[COOT] Coot 1 Tutorial - The Basics

[Paul Emsley]

Lucrezia Catapano has made a video for Coot 1. This video is one of what 
will be a series of videos showcasing Coot 1 - and this one starts at 
the beginning.


https://www.youtube.com/watch?v=Xhonm4K1y0c

Happy Jubilee,

Paul.



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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [COOT] Coot-1 missing ssm

[Sabine Schneider]

Dear all,


thank you for the suggestions. I am using the script now, but am stuck 
with the following python-error message



>ls: cannot access 
'/home/sabine/autobuild/Linux-gtk3/lib/python3.9/site-packages/numpy-*/numpy/lib/_version.py': 
No such file or directory

>guile-config - Guile version 2.2.7


However numpy etc is there, downloaded by the script in


-> 
autobuild/Linux-gtk3/lib/python3.9/site-packages/numpy-1.19.4-py3.9-linux-x86_64.egg/numpy/lib/_version.py



Can I point it to python on my sytstem? it is 3.9.7 with Numpy1.22


/home/sabine: python --version
Python 3.9.7

ls .local/lib/python3.9/site-packages/
numpy  numpy-1.22.3.dist-info  numpy.libs  pip pip-22.0.4.dist-info


I also tried the Charles Ballard experimental versions, but they failed 
unfortunately on my computer



Any ideas are very welcome! Thanks a lot!


Sabine


On 07/04/2022 01:09, Paul Emsley wrote:



On 06/04/2022 22:01, David Briggs wrote:

Hi Charles and Paul,



Yes, thank you Charles,




This installer worked exactly as advertised for my Intel MBP.



Good to know.




One bug I've come across that I've not seen reported elsewhere is 
that when dragging atoms when RSR has been activated, as well as 
dragging the atoms, the model still rotates.



On a Mac it does (did) - I had a MacBook Pro for testing and was using 
the trackpad, so I didn't know how to use "right-mouse" drag so I 
mapped view rotation to left-mouse also.



Fixed in 7fb49cdab1493c9b0b934802331def2cc64e9771





Thank you for this Paul - I think the HUD is a great idea



I will make a video for this, but briefly the HUD bar are clickable, 
the lower grey bar in the NBC HUD bars means "contributing to the 
target function but not in the refining set of residues" and the pink 
lower bar means "the active residue/the residue at the center of the 
screen"




and the depth blur looks so so good.



:-) Inspired by Oliver Clarke's twitter.


I think it will be useful if you want to make a image that highlights 
a particular residue or ligand. I turn the strength up to 6, then set 
the depth, then turn down the strength to 1 or so.



Paul.





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







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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [COOT] Coot-1 missing ssm

[Paul Emsley]

On 06/04/2022 22:01, David Briggs wrote:

Hi Charles and Paul,



Yes, thank you Charles,




This installer worked exactly as advertised for my Intel MBP.



Good to know.




One bug I've come across that I've not seen reported elsewhere is that 
when dragging atoms when RSR has been activated, as well as dragging 
the atoms, the model still rotates.



On a Mac it does (did) - I had a MacBook Pro for testing and was using 
the trackpad, so I didn't know how to use "right-mouse" drag so I mapped 
view rotation to left-mouse also.



Fixed in 7fb49cdab1493c9b0b934802331def2cc64e9771





Thank you for this Paul - I think the HUD is a great idea



I will make a video for this, but briefly the HUD bar are clickable, the 
lower grey bar in the NBC HUD bars means "contributing to the target 
function but not in the refining set of residues" and the pink lower bar 
means "the active residue/the residue at the center of the screen"




and the depth blur looks so so good.



:-) Inspired by Oliver Clarke's twitter.


I think it will be useful if you want to make a image that highlights a 
particular residue or ligand. I turn the strength up to 6, then set the 
depth, then turn down the strength to 1 or so.



Paul.




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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [COOT] Coot-1 missing ssm

[David Briggs]

Hi Charles and Paul,

This installer worked exactly as advertised for my Intel MBP.

One bug I've come across that I've not seen reported elsewhere is that when 
dragging atoms when RSR has been activated, as well as dragging the atoms, the 
model still rotates.

Hope this is useful info.

Thank you for this Paul - I think the HUD is a great idea and the depth blur 
looks so so good.

Cheers

Dave


--

Dr David C. Briggs CSci MRSB

Senior Laboratory Research Scientist

Signalling and Structural Biology Lab

The Francis Crick Institute

London, UK

==

about.me/david_briggs


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Charles Ballard - STFC UKRI 
<78bb5c0443c5-dmarc-requ...@jiscmail.ac.uk>
Sent: 06 April 2022 18:48
To: COOT@JISCMAIL.AC.UK 
Subject: Re: Coot-1 missing ssm


External Sender: Use caution.


Experimental version at



http://devtools.fg.oisin.rc-harwell.ac.uk/downloads/index.php<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdevtools.fg.oisin.rc-harwell.ac.uk%2Fdownloads%2Findex.php=04%7C01%7C%7Ca3aeef8dfcb44c96313108da17f5c79d%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637848641645726436%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000=k%2ByQMzybSg3agkoz5SaDQvvkjT5DrMydBf2vUG7j38c%3D=0>



not sure if password protected (I do not get asked).   Will extract to 
ccp4- as uses cpc4 build script.  Have to run BINARY.setup and source 
ccp4.setup-sh.  Needs tidying…





From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Paul Emsley 
Date: Wednesday, 6 April 2022 at 17:34
To: COOT@JISCMAIL.AC.UK 
Subject: Re: [COOT] Coot-1 missing ssm

Thank you Tim.


As mentioned in the Release Notes, it's quite likely that it will fail
to compile Python and/or PyGObject.

If anyone can tell me how to do it, I'd be grateful - I've probably
spent over 10 hours trying to get the thing to work.

Python needs _ctypes to compile - to do that it needs libffi. libffi is
built by the script but I don't see how to link with it.

Without ctypes, pip and meson don't work.


Paul.


On 06/04/2022 12:26, Tim Gruene wrote:
> Hi Sabine,
>
> Paul provides a build script
> https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/build-install-coot-from-scratch.html<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww2.mrc-lmb.cam.ac.uk%2Fpersonal%2Fpemsley%2Fcoot%2Fweb%2Fbuild-install-coot-from-scratch.html=04%7C01%7C%7Ca3aeef8dfcb44c96313108da17f5c79d%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637848641645726436%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000=mlT6hSP1WD51v64BcNnyMkyyMx6wTo36m647vwj1m%2Bg%3D=0>
> which takes care of the additional packages required to compile coot.
> That's much easier than running configure from the coot source tar and
> trying to fix the missing parts yourself.
>
> Best,
> Tim
>
> On Wed, 6 Apr 2022 11:59:33 +0200 Sabine Schneider
>  wrote:
>
>> Hi everyone,
>>
>> I am using Centos Stream and tried to install coot-1, but failed due
>> to an error: "ssm not found" (see below)
>> I resolved the missing mmdb2 by installing the package from source,
>> but I cannot find libSSM anywhere. Can someone point me in the right
>> direction?
>>
>> checking for LIBPNG... yes
>> checking for CAIRO... yes
>> checking for SQLite3... no
>> checking for mmdb2... yes
>> checking for ssm... no
>> configure: error: in `/home/sabine/progs/coot-1':
>> configure: error: ssm not found
>>
>> Thanks a lot!
>>
>> Sabine
>>
>>
>
>



To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCOOT%26A%3D1=04%7C01%7C%7Ca3aeef8dfcb44c96313108da17f5c79d%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637848641645726436%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000=0SLTsCyWK2ijdABcjHbScBH%2FMONjrHOT6ErTWrorm2Q%3D=0>

This message was issued to members of 
www.jiscmail.ac.uk/COOT<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCOOT=04%7C01%7C%7Ca3aeef8dfcb44c96313108da17f5c79d%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637848641645726436%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000=uDt4%2FIdPFlQh%2BWaU%2B3IfHc06jki6%2BGkHXb9r6wfsF6A%3D=0>,
 a mailing list hosted by 
www.jiscmail.ac.uk<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F=04%7

Re: [COOT] Coot-1 missing ssm

[Charles Ballard - STFC UKRI]

Experimental version at

http://devtools.fg.oisin.rc-harwell.ac.uk/downloads/index.php

not sure if password protected (I do not get asked).   Will extract to 
ccp4- as uses cpc4 build script.  Have to run BINARY.setup and source 
ccp4.setup-sh.  Needs tidying…


From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Paul Emsley 
Date: Wednesday, 6 April 2022 at 17:34
To: COOT@JISCMAIL.AC.UK 
Subject: Re: [COOT] Coot-1 missing ssm
Thank you Tim.


As mentioned in the Release Notes, it's quite likely that it will fail
to compile Python and/or PyGObject.

If anyone can tell me how to do it, I'd be grateful - I've probably
spent over 10 hours trying to get the thing to work.

Python needs _ctypes to compile - to do that it needs libffi. libffi is
built by the script but I don't see how to link with it.

Without ctypes, pip and meson don't work.


Paul.


On 06/04/2022 12:26, Tim Gruene wrote:
> Hi Sabine,
>
> Paul provides a build script
> https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/build-install-coot-from-scratch.html
> which takes care of the additional packages required to compile coot.
> That's much easier than running configure from the coot source tar and
> trying to fix the missing parts yourself.
>
> Best,
> Tim
>
> On Wed, 6 Apr 2022 11:59:33 +0200 Sabine Schneider
>  wrote:
>
>> Hi everyone,
>>
>> I am using Centos Stream and tried to install coot-1, but failed due
>> to an error: "ssm not found" (see below)
>> I resolved the missing mmdb2 by installing the package from source,
>> but I cannot find libSSM anywhere. Can someone point me in the right
>> direction?
>>
>> checking for LIBPNG... yes
>> checking for CAIRO... yes
>> checking for SQLite3... no
>> checking for mmdb2... yes
>> checking for ssm... no
>> configure: error: in `/home/sabine/progs/coot-1':
>> configure: error: ssm not found
>>
>> Thanks a lot!
>>
>> Sabine
>>
>>
>
>



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

This message was issued to members of 
www.jiscmail.ac.uk/COOT<http://www.jiscmail.ac.uk/COOT>, a mailing list hosted 
by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are 
available at https://www.jiscmail.ac.uk/policyandsecurity/

This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
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 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [COOT] Coot-1 missing ssm

[Paul Emsley]

Thank you Tim.


As mentioned in the Release Notes, it's quite likely that it will fail 
to compile Python and/or PyGObject.


If anyone can tell me how to do it, I'd be grateful - I've probably 
spent over 10 hours trying to get the thing to work.


Python needs _ctypes to compile - to do that it needs libffi. libffi is 
built by the script but I don't see how to link with it.


Without ctypes, pip and meson don't work.


Paul.


On 06/04/2022 12:26, Tim Gruene wrote:

Hi Sabine,

Paul provides a build script
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/build-install-coot-from-scratch.html
which takes care of the additional packages required to compile coot.
That's much easier than running configure from the coot source tar and
trying to fix the missing parts yourself.

Best,
Tim

On Wed, 6 Apr 2022 11:59:33 +0200 Sabine Schneider
 wrote:


Hi everyone,

I am using Centos Stream and tried to install coot-1, but failed due
to an error: "ssm not found" (see below)
I resolved the missing mmdb2 by installing the package from source,
but I cannot find libSSM anywhere. Can someone point me in the right
direction?

checking for LIBPNG... yes
checking for CAIRO... yes
checking for SQLite3... no
checking for mmdb2... yes
checking for ssm... no
configure: error: in `/home/sabine/progs/coot-1':
configure: error: ssm not found

Thanks a lot!

Sabine









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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [COOT] Coot-1 missing ssm

[Tim Gruene]

Hi Sabine,

Paul provides a build script
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/build-install-coot-from-scratch.html
which takes care of the additional packages required to compile coot.
That's much easier than running configure from the coot source tar and
trying to fix the missing parts yourself.

Best,
Tim

On Wed, 6 Apr 2022 11:59:33 +0200 Sabine Schneider
 wrote:

> Hi everyone,
> 
> I am using Centos Stream and tried to install coot-1, but failed due
> to an error: "ssm not found" (see below)
> I resolved the missing mmdb2 by installing the package from source,
> but I cannot find libSSM anywhere. Can someone point me in the right
> direction?
> 
> checking for LIBPNG... yes
> checking for CAIRO... yes
> checking for SQLite3... no
> checking for mmdb2... yes
> checking for ssm... no
> configure: error: in `/home/sabine/progs/coot-1':
> configure: error: ssm not found
> 
> Thanks a lot!
> 
> Sabine
> 
> 



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

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/


pgpOFRKTGsLCR.pgp
Description: OpenPGP digital signature

[COOT] Coot-1 missing ssm

[Sabine Schneider]

Hi everyone,

I am using Centos Stream and tried to install coot-1, but failed due to 
an error: "ssm not found" (see below)
I resolved the missing mmdb2 by installing the package from source, but 
I cannot find libSSM anywhere. Can someone point me in the right direction?


checking for LIBPNG... yes
checking for CAIRO... yes
checking for SQLite3... no
checking for mmdb2... yes
checking for ssm... no
configure: error: in `/home/sabine/progs/coot-1':
configure: error: ssm not found

Thanks a lot!

Sabine


--
--
Dr. Sabine Schneider
Heisenberg Research Group Leader
Ludwig-Maximilians University Munich
Department of Chemistry
Institute for Chemical Epigenetics
Butenandtstr. 5-13
81377 Munich, Germany

Tel.: +49 (0) 89 2180 77716
https://www.cup.lmu.de/oc/schneider/



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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[COOT] Coot 1 NCS Ghosts

[Paul Emsley]

The twitterati have spoke and I have listened.

ff8c399abd621bd8366466b2154d0783855607cd restores/re-implements the NCS 
Ghosts.


I will release 1.0.01 in a few days.

Tomorrow I will start work on the port to GTK4 - that will give me an 
idea of how hard it's going to be.


Paul.



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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [COOT] coot-1 on mac m1

[Pranav Shah]

Thanks Paul!! Will get in touch!

On Sat, 2 Apr 2022 at 17:12, Paul Emsley  wrote:

> On 02/04/2022 16:38, Paul Emsley wrote:
> >
> > There are real problems to be solved though, one of them is to
> > actually compile the beast (it's not actually the Coot code that's the
> > problem, it's the parts on which it depends).
> >
> > There is a live issue on github
> >
> > https://github.com/pemsley/coot/issues/33
> >
> > where Coot compilation via Homebrew is being discussed (including M1).
> >
> The author of the Coot Homebrew build script is @Ag_smith. You might
> like to send him some twitter-based enouragement, which is probably
> easier than doing so via github. He picked it up before 1.0 was actually
> released:
>
>
> https://twitter.com/Ag_smith/status/1478567242749325314
>
>
> Paul.
>
> 
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
>
> This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at
> https://www.jiscmail.ac.uk/policyandsecurity/
>
-- 
Best,
Pranav
--
Pranav Shah
Postdoctoral Research Fellow.

Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,
UK



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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [COOT] coot-1 on mac m1

[Paul Emsley]

On 02/04/2022 16:38, Paul Emsley wrote:


There are real problems to be solved though, one of them is to 
actually compile the beast (it's not actually the Coot code that's the 
problem, it's the parts on which it depends).


There is a live issue on github

https://github.com/pemsley/coot/issues/33

where Coot compilation via Homebrew is being discussed (including M1).

The author of the Coot Homebrew build script is @Ag_smith. You might 
like to send him some twitter-based enouragement, which is probably 
easier than doing so via github. He picked it up before 1.0 was actually 
released:



https://twitter.com/Ag_smith/status/1478567242749325314


Paul.



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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [COOT] coot-1 on mac m1

[Paul Emsley]

On 02/04/2022 01:58, Pranav Shah wrote:


Hi Paul,

This release looks really interesting! Do you have any tips on
compiling it for arm64 based archs (m1 and ilk)? There appears to be a
dependency on fftw2 which I am failing to compile on the M1.


The M1 Max might be a very comfortable natural home for Coot 1.

There are real problems to be solved though, one of them is to actually 
compile the beast (it's not actually the Coot code that's the problem, 
it's the parts on which it depends).


There is a live issue on github

https://github.com/pemsley/coot/issues/33

where Coot compilation via Homebrew is being discussed (including M1).

(Another one is the framebuffer problem)

Also, via a completely different mechanism, Charles Ballard is using 
Anvil to compile binaries using the CCP4 build system - although his 
priority (as I understand it) is to get it working within CCP4 rather 
than providing you with a build script or making stand-alone binaries.


Paul.



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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[COOT] coot-1 on mac m1

[Pranav Shah]

Hi Paul,

This release looks really interesting! Do you have any tips on
compiling it for arm64 based archs (m1 and ilk)? There appears to be a
dependency on fftw2 which I am failing to compile on the M1.

Best,
Pranav
--
Pranav Shah
Postdoctoral Research Fellow.

Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,
UK



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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [COOT] Coot 1

[Pedro Matias]

Hi Paul,

The new Coot does have a nice depth of field and that certainly helps to 
provide a 3D feeling to the image. Still, I hope you can manage to bring 
it back at some future date. Old habits die hard...


Best,

Pedro

Em 01/04/2022 12:03, Paul Emsley escreveu:


Hi Pedro,

Stereo is not available because I didn't have access to stereo at home 
and I have not been keen on touching communal equipment at the lab. My 
guess is that it needs only 100 lines or so - many of those are in 
Coot 0.9.x. I would like a chance to revisit the view matrices though 
- during a recent test of new stereo kit PyMOL was noticeably better.


I wonder actually if stereo is so necessary in Coot 1 though..? - 
here's a side-by-side.


Paul


On 01/04/2022 11:32, Pedro Matias wrote:

Hi Paul,

Is stereo definitely off the table for Coot 1 or will you add it back 
later?


If not, the I would ask CCP4 developers to *pretty please* keep coot 
0.9 as a legacy option for us users who cannot live without stereo.






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

This message was issued to members of www.jiscmail.ac.uk/COOT, a 
mailing list hosted by www.jiscmail.ac.uk, terms & conditions are 
available at https://www.jiscmail.ac.uk/policyandsecurity/


--
Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8



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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [COOT] Coot 1

[Pedro Matias]

Hi Paul,

Is stereo definitely off the table for Coot 1 or will you add it back later?

If not, the I would ask CCP4 developers to *pretty please* keep coot 0.9 
as a legacy option for us users who cannot live without stereo.


Best,

Pedro

Em 01/04/2022 11:14, Paul Emsley escreveu:

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.



To unsubscribe from the COOT list, click the 

[COOT] 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.



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

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/