Re: [COOT] Backrub rotamers in coot-1

2026-01-07 Thread Kevin M Jude 
Sorry, I should correct myself - I was messing around with coot installation on 
two different computers and got some issues mixed up. I did need to set 
DYLD_FALLBACK_LIBRARY_PATH to get libgl libraries to load, but it seems to be 
unrelated to coot finding coot.py - if I unset that variable it still works.  
It’s possible that there is different behavior between the two machines, I 
can’t check that right now.

From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Kevin M Jude 
<[email protected]>
Date: Wednesday, January 7, 2026 at 3:39 PM
To: [email protected] 
Subject: Re: Backrub rotamers in coot-1

Issue #269

From: Paul Emsley 
Date: Wednesday, January 7, 2026 at 3:30 PM
To: Kevin M Jude , [email protected] 
Subject: Re: Backrub rotamers in coot-1



On 07/01/2026 21:25, Kevin M Jude wrote:

For anyone following along at home, I guess I should mention that I also added 
a line to my .zshrc so coot could find coot.py and the -* files

export DYLD_FALLBACK_LIBRARY_PATH="$(brew 
--prefix)/lib:$DYLD_FALLBACK_LIBRARY_PATH”


Hi Kevin,

Interesting. It should not be needed. I don't need it.

We need Yoshitaka Moriwaki in the chat. Please raise this as an issue on 
github.com pemsley/coot.

Paul.




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Re: [COOT] Backrub rotamers in coot-1

2026-01-07 Thread Kevin M Jude 
Issue #269

From: Paul Emsley 
Date: Wednesday, January 7, 2026 at 3:30 PM
To: Kevin M Jude , [email protected] 
Subject: Re: Backrub rotamers in coot-1



On 07/01/2026 21:25, Kevin M Jude wrote:

For anyone following along at home, I guess I should mention that I also added 
a line to my .zshrc so coot could find coot.py and the -* files

export DYLD_FALLBACK_LIBRARY_PATH="$(brew 
--prefix)/lib:$DYLD_FALLBACK_LIBRARY_PATH”


Hi Kevin,

Interesting. It should not be needed. I don't need it.

We need Yoshitaka Moriwaki in the chat. Please raise this as an issue on 
github.com pemsley/coot.

Paul.




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Re: [COOT] Backrub rotamers in coot-1

2026-01-07 Thread Paul Emsley 


On 07/01/2026 21:25, Kevin M Jude wrote:


For anyone following along at home, I guess I should mention that I 
also added a line to my .zshrc so coot could find coot.py and the -* files


export DYLD_FALLBACK_LIBRARY_PATH="$(brew 
--prefix)/lib:$DYLD_FALLBACK_LIBRARY_PATH”



Hi Kevin,

Interesting. It should not be needed. I don't need it.

We need Yoshitaka Moriwaki in the chat. Please raise this as an issue on 
github.com pemsley/coot.


Paul.




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Re: [COOT] Backrub rotamers in coot-1

2026-01-07 Thread Kevin M Jude 
Super, thanks.

For anyone following along at home, I guess I should mention that I also added 
a line to my .zshrc so coot could find coot.py and the -* files

export DYLD_FALLBACK_LIBRARY_PATH="$(brew 
--prefix)/lib:$DYLD_FALLBACK_LIBRARY_PATH”


From: Paul Emsley 
Date: Wednesday, January 7, 2026 at 8:52 AM
To: Kevin M Jude , [email protected] 
Subject: Re: Backrub rotamers in coot-1



On 07/01/2026 00:14, Kevin M Jude wrote:
OK, I first had to “import coot”.
Ah yes, I should have mentioned that.
 Then with:

coot.set_rotamer_search_mode(ROTAMERSEARCHLOWRES)

I got the error
NameError: name 'ROTAMERSEARCHLOWRES' is not defined
but I tried again with

coot.set_rotamer_search_mode(coot.ROTAMERSEARCHLOWRES)

and that worked. Thanks!

Is there an equivalent to the ~/.coot startup file where I can add this to make 
it a default setting?

Yes. Coot now follows the XDG Base Directory Specification,

so ~/.config/Coot/startup.py

Paul.




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Re: [COOT] Backrub rotamers in coot-1

2026-01-07 Thread Paul Emsley 


On 07/01/2026 00:14, Kevin M Jude wrote:

OK, I first had to “import coot”.

Ah yes, I should have mentioned that.

 Then with:

coot.set_rotamer_search_mode(ROTAMERSEARCHLOWRES)

I got the error
NameError: name 'ROTAMERSEARCHLOWRES' is not defined
but I tried again with

coot.set_rotamer_search_mode(coot.ROTAMERSEARCHLOWRES)

and that worked. Thanks!


Is there an equivalent to the ~/.coot startup file where I can add 
this to make it a default setting?


Yes. Coot now follows the XDG Base Directory Specification,

so ~/.config/Coot/startup.py

Paul.




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Re: [COOT] Backrub rotamers in coot-1

2026-01-06 Thread Kevin M Jude 
OK, I first had to “import coot”. Then with:

coot.set_rotamer_search_mode(ROTAMERSEARCHLOWRES)

I got the error
NameError: name 'ROTAMERSEARCHLOWRES' is not defined
but I tried again with

coot.set_rotamer_search_mode(coot.ROTAMERSEARCHLOWRES)

and that worked. Thanks!

Is there an equivalent to the ~/.coot startup file where I can add this to make 
it a default setting? Apologies if that’s documented somewhere, there are so 
many years of coot documentation online that I can’t get google to direct me to 
the new stuff.


--

Kevin M. Jude, PhD

Structural Biology Research Specialist, Garcia Lab

Howard Hughes Medical Institute

Stanford University School of Medicine

Beckman B177, 279 Campus Drive, Stanford CA 94305



From: Paul Emsley 
Date: Monday, January 5, 2026 at 8:32 PM
To: Kevin M Jude , [email protected] 
Subject: Re: Backrub rotamers in coot-1



On 05/01/2026 20:37, Kevin M Jude wrote:

Is there a way to turn on backrub rotamers in coot 1.20 for Mac. In 0.9.x I 
have a toolbar button to toggle back rub rotamers (I keep it always on), but I 
don’t know of any other way to toggle the setting.

coot.set_rotamer_search_mode(m)

where m is

ROTAMERSEARCHLOWRES # backrub

ROTAMERSEARCHHIGHRES # old


“backrub rotamers for chain” is overkill for me, I just want to use autofit 
rotamer for specific residues.


Copy your working fragment to a new molecule

work on the (new molecule) fragment

Replace Fragment (move the atoms of the original model to where the new 
molecule fragment atoms are)


Paul.




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Re: [COOT] Backrub rotamers in coot-1

2026-01-05 Thread Paul Emsley 


On 05/01/2026 20:37, Kevin M Jude wrote:


Is there a way to turn on backrub rotamers in coot 1.20 for Mac. In 
0.9.x I have a toolbar button to toggle back rub rotamers (I keep it 
always on), but I don’t know of any other way to toggle the setting.


coot.set_rotamer_search_mode(m)

where m is

ROTAMERSEARCHLOWRES # backrub

ROTAMERSEARCHHIGHRES # old


“backrub rotamers for chain” is overkill for me, I just want to use 
autofit rotamer for specific residues.



Copy your working fragment to a new molecule

work on the (new molecule) fragment

Replace Fragment (move the atoms of the original model to where the new 
molecule fragment atoms are)



Paul.




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[COOT] Backrub rotamers in coot-1

2026-01-05 Thread Kevin M Jude 
Is there a way to turn on backrub rotamers in coot 1.20 for Mac. In 0.9.x I 
have a toolbar button to toggle back rub rotamers (I keep it always on), but I 
don’t know of any other way to toggle the setting. “backrub rotamers for chain” 
is overkill for me, I just want to use autofit rotamer for specific residues.


--

Kevin M. Jude, PhD

Structural Biology Research Specialist, Garcia Lab

Howard Hughes Medical Institute

Stanford University School of Medicine

Beckman B177, 279 Campus Drive, Stanford CA 94305





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