Re: [COOT] Coot-1 missing ssm

2022-04-07 Thread 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.





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Re: [COOT] Coot-1 missing ssm

2022-04-06 Thread 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.




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Re: [COOT] Coot-1 missing ssm

2022-04-06 Thread 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
>>
>>
>
>



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Re: [COOT] Coot-1 missing ssm

2022-04-06 Thread 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
>>
>>
>
>



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Re: [COOT] Coot-1 missing ssm

2022-04-06 Thread 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









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Re: [COOT] Coot-1 missing ssm

2022-04-06 Thread 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



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