - which 
makes GTK3 Coot almost usable (on an Intel MacBook Pro, maybe on an M1 
it is *actually* usable).



Paul.


On 30/09/2022 16:17, William G. Scott wrote:

homebrew heavy-handedly wiped out coocanvas v. 2 when upgrading.

I made a temp fix with a sym link as follows:

ln -s /usr/local/Cellar/goocanvas/3.0.0/lib/libgoocanvas-3.0.9.dylib 
/usr/local/lib/libgoocanvas-2.0.9.dylib

your path prefix will be different, but you get the idea.




On Sep 30, 2022, at 7:38 AM, tim smith  wrote:

Hi All,

I am having an issue with installing coot. Here is the outcome when I type coot 
in command line. I am using M1 mac pro. Thank you.

Best regards
Tim


CSI363227 ~ % coot
dyld[11265]: Library not loaded: 
'/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
   Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin'
   Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib' 
(no such file), 
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no such 
file), '/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no 
such file), 
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no such 
file)
/opt/homebrew/bin/coot: line 211: 11265 Abort trap: 6   $coot_bin "$@"
Coot crashed.



CSI363227 ~ % coot --version
dyld[11238]: Library not loaded: 
'/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
   Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin'
   Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib' 
(no such file), 
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no such 
file), '/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no 
such file), 
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no such 
file)
/opt/homebrew/bin/coot: line 211: 11238 Abort trap: 6   $coot_bin "$@"
Coot crashed.

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Re: [ccp4bb] Coot installation issue

[William G. Scott]

homebrew heavy-handedly wiped out coocanvas v. 2 when upgrading.

I made a temp fix with a sym link as follows:

ln -s /usr/local/Cellar/goocanvas/3.0.0/lib/libgoocanvas-3.0.9.dylib 
/usr/local/lib/libgoocanvas-2.0.9.dylib

your path prefix will be different, but you get the idea.



> On Sep 30, 2022, at 7:38 AM, tim smith  wrote:
> 
> Hi All,
> 
> I am having an issue with installing coot. Here is the outcome when I type 
> coot in command line. I am using M1 mac pro. Thank you. 
> 
> Best regards
> Tim
> 
> 
> CSI363227 ~ % coot
> dyld[11265]: Library not loaded: 
> '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
>   Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin'
>   Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib' 
> (no such file), 
> '/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no 
> such file), 
> '/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no such 
> file), '/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' 
> (no such file)
> /opt/homebrew/bin/coot: line 211: 11265 Abort trap: 6   $coot_bin "$@"
> Coot crashed.
> 
> 
> 
> CSI363227 ~ % coot --version
> dyld[11238]: Library not loaded: 
> '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
>   Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin'
>   Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib' 
> (no such file), 
> '/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no 
> such file), 
> '/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no such 
> file), '/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' 
> (no such file)
> /opt/homebrew/bin/coot: line 211: 11238 Abort trap: 6   $coot_bin "$@"
> Coot crashed.
> 
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[ccp4bb] Coot installation issue

[tim smith]

Hi All,

I am having an issue with installing coot. Here is the outcome when I type
coot in command line. I am using M1 mac pro. Thank you.

Best regards
Tim


CSI363227 ~ % coot
dyld[11265]: Library not loaded:
'/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
  Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin'
  Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
(no such file),
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no
such file),
'/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no
such file),
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no
such file)
/opt/homebrew/bin/coot: line 211: 11265 Abort trap: 6   $coot_bin
"$@"
Coot crashed.



CSI363227 ~ % coot --version
dyld[11238]: Library not loaded:
'/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
  Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin'
  Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
(no such file),
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no
such file),
'/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no
such file),
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no
such file)
/opt/homebrew/bin/coot: line 211: 11238 Abort trap: 6   $coot_bin
"$@"
Coot crashed.



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Re: [ccp4bb] Coot RNA bases Mutate

[Paul Emsley]

On 06/08/2022 09:08, Cryo EM wrote:

Hi everyone,

I am trying to mutate modified RNA nucleotide to standard nucleotide 
by coot using "Simple Mutate" button. But it is not working despite 
selecting the correct residue from the standard base list that pop up 
on clicking "simple mutate button". Does anyone and an idea what 
could be the problem? Or is this wrong way to do that?


I am using coot 0.9.8.3 EL (Ccp4) on my Mac.



What does it say in the terminal? - that should give you a clue. My 
guess is that coot can't auto-superpose onto a non-standard nucleotide.


Try "Replace Residue" instead.

Paul



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[ccp4bb] Coot RNA bases Mutate

[Cryo EM]

Hi everyone,

I am trying to mutate modified RNA nucleotide to standard nucleotide by
coot using "Simple Mutate" button. But it is not working despite selecting
the correct residue from the standard base list that pop up on clicking
"simple mutate button". Does anyone and an idea what could be the problem?
Or is this wrong way to do that?

I am using coot 0.9.8.3 EL (Ccp4) on my Mac.

Thanks



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Re: [ccp4bb] Coot sporadically crashes

[Goldman, Adrian]

Hi no - Mac. I’ll have a look next time it occurs. 

Adrian 

Sent from my iPhone

> On 9 Jul 2022, at 14:41, Paul Emsley  wrote:
> 
> On 09/07/2022 12:36, Goldman, Adrian wrote:
>> On a related theme, Paul, I often find that the undo button doesn’t work, 
>> but I can’t figure out why it sometimes does and sometimes doesn’t.  Is this 
>> something to do with how I open .pdb files - that somehow Coot can’t find 
>> the backup files, even though they exist?  What should I do to rectify this 
>> problem?
> 
> 
> There should be some diagnostic message in the console/terminal.
> 
> Are you using Windows?
> 
> Paul.
> 
> 
> 
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Re: [ccp4bb] Coot sporadically crashes

[Paul Emsley]

On 09/07/2022 12:36, Goldman, Adrian wrote:
On a related theme, Paul, I often find that the undo button doesn’t 
work, but I can’t figure out why it sometimes does and sometimes 
doesn’t.  Is this something to do with how I open .pdb files - that 
somehow Coot can’t find the backup files, even though they exist? 
 What should I do to rectify this problem?



There should be some diagnostic message in the console/terminal.

Are you using Windows?

Paul.



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Re: [ccp4bb] Coot sporadically crashes

[Goldman, Adrian]

On a related theme, Paul, I often find that the undo button doesn’t work, but I 
can’t figure out why it sometimes does and sometimes doesn’t.  Is this 
something to do with how I open .pdb files - that somehow Coot can’t find the 
backup files, even though they exist?  What should I do to rectify this problem?

thanks a lot,

Adrian

On 8 Jul 2022, at 18:49, Paul Emsley 
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:


 Is there an option to save the session automatically every 10-15 minutes or so?




And now to actually answer your question:

yes: Edit -> Settings ->Enable Quick-Save Check-pointing... (the default is 30 
seconds)





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Re: [ccp4bb] Coot sporadically crashes

[Oganesyan, Vaheh]

Thank you, Paul!

From: CCP4 bulletin board  On Behalf Of Paul Emsley
Sent: Friday, July 8, 2022 11:50 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot sporadically crashes



 Is there an option to save the session automatically every 10-15 minutes or so?





And now to actually answer your question:

yes: Edit -> Settings ->Enable Quick-Save Check-pointing... (the default is 30 
seconds)







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Re: [ccp4bb] Coot sporadically crashes

[Paul Emsley]

 Is there an option to save the session automatically every 10-15 
minutes or so?







And now to actually answer your question:

yes: Edit -> Settings ->Enable Quick-Save Check-pointing... (the default 
is 30 seconds)






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Re: [ccp4bb] Coot sporadically crashes

[Paul Emsley]

On 08/07/2022 16:30, Oganesyan, Vaheh wrote:


Hi All,

Sorry for posting on CCP4BB.



This is an appropriate venue for such a message.


Coot installed together with latest CCP4 on Win10 crashes time to time 
with no messages/warnings. Is there an option to save the session 
automatically every 10-15 minutes or so?



Coot backs up your model at every edit. Look in the coot-backup 
directory to find the latest update (actually it saves the model before 
the last edit - that's how undo & redo work in Coot).


Additionally there is the "Quick-save-as" function - bound to Ctrl-S - 
it saves the session file and all edited models with versioning (hence 
the "as" part, merely "Quick-save" would imply overwriting your file - 
and I didn't want Coot to do that).



Paul




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[ccp4bb] Coot sporadically crashes

[Oganesyan, Vaheh]

Hi All,

Sorry for posting on CCP4BB.

Coot installed together with latest CCP4 on Win10 crashes time to time with no 
messages/warnings. Is there an option to save the session automatically every 
10-15 minutes or so?

Thank you.

Vaheh



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Re: [ccp4bb] coot 0.9.8.1 and phenix mtz files

[Paul Emsley]

On 27/05/2022 19:22, Jan Abendroth wrote:

Hi all,
not sure if this appropriate for this BB, since right at the interface 
between CCP4, Coot and Phenix.


I wonder if someone else also experiences these issues after upgrading 
to CCP4 8.0 (or 8.001) and with that to Coot 0.9.8.1. This happens 
both on OSX and windows.


  * coot /mydata/.pdb /mydata/.mtz


coot --pdb mydata.pdb --auto mydata.mtz

I removed the globbed data files for style reasons (Bernhard didn't 
think that was a good idea).



  * will only open up the PDB but ont the mtz file. The latter can be
opened via the Load menu.


Yes.


  * The Coot window launched from the phenix gui does not displany the
pdb or the map.


That doesn't sound good. I don't know what's going on there - I'd need 
to see the console log.



Paul.




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[ccp4bb] coot 0.9.8.1 and phenix mtz files

[Jan Abendroth]

Hi all,
not sure if this appropriate for this BB, since right at the interface
between CCP4, Coot and Phenix.

I wonder if someone else also experiences these issues after upgrading to
CCP4 8.0 (or 8.001) and with that to Coot 0.9.8.1. This happens both on OSX
and windows.

   - coot *mydata*.pdb *mydata*.mtz
   will only open up the PDB but ont the mtz file. The latter can be opened
   via the Load menu.
   - The Coot window launched from the phenix gui does not displany the pdb
   or the map.

Any pointers would be appreciated.

Thanks!
Jan

-- 
Jan Abendroth
UCB BioSciences
Seattle / Bainbridge Island, WA, USA
home: jan.abendr...@gmail.com
work: jan.abendr...@ucb.com



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Re: [ccp4bb] Coot and Pandda questions

[Paul Emsley]

On 06/04/2022 07:05, Laurent wrote:

Good morning (French time…)

Two unrelated questions…
Using Coot, I would like to define some key binding… How can I find 
the command that is actually issued from an option in the 
« calculate » menu ? I would like to define a key binding for the 
function « NCS Tools -> Update NCS ghost using local match ».



This is what the coot source code says:

--

def update_ncs_ghosts_by_local_sphere():
    """Update NCS ghosts based on local environment (residues within 6A of
    (and including) the active residue).

    Typically one would bind this function to a key."""

--


add_key_binding("NCS Matrix Update", "U", lambda: 
update_ncs_ghosts_by_local_sphere())


You will need to use the ncs module in the new version.


Paul.



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Re: [ccp4bb] Coot and Pandda questions

[Tobias Krojer]

Hi Laurent,

I wrote a minimalistic version of pandda.inspect which works with any version 
of ccp4 or operating system. Event maps etc. need to be converted to mtz files 
beforehand, but suitable scripts and documentation are included in the Github 
repository below:

https://github.com/tkrojer/pandda_inspect_tools

Let me know in case you have any problems.

Best,
Tobias


From: CCP4 bulletin board  on behalf of Laurent 

Reply to: Laurent 
Date: Wednesday, 6 April 2022 at 08:05
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] Coot and Pandda questions

Good morning (French time…)

Two unrelated questions…
Using Coot, I would like to define some key binding… How can I find the command 
that is actually issued from an option in the « calculate » menu ? I would like 
to define a key binding for the function « NCS Tools -> Update NCS ghost using 
local match ».

About Pandda… Nick Pearce helped me about my previous request about pandda… I 
am now able to run pandda_analysis, but pandda_inspect still issues an error. I 
would therefore like to install ccp4 7.0 instead of the ccp4 7.1 (Pandda web 
site states that 7.0 should work). Is it possible to find old CCP4 versions to 
download and install (I am working with MacOS)?

Thanks for your help,

Laurent

[Image removed by sender. logo-ipbs]
Laurent Maveyraud
Professor of Biophysics | University of Toulouse | Structural Biophysics Team

Doctoral School Biology - Health - Biotechnologies

[Image removed by sender.]+33 5 61 17 54 35 | +33 6 46 04 21 11 | 
laurent.maveyr...@ipbs.fr<mailto:laurent.maveyr...@ipbs.fr> | [Image removed by 
sender.] L. Maveyraud<https://fr.linkedin.com/in/laurent-maveyraud-8b394a5> | 
[Image removed by sender.] L. Maveyraud<https://orcid.org/-0003-4610-8319>

[Image removed by sender.]UMR5089 | CNRS - UT3 | 205 Route de Narbonne BP 64182 
- 31077 Toulouse Cedex 4

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<https://www.ipbs.fr/structural-biophysics> | pict.ipbs.fr 
<https://cribligand.ipbs.fr>

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[ccp4bb] Coot and Pandda questions

[Laurent]

Good morning (French time…)

Two unrelated questions…
Using Coot, I would like to define some key binding… How can I find the command 
that is actually issued from an option in the « calculate » menu ? I would like 
to define a key binding for the function « NCS Tools -> Update NCS ghost using 
local match ». 

About Pandda… Nick Pearce helped me about my previous request about pandda… I 
am now able to run pandda_analysis, but pandda_inspect still issues an error. I 
would therefore like to install ccp4 7.0 instead of the ccp4 7.1 (Pandda web 
site states that 7.0 should work). Is it possible to find old CCP4 versions to 
download and install (I am working with MacOS)?

Thanks for your help,

Laurent

 
Laurent Maveyraud
Professor of Biophysics | University of Toulouse | Structural Biophysics Team
Doctoral School Biology - Health - Biotechnologies
+33 5 61 17 54 35 | +33 6 46 04 21 11 | laurent.maveyr...@ipbs.fr 
 | L. Maveyraud 
 | L. Maveyraud 

 UMR5089 | CNRS - UT3 | 205 Route de Narbonne BP 64182 - 31077 Toulouse Cedex 4
 ipbs.fr  | Team Website  
| pict.ipbs.fr   
      @IpbsToulouse  
  ipbs.cnrs 
 




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Re: [ccp4bb] Coot 1

[Harry Powell - CCP4BB]

Isn’t that what we all say every year on the day after March finishes?

Harry

> On 1 Apr 2022, at 23:46, Paul Emsley  wrote:
> 
> That, for the record, is more or less what Ralf said 18 years ago.
> On 01/04/2022 23:38, Pavel Afonine wrote:
>> It's April 1st today, isn't it? -;)
>> 
>> 
>> On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley  wrote:
>> Coot 1
>> 
>> 18 years after the release of Coot 0 it's time that I actually released 
>> Coot 1.
>> 
> 
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> 



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[ccp4bb] RES: [ccp4bb] Coot 1

[Rafael Marques]

If Paul had said that there is also a Windows version I would be sure that it 
was April fools’ joke. I can’t wait to use it 😊

Best


Rafael Marques da Silva
Mestrando em Física Biomolecular
Universidade de São Paulo

Bacharel em Ciências Biológicas
Universidade Federal de São Carlos

phone: +55 16 99766-0021

   "A sorte acompanha uma mente bem treinada"


De: Jurgen Bosch<mailto:jxb...@case.edu>
Enviado:sexta-feira, 1 de abril de 2022 19:59
Para: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Assunto: Re: [ccp4bb] Coot 1

Yay!!

I can now blend it with blender.

Jürgen
__
Jürgen Bosch, PhD, MBA
Center for Global Health & Diseases
Case Western Reserve University

https://www.linkedin.com/in/jubosch/

CEO & Co-Founder at InterRayBio, LLC


Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology


On Apr 1, 2022, at 18:46, Paul Emsley 
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:


That, for the record, is more or less what Ralf said 18 years ago.
On 01/04/2022 23:38, Pavel Afonine wrote:
It's April 1st today, isn't it? -;)


On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley 
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
Coot 1

18 years after the release of Coot 0 it's time that I actually released
Coot 1.



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Re: [ccp4bb] Coot 1

[Jurgen Bosch]

Yay!!

I can now blend it with blender.

Jürgen

__
Jürgen Bosch, PhD, MBA
Center for Global Health & Diseases
Case Western Reserve University

https://www.linkedin.com/in/jubosch/

CEO & Co-Founder at InterRayBio, LLC

Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology

On Apr 1, 2022, at 18:46, Paul Emsley  wrote:



That, for the record, is more or less what Ralf said 18 years ago.
On 01/04/2022 23:38, Pavel Afonine wrote:

It's April 1st today, isn't it? -;)


On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley 
wrote:

> Coot 1
>
> 18 years after the release of Coot 0 it's time that I actually released
> Coot 1.
>
>
--

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Re: [ccp4bb] Coot 1

[Paul Emsley]

That, for the record, is more or less what Ralf said 18 years ago.

On 01/04/2022 23:38, Pavel Afonine wrote:

It's April 1st today, isn't it? -;)


On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley  
wrote:


Coot 1

18 years after the release of Coot 0 it's time that I actually
released
Coot 1.





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Re: [ccp4bb] Coot 1

[Pavel Afonine]

It's April 1st today, isn't it? -;)


On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley 
wrote:

> Coot 1
>
> 18 years after the release of Coot 0 it's time that I actually released
> Coot 1.
>
> Coot 1 is a major change beyond Coot 0. It has required a lot of writing
> and rewriting [1]
> and has been the preponderance of my work since 2017. I have had to
> learn how to program
> graphics from scratch using the new style. Much of the GUI internals has
> been
> rewritten [2].
>
> My experience with 0.9 was that I sat on it, bug-fixing for a long time,
> releasing it
> too late. I don't want to repeat that mistake. So here we are, there's a
> lot of good new
> stuff in Coot 1, but it's not as slick as it might be (or will become).
>
>o Update graphics to use OpenGL 3.3
>o Update Python to use version 3.9
>o Update GTK+ to use version 3
>
> While many of the features that were available in 0.9.x have been
> reworked or
> re-implemented, there are some gaps. Dropped features include
> Cross-hairs, Stereo, Pisa
> interface, built-in key-bindings, NCS Ghosts, Edit Phi/Psi,
> anti-aliasing, Kleywegt
> plots, the clipping dialog, Chemical Feature Clustering,
> Dynamically-Transformed/NCS
> Maps, LSQ plane distances, dynamic distances, CABLAM-markup, the test
> suite,
> user-defined colour schemes, anisotropic atoms, CURLEW, Scheme GUI
> scripting,
> Skeletonization and Baton-Building.
>
> "So, is there anything that _does_ work?" - you might ask...
>
> The GUI has been updated, I have tried to cut down on the number of
> dialogs, the Real
> Space Refinement in particular has seen quite a lot of work. The GUI now
> uses dark mode
> if the theme is installed [3]. Several menu items have been relocated.
> More menus are now
> alphabetically ordered [4].
>
> The graphics is, by default, now based on triangles instead of lines
> which affords a
> more pleasing representation (density maps can be represented using both
> modes) and one
> can have a more expeditious if not pleasant experience with a fast
> graphics card and a
> big screen. The various graphics effects and filters can be tailored to
> some extent by
> changing the configuration using the GUI or by editing/replacing the
> shaders.
> Full-screen mode is now an option [5].
>
> Overall, the GUI has only had light testing. At the moment, it's
> probably best to
> avoid closing dialogs using the window manager. The "OK" button now
> appears after the
> "Cancel" button in dialogs.
>
> Python scripting now has uses a history from previous sessions and the
> functions need
> to be used with namespaces/modules (e.g. "coot", or "coot_utils"). Coot
> (or coot) is
> now a module that can be imported into python.
>
> This build compiles with the RDKit and optionally MoleculestoTriangles
> from Martin Noble.
>
> The map and the model can now be exported to glTF files (for use in
> Blender and other
> 3D modelling software).
>
> The build script for Coot 1, called build-it-3-3 can be found in the
> "Build from Scratch"
> menu on the web page (you will need to have already installed cmake and
> Gtk+). The catch
> though is that (at least in my hands) Python and friends are
> frustratingly difficult to
> install, so it's possible/likely that the build script won't work.
> Likewise,
> the script doesn't work for Mac OS either. But it is currently the best
> method to get
> binaries so I will support it if you try it [6]. (Homebrew might be
> another method.)
>
> Bernhard Lohkamp has been working on the WinCoot version - I will defer
> WinCoot
> questions to him.
>
> Mac Coot is now native (no X11/XQuartz needed). I would be interested to
> see how a
> natively-compiled [7] version works on an M1 Max processor [8,9].
>
> Judging from previous experience, a few rapid iterations of bug-fix
> releases will be
> needed. After this, the version numbers will become sane - it's my plan
> to release a new
> major version every year or so.
>
>
> https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.tar.gz
>
> Normally I don't cross-post releases, but this one I thought I should.
>
>
> [1] new as in OpenGL 3.3 or later - using shaders - I don't mean Vulkan
> (that's for the
>  future)
> [2] the patch from the 0.9.x version is 285k lines
> [3] I recommend it
> [4] rather than chronologically
> [5] double-tap Esc key (the first time) to revert to standard display
> [6] I have be working with CCP4 collaborators to use their system to
> build Coot binaries.
>  Hopefully the binaries will be available stand-alone, as well as
> integrated into
>  the CCP4 Suite via that method
> [7] so that's a different meaning of "native"
> [8] the little testing I have done on a recent intel MacBook Pro shows
> unimpressive
>  performance (Iris graphics, retina display)
> [9] Thanks to my Mac-using colleagues for their feedback.
>
> 
>
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[ccp4bb] Coot 1

[Paul Emsley]

Coot 1

18 years after the release of Coot 0 it's time that I actually released 
Coot 1.


Coot 1 is a major change beyond Coot 0. It has required a lot of writing 
and rewriting [1]
and has been the preponderance of my work since 2017. I have had to 
learn how to program
graphics from scratch using the new style. Much of the GUI internals has 
been

rewritten [2].

My experience with 0.9 was that I sat on it, bug-fixing for a long time, 
releasing it
too late. I don't want to repeat that mistake. So here we are, there's a 
lot of good new

stuff in Coot 1, but it's not as slick as it might be (or will become).

  o Update graphics to use OpenGL 3.3
  o Update Python to use version 3.9
  o Update GTK+ to use version 3

While many of the features that were available in 0.9.x have been 
reworked or
re-implemented, there are some gaps. Dropped features include 
Cross-hairs, Stereo, Pisa
interface, built-in key-bindings, NCS Ghosts, Edit Phi/Psi, 
anti-aliasing, Kleywegt
plots, the clipping dialog, Chemical Feature Clustering, 
Dynamically-Transformed/NCS

Maps, LSQ plane distances, dynamic distances, CABLAM-markup, the test suite,
user-defined colour schemes, anisotropic atoms, CURLEW, Scheme GUI 
scripting,

Skeletonization and Baton-Building.

"So, is there anything that _does_ work?" - you might ask...

The GUI has been updated, I have tried to cut down on the number of 
dialogs, the Real
Space Refinement in particular has seen quite a lot of work. The GUI now 
uses dark mode
if the theme is installed [3]. Several menu items have been relocated. 
More menus are now

alphabetically ordered [4].

The graphics is, by default, now based on triangles instead of lines 
which affords a
more pleasing representation (density maps can be represented using both 
modes) and one
can have a more expeditious if not pleasant experience with a fast 
graphics card and a
big screen. The various graphics effects and filters can be tailored to 
some extent by
changing the configuration using the GUI or by editing/replacing the 
shaders.

Full-screen mode is now an option [5].

Overall, the GUI has only had light testing. At the moment, it's 
probably best to
avoid closing dialogs using the window manager. The "OK" button now 
appears after the

"Cancel" button in dialogs.

Python scripting now has uses a history from previous sessions and the 
functions need
to be used with namespaces/modules (e.g. "coot", or "coot_utils"). Coot 
(or coot) is

now a module that can be imported into python.

This build compiles with the RDKit and optionally MoleculestoTriangles 
from Martin Noble.


The map and the model can now be exported to glTF files (for use in 
Blender and other

3D modelling software).

The build script for Coot 1, called build-it-3-3 can be found in the 
"Build from Scratch"
menu on the web page (you will need to have already installed cmake and 
Gtk+). The catch
though is that (at least in my hands) Python and friends are 
frustratingly difficult to

install, so it's possible/likely that the build script won't work. Likewise,
the script doesn't work for Mac OS either. But it is currently the best 
method to get
binaries so I will support it if you try it [6]. (Homebrew might be 
another method.)


Bernhard Lohkamp has been working on the WinCoot version - I will defer 
WinCoot

questions to him.

Mac Coot is now native (no X11/XQuartz needed). I would be interested to 
see how a

natively-compiled [7] version works on an M1 Max processor [8,9].

Judging from previous experience, a few rapid iterations of bug-fix 
releases will be
needed. After this, the version numbers will become sane - it's my plan 
to release a new

major version every year or so.

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.tar.gz

Normally I don't cross-post releases, but this one I thought I should.


[1] new as in OpenGL 3.3 or later - using shaders - I don't mean Vulkan 
(that's for the

    future)
[2] the patch from the 0.9.x version is 285k lines
[3] I recommend it
[4] rather than chronologically
[5] double-tap Esc key (the first time) to revert to standard display
[6] I have be working with CCP4 collaborators to use their system to 
build Coot binaries.
    Hopefully the binaries will be available stand-alone, as well as 
integrated into

    the CCP4 Suite via that method
[7] so that's a different meaning of "native"
[8] the little testing I have done on a recent intel MacBook Pro shows 
unimpressive

    performance (Iris graphics, retina display)
[9] Thanks to my Mac-using colleagues for their feedback.



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Re: [ccp4bb] Coot on Mac OSX Monterey

[Nicholas Clark]

Dr. Pearl,

I have used the pre-built installer here:
http://scottlab.ucsc.edu/xtal/wiki/index.php/Stand-Alone_Coot

This worked  on my Mac running Monterey OS with an intel i7.

Best regards,

Nick Clark

On Fri, Feb 11, 2022 at 4:53 PM Laurence Pearl 
wrote:

> Does anyone know where I can download a pre-built Coot that will work on
> OS X Monterey  (12.2) on an iMac with an Intel i7 ?
>
> The packages I can find all fail at the File finder which comes up blank.
> X11 latest is installed.
>
> Laurence
>
>
> 
> Laurence H. Pearl PhD FRS FMedSci
>
> Professor of Structural Biology
> Genome Damage and Stability Centre
> School of Life Sciences, University of Sussex
> Brighton, BN1 9RQ, UK
>
> +44-(0)1273 678349
>
> 
> "Live Modestly and do Serious Things .. "
> - Dorothy Crowfoot Hodgkin
>
> 
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
>
-- 
Nicholas D. Clark
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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Re: [ccp4bb] Coot on Mac OSX Monterey

[Paul Emsley]

On 11/02/2022 21:53, Laurence Pearl wrote:
Does anyone know where I can download a pre-built Coot that will work 
on OS X Monterey  (12.2) on an iMac with an Intel i7 ?


The packages I can find all fail at the File finder which comes up 
blank. X11 latest is installed.


Not an answer to your question but a question about the bug: Classic or 
Modern? Try the other one just to check.


Paul.



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[ccp4bb] Coot on Mac OSX Monterey

[Laurence Pearl]

Does anyone know where I can download a pre-built Coot that will work on OS X 
Monterey  (12.2) on an iMac with an Intel i7 ?

The packages I can find all fail at the File finder which comes up blank. X11 
latest is installed.

Laurence


Laurence H. Pearl PhD FRS FMedSci

Professor of Structural Biology
Genome Damage and Stability Centre
School of Life Sciences, University of Sussex
Brighton, BN1 9RQ, UK

+44-(0)1273 678349

"Live Modestly and do Serious Things .. "
- Dorothy Crowfoot Hodgkin







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Re: [ccp4bb] COOT FLEV error

[Xavier Brazzolotto]

This is probably a FLEV specific issue.
Have you tried external software such as LigPlot+ or Schrodinger’s Maestro to 
see if they can better handle the modified residue ?

> Le 27 janv. 2022 à 01:03, Sergio A. Sampieri  a écrit :
> 
> Greetings all,
> 
> Sorry for the naive question, but I'm having problems trying to FLEV a 
> modified residue in COOT.
> 
> I have modeled a modified CYS into an structure following these steps:
> 
> Generate a SMILES string for L-cysteine bonded the modification.  
> C1=CC=C(C=C1)C(=O)SCC(C(O)=O)N. 
> https://pubchem.ncbi.nlm.nih.gov/compound/262741 
> 
> Input the SMILES string to PHENIX eLBOW using the graphical user interface 
> with quantum optimization enabled to generate restraints (.cif) and 
> coordinates (.pdb).
> Used the eLBOW graphical user interface to change the atom names for the 
> backbone atoms of the modified cysteine to the standard ones for amino acids 
> (N, CA, C, O, OXT, CB), (additional atom names remain as they are)
> Save the new coordinates and restraints.
>  Modified the cif file, especially the definition as a L-peptide and not as 
> Ligand.
> Move the modified cysteine saved in step 5 into the density using Coot.
> Delete the extra OXT atom of the cysteine carboxylate and save the 
> coordinates of the modified Cys.
> In coot "replace residue" CYS with the Modified CYS ("MCY").
> Refine the structure.
> Open the refined model in COOT, and the cif dictionary generated.
> 
> But when trying to FLEV the modified residue I get the next errors:
> 
> WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for 
> atom name: " OXT" ele : O:
> Failed to get atom index for atom name " OXT"" in residue of type MCY [spec: 
> 1 "A" 165 ""]
> [17:43:23] Explicit valence for atom # 12 O, 3, is greater than permitted
> std::exception
> WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for 
> atom name: " OXT" ele : O:
> Failed to get atom index for atom name " OXT"" in residue of type MCY [spec: 
> 1 "A" 165 ""]
> [17:43:23] Explicit valence for atom # 12 O, 3, is greater than permitted
> std::exception
> WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for 
> atom name: " OXT" ele : O:
> ERROR:: (runtime error) in fle_view_with_rdkit(): Failed to get atom index 
> for atom name " OXT"" in residue of type MCY [spec: 1 "A" 165 ""]
> 
> Also tried to modify the atom names in the CIF file but still get the same 
> error (with different atom numbers instead of OXT, O09 and so):
> 
> WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for 
> atom name: " C10" ele : C:
> ERROR:: (runtime error) in fle_view_with_rdkit(): Failed to get atom index 
> for atom name " C10"" in residue of type MCY [spec: 1 "A" 165 ""]
> 
> Any help or ideas would be greatly appreciated, thanks in advance, stay safe!
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 
> 
Xavier Brazzolotto, PhD
Département de Toxicologie et Risques Chimiques
Institut de Recherche Biomédicale des Armées
BP 73
91223 Brétigny sur Orge
France

Phone   +33 (0) 1 78 65 14 00
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[ccp4bb] COOT FLEV error

[Sergio A. Sampieri]

Greetings all,

Sorry for the naive question, but I'm having problems trying to FLEV a
modified residue in COOT.

I have modeled a modified CYS into an structure following these steps:


   1. Generate a SMILES string for L-cysteine bonded the modification.
   C1=CC=C(C=C1)C(=O)SCC(C(O)=O)N.
   https://pubchem.ncbi.nlm.nih.gov/compound/262741
   2. Input the SMILES string to PHENIX eLBOW using the graphical user
   interface with quantum optimization enabled to generate restraints (.cif)
   and coordinates (.pdb).
   3. Used the eLBOW graphical user interface to change the atom names for
   the backbone atoms of the modified cysteine to the standard ones for amino
   acids (N, CA, C, O, OXT, CB), (additional atom names remain as they are)
   4. Save the new coordinates and restraints.
   5.  Modified the cif file, especially the definition as a L-peptide and
   not as Ligand.
   6. Move the modified cysteine saved in step 5 into the density using
   Coot.
   7. Delete the extra OXT atom of the cysteine carboxylate and save the
   coordinates of the modified Cys.
   8. In coot "replace residue" CYS with the Modified CYS ("MCY").
   9. Refine the structure.
   10. Open the refined model in COOT, and the cif dictionary generated.


But when trying to FLEV the modified residue I get the next errors:

WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for
atom name: " OXT" ele : O:
Failed to get atom index for atom name " OXT"" in residue of type MCY
[spec: 1 "A" 165 ""]
[17:43:23] Explicit valence for atom # 12 O, 3, is greater than permitted
std::exception
WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for
atom name: " OXT" ele : O:
Failed to get atom index for atom name " OXT"" in residue of type MCY
[spec: 1 "A" 165 ""]
[17:43:23] Explicit valence for atom # 12 O, 3, is greater than permitted
std::exception
WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for
atom name: " OXT" ele : O:
ERROR:: (runtime error) in fle_view_with_rdkit(): Failed to get atom index
for atom name " OXT"" in residue of type MCY [spec: 1 "A" 165 ""]

Also tried to modify the atom names in the CIF file but still get the same
error (with different atom numbers instead of OXT, O09 and so):

WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for
atom name: " C10" ele : C:
ERROR:: (runtime error) in fle_view_with_rdkit(): Failed to get atom index
for atom name " C10"" in residue of type MCY [spec: 1 "A" 165 ""]

Any help or ideas would be greatly appreciated, thanks in advance, stay
safe!



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[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] COOT RSR

[Schreuder, Herman /DE]

Hi Paul,

For me, dummy waters are waters placed in very early models, where it is not 
yet clear whether the density belongs to a water, a rearranged side chain or a 
ligand. In the course of the refinement process, it becomes clear to which 
category the density really belongs. Especially for larger rebuilding, I find 
it helpful to use such waters.

A real water is for me a nicely defined, hydrogen bonded water in a 
well-refined structure. However, in this stage one does not need any RSR 
anymore.

Best regards,
Herman

Von: CCP4 bulletin board  Im Auftrag von Paul Emsley
Gesendet: Montag, 22. November 2021 22:09
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [ccp4bb] COOT RSR




What's the difference between a dummy water and a real one?

Paul


On 22/11/2021 14:34, Schreuder, Herman /DE wrote:
Dear Paul,

I agree with Oliver and Norbert, in the early phases of refinement, when a lot 
of rebuilding has to be done, the coot RSR is not very helpful and in general I 
leave it to buster do refine the rebuilt regions. Knowing now that (dummy) 
waters may be the culprit, I will remove them. However, it would be much more 
convenient if the  repulsions with water molecules would not be taken into 
account.

Thank you,
Herman

Von: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK> 
Im Auftrag von Norbert Straeter
Gesendet: Sonntag, 21. November 2021 12:24
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: Re: [ccp4bb] COOT RSR

Dear Paul,

I agree to Oliver. In situations where you want to fit a "dummy water" to a 
difference density peak (to determine distances to the environment) or try the 
fit of solvent molecules to yet unexplained density, it would be nice to first 
obtain an optimal fit and next think about the environment and possible bumps 
and partial occupancy. I had this problem already several times, that I could 
not get a good fit because of the model repulsions. Even if two partially 
occupied waters are at closed distance the repulsions appear to be active in 
RSR. It is not about the old method being better.

Best wishes,

Norbert



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Re: [ccp4bb] AW: [ccp4bb] COOT RSR

[Norbert Straeter]

Dear Paul,

with "dummy water" I refer to a water molecule, which I place at the center of 
a (usually positive) difference electron density peak to be able to measure the 
distances to the environment and decide, what the density actually might be. I 
do that quite often. It could also be any other atom, of course.

Best wishes,

Norbert



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Re: [ccp4bb] AW: [ccp4bb] COOT RSR

[Paul Emsley]

What's the difference between a dummy water and a real one?

Paul


On 22/11/2021 14:34, Schreuder, Herman /DE wrote:


Dear Paul,

I agree with Oliver and Norbert, in the early phases of refinement, 
when a lot of rebuilding has to be done, the coot RSR is not very 
helpful and in general I leave it to buster do refine the rebuilt 
regions. Knowing now that (dummy) waters may be the culprit, I will 
remove them. However, it would be much more convenient if the 
repulsions with water molecules would not be taken into account.


Thank you,

Herman

*Von:* CCP4 bulletin board  *Im Auftrag von 
*Norbert Straeter

*Gesendet:* Sonntag, 21. November 2021 12:24
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* Re: [ccp4bb] COOT RSR

Dear Paul,

I agree to Oliver. In situations where you want to fit a "dummy water" 
to a difference density peak (to determine distances to the 
environment) or try the fit of solvent molecules to yet unexplained 
density, it would be nice to first obtain an optimal fit and next 
think about the environment and possible bumps and partial occupancy. 
I had this problem already several times, that I could not get a good 
fit because of the model repulsions. Even if two partially occupied 
waters are at closed distance the repulsions appear to be active in 
RSR. It is not about the old method being better.


Best wishes,

Norbert



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[ccp4bb] AW: [ccp4bb] COOT RSR

[Schreuder, Herman /DE]

Dear Paul,

I agree with Oliver and Norbert, in the early phases of refinement, when a lot 
of rebuilding has to be done, the coot RSR is not very helpful and in general I 
leave it to buster do refine the rebuilt regions. Knowing now that (dummy) 
waters may be the culprit, I will remove them. However, it would be much more 
convenient if the  repulsions with water molecules would not be taken into 
account.

Thank you,
Herman

Von: CCP4 bulletin board  Im Auftrag von Norbert Straeter
Gesendet: Sonntag, 21. November 2021 12:24
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] COOT RSR

Dear Paul,

I agree to Oliver. In situations where you want to fit a "dummy water" to a 
difference density peak (to determine distances to the environment) or try the 
fit of solvent molecules to yet unexplained density, it would be nice to first 
obtain an optimal fit and next think about the environment and possible bumps 
and partial occupancy. I had this problem already several times, that I could 
not get a good fit because of the model repulsions. Even if two partially 
occupied waters are at closed distance the repulsions appear to be active in 
RSR. It is not about the old method being better.

Best wishes,

Norbert



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Re: [ccp4bb] COOT RSR

[Norbert Straeter]

Dear Paul,

I agree to Oliver. In situations where you want to fit a "dummy water" to a 
difference density peak (to determine distances to the environment) or try the 
fit of solvent molecules to yet unexplained density, it would be nice to first 
obtain an optimal fit and next think about the environment and possible bumps 
and partial occupancy. I had this problem already several times, that I could 
not get a good fit because of the model repulsions. Even if two partially 
occupied waters are at closed distance the repulsions appear to be active in 
RSR. It is not about the old method being better.

Best wishes,

Norbert



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Re: [ccp4bb] COOT RSR

[Paul Emsley]

On 20/11/2021 11:31, Weiergräber, Oliver H. wrote:

Dear Paul,

>From my experience, I agree that an option to inactivate the anti-bumping 
restraints in RSR would be very useful.
To be honest, my impression is that it tends to be a hindrance rather than 
helping, at least in cases where extensive rebuilding is required.

Best regards
Oliver



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Paul Emsley 
[pems...@mrc-lmb.cam.ac.uk]
Sent: 20 November 2021 11:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] COOT RSR

On 20/11/2021 09:42, Matthew Snee wrote:

I had a bit of trouble getting used to the new COOT real space refine... it 
took me an embarrassingly long time to work out that there is nothing wrong 
with the fitting/restraints..

You are not alone in finding Coot's RSR unintuitive (at least initially).

it just doesn't seem to allow clashes with parts of the model that aren't in 
the selected RSR zone even when the fit would be perfect.

That's right.

To help out, I have added dynamic interaction analysis: use CURLEW to download the 
Refinement Tools and then use Refine -> Contact Dots On. Now when you use RSR 
you can see what's bumping into what (I usually have this feature turned on).

Is there a quick way to toggle this feature on/off?
No.
It seems like a nice addition, but it can cause problems where one incorrect 
part of a partially built model prevents me building another, or for cases 
where two different residues/ligands occupy the same space at partial occupancy.


The solution is to move the wrong parts of the model out of the way first - or 
include them in the set of refining residues.

Paul.


Hello Oliver,

I am willing to change the real space refinement if I see a reason to do 
so.  If you can show me an example where the old method is easier then 
I'd be interested to watch it.


Paul.



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Re: [ccp4bb] COOT RSR

[Weiergräber , Oliver H .]

Dear Paul,

>From my experience, I agree that an option to inactivate the anti-bumping 
>restraints in RSR would be very useful.
To be honest, my impression is that it tends to be a hindrance rather than 
helping, at least in cases where extensive rebuilding is required.

Best regards
Oliver

==
  PD Dr. Oliver H. Weiergräber
  Institut für Biologische Informationsprozesse
  IBI-7: Strukturbiochemie
  Tel.: +49 2461 61-2028
  Fax: +49 2461 61-9540
==



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Paul Emsley 
[pems...@mrc-lmb.cam.ac.uk]
Sent: 20 November 2021 11:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] COOT RSR

On 20/11/2021 09:42, Matthew Snee wrote:

I had a bit of trouble getting used to the new COOT real space refine... it 
took me an embarrassingly long time to work out that there is nothing wrong 
with the fitting/restraints..

You are not alone in finding Coot's RSR unintuitive (at least initially).

it just doesn't seem to allow clashes with parts of the model that aren't in 
the selected RSR zone even when the fit would be perfect.

That's right.

To help out, I have added dynamic interaction analysis: use CURLEW to download 
the Refinement Tools and then use Refine -> Contact Dots On. Now when you use 
RSR you can see what's bumping into what (I usually have this feature turned 
on).

Is there a quick way to toggle this feature on/off?
No.
It seems like a nice addition, but it can cause problems where one incorrect 
part of a partially built model prevents me building another, or for cases 
where two different residues/ligands occupy the same space at partial occupancy.


The solution is to move the wrong parts of the model out of the way first - or 
include them in the set of refining residues.

Paul.




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Prof. Dr. Frauke Melchior





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Re: [ccp4bb] COOT RSR

[Paul Emsley]

On 20/11/2021 09:42, Matthew Snee wrote:


I had a bit of trouble getting used to the new COOT real space 
refine... it took me an embarrassingly long time to work out that 
there is nothing wrong with the fitting/restraints..


You are not alone in finding Coot's RSR unintuitive (at least initially).

it just doesn't seem to allow clashes with parts of the model that 
aren't in the selected RSR zone even when the fit would be perfect.


That's right.

To help out, I have added dynamic interaction analysis: use CURLEW to 
download the Refinement Tools and then use Refine -> Contact Dots On. 
Now when you use RSR you can see what's bumping into what (I usually 
have this feature turned on).




Is there a quick way to toggle this feature on/off?

No.
It seems like a nice addition, but it can cause problems where one 
incorrect part of a partially built model prevents me building 
another, or for cases where two different residues/ligands occupy the 
same space at partial occupancy.


The solution is to move the wrong parts of the model out of the way 
first - or include them in the set of refining residues.


Paul.




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[ccp4bb] COOT RSR

[Matthew Snee]

Hi all

I had a bit of trouble getting used to the new COOT real space refine... it 
took me an embarrassingly long time to work out that there is nothing wrong 
with the fitting/restraints.. it just doesn't seem to allow clashes with parts 
of the model that aren't in the selected RSR zone even when the fit would be 
perfect.

Is there a quick way to toggle this feature on/off?
It seems like a nice addition, but it can cause problems where one incorrect 
part of a partially built model prevents me building another, or for cases 
where two different residues/ligands occupy the same space at partial occupancy.

Best wishes

Matthew.

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[ccp4bb] coot and chimera remote access problem

[Victor Banerjee]

Hi,
I am trying to open coot remote using ssh -X or -Y but this is what I am 
getting 

[vbanerjee@c110279 ~]$ coot
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: 
/opt/xtal/ccp4-7.1/lib/data/monomers/
There are 244 data in /opt/xtal/ccp4-7.1/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/ALA.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/ASP.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/ASN.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/c/CYS.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/GLN.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/GLY.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/GLU.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/p/PHE.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/h/HIS.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/i/ILE.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/l/LYS.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/l/LEU.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/m/MET.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/m/MSE.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/p/PRO.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/ARG.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/s/SER.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/t/THR.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/v/VAL.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/t/TRP.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/t/TYR.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/p/PO4.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/s/SO4.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/GOL.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/c/CIT.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/e/EDO.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/A.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/c/C.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/G.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/u/U.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DA.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DC.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DG.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DT.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/h/HOH.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/n/NA.cif
Spacegroup: P 1
The program 'coot-bin' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadValue (integer parameter out of range for operation)'.
  (Details: serial 321 error_code 2 request_code 149 minor_code 3)
  (Note to programmers: normally, X errors are reported asynchronously;
   that is, you will receive the error a while after causing it.
   To debug your program, run it with the --sync command line
   option to change this behavior. You can then get a meaningful
   backtrace from your debugger if you break on the gdk_x_error() function.)
. -- Coot crashed - trying to diagnose -
ldd -r on guile gives:
linux-vdso.so.1 =>  (0x7fd0fd847000)
libguile.so.17 => /opt/xtal/ccp4-7.1/libexec/../lib/libguile.so.17 
(0x7fd0fd326000)
libgmp.so.10 => /opt/xtal/ccp4-7.1/libexec/../lib/libgmp.so.10 
(0x7fd0fd0a5000)
libcrypt.so.1 => /lib64/libcrypt.so.1 (0x7fd0fce6e000)
libm.so.6 => /lib64/libm.so.6 (0x7fd0fcb6c000)
libltdl.so.7 => /opt/xtal/ccp4-7.1/libexec/../lib/libltdl.so.7 
(0x7fd0fc962000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x7fd0fc746000)
libc.so.6 => /lib64/libc.so.6 (0x7fd0fc378000)
/lib64/ld-linux-x86-64.so.2 (0x7fd0fd628000)
libfreebl3.so => /lib64/libfreebl3.so (0x7fd0fc175000)
libdl.so.2 => /lib64/libdl.so.2 (0x7fd0fbf71000)
Guile 1.8.8
Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 
2008 Free Software Foundation
Guile may be distributed under the terms of the GNU General Public Licence;
certain other uses are permitted as well.  For details, see the file
`COPYING', which is included in the Guile distribution.
There is no warranty, to the extent permitted by law.
catching the crash log:
coot-exe: "/opt/xtal/ccp4-7.1/libexec/coot-bin"
/usr/bin/ls
-rwxr-xr-x. 1 root root 9169416 Sep 10 05:47 /opt/xtal/ccp4-7.1/libexec/coot-bin
coot-version: 
/opt/xtal/ccp4-7.1/libexec/coot-bin
Builder_info: CCP4, Oxfordshire
Enabled: Enhanced-ligand-tools C++-11 Threads Boost-based-thread-pool Goocanvas 
GSL SQLite3 LibCurl 
Binary type: Linux-x86_64-scientific-linux-6.10-python-gtk2
git commit: 0b823e493e00c1199103369ddab6641e14560d00
Builder_info: CCP

[ccp4bb] coot problems on Mac with external display

[Ursula Schulze-Gahmen]

I apologize if this question has been raised before. But I am still
struggling with running Coot 0.95 on my mac laptop (Catalina) with an
external display.
Coot is functioning normal without the external display. But with external
display, the window for displaying models doesn't open properly. Is there a
fix for this situation?
I am using the Coot version from sbgrid, ccp4 7.1. I am running XQuartz
2.8.1 for the graphics.

Thanks

Ursula

-- 
Ursula Schulze-Gahmen, PhD
Staff Research Scientist
The J David Gladstone Institutes
1650 Owens St.
San Francisco, CA 94158
(415) 734 4835



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[ccp4bb] Coot Crashing on MacOS 10.10

[Abhishek A. Jalan]

Dear all,

I installed the ccp4-7.1 and it loads fine but coot crashes with the
following error message.  I would really appreciate any help.


 [1m(filter-fileselection-filenames-state) [0m
 [1m(get-active-map-drag-flag) [0m
 [1m(use-graphics-interface-state) [0m
INFO:: coot.py imported
INFO:: coot_python initialized
Running python script
/Applications/ccp4-7.1/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Morning Aaj30, Welcome to Coot version 0.9.6
 [1m(set-display-intro-string "Good Morning Aaj30, Welcome to Coot
version 0.9.6") [0m
Coot Python Scripting GUI code found and loaded.
Coot Python Scripting GUI code found and loaded.
 [1m(use-graphics-interface-state) [0m
Running python script /Users/aaj30/.coot-preferences/coot_preferences.py
 [1m(set-filter-fileselection-filenames 0) [0m
 [1m(unset-sticky-sort-by-date) [0m
 [1m(set-colour-map-rotation-on-read-pdb 21.00) [0m
 [1m(set-colour-map-rotation-on-read-pdb-c-only-flag 1) [0m
 [1m(set-density-size 12.60) [0m
 [1m(set-swap-difference-map-colours 0) [0m
 [1m(set-colour-map-rotation-for-map 14.00) [0m
 [1m(set-active-map-drag-flag 1) [0m
 [1m(set-idle-function-rotate-angle 1.00) [0m
Running python script /Users/aaj30/.coot-preferences/coot_toolbuttons.py
Running python script /Users/aaj30/.coot-preferences/template_key_bindings.py
Running python script /Users/aaj30/.coot-preferences/xenops_symmetry.py
 [1m(set-show-symmetry-master 1) [0m
 [1m(filter-fileselection-filenames-state) [0m
 [1m(get-active-map-drag-flag) [0m
 [1m(use-graphics-interface-state) [0m
Coot Scheme Scripting GUI code found and loaded.
Good morning aaj30. Welcome to Coot 0.9.6.
 [1m(set-display-intro-string "Good morning aaj30. Welcome to Coot 0.9.6") [0m
 [1m(set-display-lists-for-maps 0) [0m
load /Users/aaj30/.coot-preferences/coot-preferences.scm
 [1m(set-filter-fileselection-filenames 0) [0m
 [1m(unset-sticky-sort-by-date) [0m
 [1m(set-colour-map-rotation-on-read-pdb 21.00) [0m
 [1m(set-colour-map-rotation-on-read-pdb-c-only-flag 1) [0m
 [1m(set-density-size 12.60) [0m
 [1m(set-swap-difference-map-colours 0) [0m
 [1m(set-colour-map-rotation-for-map 14.00) [0m
 [1m(set-active-map-drag-flag 1) [0m
 [1m(set-idle-function-rotate-angle 1.00) [0m
load /Users/aaj30/.coot-preferences/xenops-symmetry.scm
 [1m(set-show-symmetry-master 1) [0m
 [1m(filter-fileselection-filenames-state) [0m
 [1m(get-active-map-drag-flag) [0m
Loading ~/.coot
. -- Coot crashed - trying to diagnose -
Guile 1.8.8
Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005,
2006, 2007, 2008 Free Software Foundation
Guile may be distributed under the terms of the GNU General Public Licence;
certain other uses are permitted as well.  For details, see the file
`COPYING', which is included in the Guile distribution.
There is no warranty, to the extent permitted by law.
catching the crash log:
/bin/ls
/Applications/ccp4-7.1/libexec/coot-bin
/usr/bin/uname
coot-exe: "/Applications/ccp4-7.1/libexec/coot-bin"
-rwxr-xr-x  1 aaj30  staff  9877812 Sep 10 12:15
/Applications/ccp4-7.1/libexec/coot-bin
coot-version:
Builder_info: CCP4, Oxfordshire, UK
Enabled: Enhanced-ligand-tools C++-11 Threads Boost-based-thread-pool
Goocanvas GSL LibCurl
Binary type: Darwin-MacOSX-10.9.5-x86_64-python-gtk2
git commit: 0b823e493e00c1199103369ddab6641e14560d00
Builder_info: CCP4, Oxfordshire, UK
[with python 2.7.16 embedded]
[with guile 1.8.8 embedded]
0.9.6 (revision-count 10625)
platform:
Darwin bt-nac-g137.nac.uni-bayreuth.de 14.5.0 Darwin Kernel Version
14.5.0: Sun Jun  4 21:40:08 PDT 2017;
root:xnu-2782.70.3~1/RELEASE_X86_64 x86_64
core: #f
No core file found.  No debugging





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Re: [ccp4bb] Coot under WSL2

[Clement Degut]

Hi all,

If anyone is interested in the question, coot (and any graphical
application I tried) is now fully functional in Windows 11 and the newest
WSLg.
No configuration is needed, everything works out of the box, with full
hardware acceleration.

Clément

On Wed, 25 Mar 2020 at 15:58, Clement Degut 
wrote:

> Update to my update
>
> It is possible to have coot fully functional under WSL2 with the native
> openGL on.
> The caveat is :
> - You need a full linux desktop environment installed (xfce4 for me)
> - You need to use the host X server (VcSrv in my case) as single window,
> so you lose a bit of the seamless integration with windows in that case,
> but you have to do that only with coot (or any openGL software)
> after starting the DE, coot will work normally with very decent speed, the
> upcoming direct hardware access for the VM may also improve performance.
>
> In these conditions full CCP4 (or everything I tried at least) can work
> relatively seamlessly in windows while using the linux version.
> (it actually works better than the actual windows version imho)
>
> Clément
>
>
> On Thu, 19 Mar 2020 at 14:56, Clement Degut 
> wrote:
>
>> Immediate update :
>>
>> If you use VcXserv, you need to start it with all default option, and
>> generate a config file.
>> Then change in the file wgl to False.
>> Restart computer (yes)
>> And start VcXserv with the modified config.
>> If you simply deactivate native openGl via the gui nothing is working
>> anymore for some reason, it must change another option somewhere.
>>
>> doing that the display of coot is perfectly fine, just a bit laggy, as i
>> guess it's full software render, but usable (with a beefy CPU).
>>
>> Clément
>>
>> On Thu, 19 Mar 2020 at 14:48, Clement Degut 
>> wrote:
>>
>>> The performance are massively improved in WSL2 versus WSL1, so maybe
>>> it's why you had bad memory of it ?
>>> WSL2 is currently only available in insider fast ring, but will be for
>>> everyone with next major update (v2004) in few weeks.
>>>
>>> The main problem is, while you can use the right toolbar by simply
>>> detaching it, selecting residues is almost impossible as the pointer is
>>> still using the main UI as reference, but the 3D display  is away, so you
>>> need to click far from the residus you try to select.
>>>
>>> I am playing around with the xserver options, but am not sure what I am
>>> doing with that windows X server.
>>> I'll update if I find a solution.
>>>
>>> Clément
>>>
>>> On Thu, 19 Mar 2020 at 13:31, Paul Emsley 
>>> wrote:
>>>
 On 19/03/2020 12:43, Clement Degut wrote:
 >
 > I have been recently trying to use ccp4 in windows subsystem for
 Linux 2 (Ubuntu distribution), everything i
 > tried run perfectly smoothly, including graphical interfaces.

 I am pleasantly surprised - when I tried that (some time ago) the
 graphics performance as terrible. Perhaps
 you have better hardware.

 > My only problem is with coot (latest build), the interface is working
 fine, as well as the 3D graphical. The
 > only problem is that the graphical window is offset from the rest of
 the UI (see screenshot).
 > So although it looks like everything would work smoothly it's not
 really usable.

 What, would you say, is the biggest problem?

 > I guess it comes from the absence of GPU access under WSL2 and so no
 proper display driver, but does anyone
 > had this problem? (and managed to solve it).

 FWIW, I have not seen this problem before (and don't know how to fix it)

 It seems to me an X server problem (or configuration issue). Have you
 tweaked or disabled the native OpenGL
 options on the X server?

 > Would be very useful for people working from home without a full
 linux dual boot.

 Hmm.

 > In a more general note, it seems that WSL2 will be able to replace
 windows specific build very effectively
 > in the very near future.

 For everything other than OpenGL graphics (and maybe the Cloud would
 also be problematic), yes, it seems so.

 Paul.

>>>



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[ccp4bb] Coot 0.9.6.EL Linux Ubuntu

[Andrea Smith]

Hi,

I updated my ccp4 and it came with Coot 0.9.6.EL where the sequence view does 
not show the numbers of amino acids in the sequence and some letters overlap - 
anyone having the same problem? Do I need to install some other version?

Thanks,
Andrea



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Re: [ccp4bb] COOT running on Macbook Pro M1 chip

[WENHE ZHONG]

It helps :) Thanks.

Wim

On Thu, 16 Sept 2021 at 20:40, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Maybe turning off smooth re-centering would help our mac-using friends ;-?
>
>
> Sent from ProtonMail mobile
>
>
>
>  Original Message 
> On 16 Sep 2021, 11:29, Weiergräber, Oliver H. <
> o.h.weiergrae...@fz-juelich.de> wrote:
>
>
> Hi,
>
> You may want to check the number of "steps" used in re-centring.
> This setting strongly affects the perceived speed ;-)
>
> Best regards
> Oliver
>
> ==
> PD Dr. Oliver H. Weiergräber
> Institut für Biologische Informationsprozesse
> IBI-7: Strukturbiochemie
> Tel.: +49 2461 61-2028
> Fax: +49 2461 61-9540
> ==
>
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kay
> Diederichs [kay.diederi...@uni-konstanz.de]
> Sent: 16 September 2021 12:19
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] COOT running on Macbook Pro M1 chip
>
> Dear Wim,
>
> on my M1 Macbook Air, coot 0.9.6 (latest from CCP4) works smoothly/fast.
> What is your XQuartz version? I have 2.8.1 .
>
> HTH,
> Kay
>
> On Thu, 16 Sep 2021 15:40:53 +0800, WENHE ZHONG  GMAIL.COM> wrote:
>
> >Dear CCP4 community,
> >
> >The COOT is not running smoothly on my M1 chip Macbook. For example, when
> >both model and the electron density map are displayed, the moving from one
> >residue to the next (pressing SPACE bar) is lagging/slow (>2s). This only
> >happened to my old computer, but I am surprised to find it happens in the
> >newest macbook.
> >
> >Anyone have this problem and has a solution? Thanks.
> >
> >Best regards,
> >Wim
> >
> >
> >
> >To unsubscribe from the CCP4BB list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
> >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
> >
>
> 
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> Karsten Beneke (stellv. Vorsitzender), Dr. Astrid Lambrecht,
> Prof. Dr. Frauke Melchior
>
> 
>
> 
>
> 
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Re: [ccp4bb] COOT running on Macbook Pro M1 chip

[Paul Emsley]

On 16/09/2021 08:40, WENHE ZHONG wrote:

Dear CCP4 community,

The COOT is not running smoothly on my M1 chip Macbook. For example, 
when both model and the electron density map are displayed, the moving 
from one residue to the next (pressing SPACE bar) is lagging/slow 
(>2s). This only happened to my old computer, but I am surprised to 
find it happens in the newest macbook.



Give us some numbers. Try the spin test

https://pemsley.github.io/coot/blog/2018/06/06/coot-spin-test.html

Paul.



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Re: [ccp4bb] COOT running on Macbook Pro M1 chip

[Jon Cooper]

Maybe turning off smooth re-centering would help our mac-using friends ;-?

Sent from ProtonMail mobile

 Original Message 
On 16 Sep 2021, 11:29, Weiergräber, Oliver H. wrote:

> Hi,
>
> You may want to check the number of "steps" used in re-centring.
> This setting strongly affects the perceived speed ;-)
>
> Best regards
> Oliver
>
> ==
> PD Dr. Oliver H. Weiergräber
> Institut für Biologische Informationsprozesse
> IBI-7: Strukturbiochemie
> Tel.: +49 2461 61-2028
> Fax: +49 2461 61-9540
> ==
>
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kay Diederichs 
> [kay.diederi...@uni-konstanz.de]
> Sent: 16 September 2021 12:19
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] COOT running on Macbook Pro M1 chip
>
> Dear Wim,
>
> on my M1 Macbook Air, coot 0.9.6 (latest from CCP4) works smoothly/fast. What 
> is your XQuartz version? I have 2.8.1 .
>
> HTH,
> Kay
>
> On Thu, 16 Sep 2021 15:40:53 +0800, WENHE ZHONG 
>  wrote:
>
>>Dear CCP4 community,
>>
>>The COOT is not running smoothly on my M1 chip Macbook. For example, when
>>both model and the electron density map are displayed, the moving from one
>>residue to the next (pressing SPACE bar) is lagging/slow (>2s). This only
>>happened to my old computer, but I am surprised to find it happens in the
>>newest macbook.
>>
>>Anyone have this problem and has a solution? Thanks.
>>
>>Best regards,
>>Wim
>>
>>
>>
>>To unsubscribe from the CCP4BB list, click the following link:
>>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>>This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>>list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
>>https://www.jiscmail.ac.uk/policyandsecurity/
>>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> https://www.jiscmail.ac.uk/policyandsecurity/
>
> 
> 
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Dr. Astrid Lambrecht,
> Prof. Dr. Frauke Melchior
> 
> 
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] COOT running on Macbook Pro M1 chip

[Weiergräber , Oliver H .]

Hi,

You may want to check the number of "steps" used in re-centring.
This setting strongly affects the perceived speed ;-)

Best regards
Oliver

==
  PD Dr. Oliver H. Weiergräber
  Institut für Biologische Informationsprozesse
  IBI-7: Strukturbiochemie
  Tel.: +49 2461 61-2028
  Fax: +49 2461 61-9540
==



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kay Diederichs 
[kay.diederi...@uni-konstanz.de]
Sent: 16 September 2021 12:19
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] COOT running on Macbook Pro M1 chip

Dear Wim,

on my M1 Macbook Air, coot 0.9.6 (latest from CCP4) works smoothly/fast. What 
is your XQuartz version? I have 2.8.1 .

HTH,
Kay

On Thu, 16 Sep 2021 15:40:53 +0800, WENHE ZHONG  
wrote:

>Dear CCP4 community,
>
>The COOT is not running smoothly on my M1 chip Macbook. For example, when
>both model and the electron density map are displayed, the moving from one
>residue to the next (pressing SPACE bar) is lagging/slow (>2s). This only
>happened to my old computer, but I am surprised to find it happens in the
>newest macbook.
>
>Anyone have this problem and has a solution? Thanks.
>
>Best regards,
>Wim
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
>https://www.jiscmail.ac.uk/policyandsecurity/
>



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Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Dr. Astrid Lambrecht,
Prof. Dr. Frauke Melchior





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Re: [ccp4bb] COOT running on Macbook Pro M1 chip

[Sebastiano Pasqualato]

Hi Claude,
Pymol 2.4.0 (installed via homebrew) works fine for me in Apple M1 MacBook Pro, 
2020.
Ciao,
S

> On 16 Sep 2021, at 12:12, Claude Sauter  wrote:
> 
> Dear all,
> 
> to continue on the same theme, a colleague biochemist asked me a couple of 
> days ago if there is any incompatibility between PyMOL and other softwares 
> used in structural biology and new mac M1 chips. Being a Linux user, I have 
> no clue. Could mac users share their experience?
> 
> Thanks
> Best regards,
> Claude
> 
> Le 16/09/2021 à 09:40, WENHE ZHONG a écrit :
>> Dear CCP4 community,
>> 
>> The COOT is not running smoothly on my M1 chip Macbook. For example, when 
>> both model and the electron density map are displayed, the moving from one 
>> residue to the next (pressing SPACE bar) is lagging/slow (>2s). This only 
>> happened to my old computer, but I am surprised to find it happens in the 
>> newest macbook.
>> 
>> Anyone have this problem and has a solution? Thanks.
>> 
>> Best regards,
>> Wim
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 
>> 
> -- 
> Dr Claude Sauter
> Directeur de Recherche
> Institut de Biologie Moléculaire et Cellulaire (IBMC-ARN-CNRS)
> Biologie des ARNt et pathogénicité  tel +33 (0)388 417 102
> 2 allée Conrad Roentgen fax +33 (0)388 602 218
> F-67084 Strasbourg - France  http://cj.sauter.free.fr/xtal 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 
> 



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Re: [ccp4bb] COOT running on Macbook Pro M1 chip

[Kay Diederichs]

Dear Wim,

on my M1 Macbook Air, coot 0.9.6 (latest from CCP4) works smoothly/fast. What 
is your XQuartz version? I have 2.8.1 .

HTH,
Kay

On Thu, 16 Sep 2021 15:40:53 +0800, WENHE ZHONG  
wrote:

>Dear CCP4 community,
>
>The COOT is not running smoothly on my M1 chip Macbook. For example, when
>both model and the electron density map are displayed, the moving from one
>residue to the next (pressing SPACE bar) is lagging/slow (>2s). This only
>happened to my old computer, but I am surprised to find it happens in the
>newest macbook.
>
>Anyone have this problem and has a solution? Thanks.
>
>Best regards,
>Wim
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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>



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Re: [ccp4bb] COOT running on Macbook Pro M1 chip

[Claude Sauter]

  
  

  Dear all,
  
  
  to continue on the same theme, a
colleague biochemist asked me a couple of days ago if there is
any incompatibility between PyMOL and other softwares used in
structural biology and new mac M1 chips. Being a Linux user, I
have no clue. Could mac users share their experience?
  
  
  Thanks
  Best regards,
  Claude


Le 16/09/2021 à 09:40, WENHE ZHONG a
  écrit :


  
  
Dear CCP4 community,



The COOT is not running smoothly on my M1 chip Macbook. For
  example, when both model and the electron density map are
  displayed, the moving from one residue to the next (pressing
  SPACE bar) is lagging/slow (>2s). This only happened to my
  old computer, but I am surprised to find it happens in the
  newest macbook.


Anyone have this problem and has a solution? Thanks.


Best regards,
Wim


  
  
  
  To unsubscribe from the CCP4BB list, click the
following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
  



-- 
Dr Claude Sauter
Directeur de Recherche
Institut de Biologie Moléculaire et Cellulaire (IBMC-ARN-CNRS)
Biologie des ARNt et pathogénicité  tel +33 (0)388 417 102
2 allée Conrad Roentgen fax +33 (0)388 602 218
F-67084 Strasbourg - France  http://cj.sauter.free.fr/xtal

  



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[ccp4bb] COOT running on Macbook Pro M1 chip

[WENHE ZHONG]

Dear CCP4 community,

The COOT is not running smoothly on my M1 chip Macbook. For example, when
both model and the electron density map are displayed, the moving from one
residue to the next (pressing SPACE bar) is lagging/slow (>2s). This only
happened to my old computer, but I am surprised to find it happens in the
newest macbook.

Anyone have this problem and has a solution? Thanks.

Best regards,
Wim



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