Re: [COOT] Mac Coot 1.0.06-pre mutate sequence not working

2022-06-25 Thread Sun, Chen 
Hi Paul,

Thank you for your timely response. However, I can’t reinstall coot right now. 
It said not to be found.


Warning: No available formula with the name "./coot.rb".
==> Searching for similarly named formulae...
Error: No similarly named formulae found.
==> Searching for a previously deleted formula (in the last month)...
Error: No previously deleted formula found.

Thanks,
Chen
From: Paul Emsley 
Date: Saturday, June 25, 2022 at 4:47 PM
To: Sun, Chen , COOT@JISCMAIL.AC.UK 
Subject: Re: Mac Coot 1.0.06-pre mutate sequence not working
* External Email - Caution *


On 25/06/2022 17:57, Sun, Chen wrote:
Hi Paul,

Now the copy molecule is not working. The save coordinate also failed to launch 
after I have mutated a long sequence.


OK, copy_molecule is fixed.


It doesn’t allow me to save the session. Please see the error message below.



on_glarea_key_press_notify() key not found in map: 65505

debug:: safe_python_command() PyRun_SimpleString() import coot_gui; 
coot_gui.molecule_chooser_gui("Molecule to Copy...", lambda imol: 
coot.copy_molecule(imol))

Selected: imol=

Traceback (most recent call last):

  File 
"/opt/homebrew/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/coot/coot_gui.py"<mailto:/opt/homebrew/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/coot/coot_gui.py>,
 line 931, in on_ok_button_clicked

callback_function(imol_model)

  File "", line 1, in 

NameError: name 'coot' is not defined

Traceback (most recent call last):

  File 
"/opt/homebrew/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/coot/coot_gui.py"<mailto:/opt/homebrew/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/coot/coot_gui.py>,
 line 931, in on_ok_button_clicked

callback_function(imol_model)

  File "", line 1, in 

NameError: name 'coot' is not defined



OK, save state dialog is fixed now also. Same deal to install of course.

Alternatively, use Ctrl-S to save the session.

Thanks,

Paul.




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Re: [COOT] Mac Coot 1.0.06-pre mutate sequence not working

2022-06-25 Thread Paul Emsley 


On 25/06/2022 17:57, Sun, Chen wrote:


Hi Paul,

Now the copy molecule is not working. The save coordinate also failed 
to launch after I have mutated a long sequence.




OK, copy_molecule is fixed.


It doesn’t allow me to save the session. Please see the error message 
below.


on_glarea_key_press_notify() key not found in map: 65505

debug:: safe_python_command() PyRun_SimpleString() import coot_gui; 
coot_gui.molecule_chooser_gui("Molecule to Copy...", lambda imol: 
coot.copy_molecule(imol))


Selected: imol=

Traceback (most recent call last):

File 
"/opt/homebrew/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/coot/coot_gui.py", 
line 931, in on_ok_button_clicked


callback_function(imol_model)

File "", line 1, in 

NameError: name 'coot' is not defined

Traceback (most recent call last):

File 
"/opt/homebrew/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/coot/coot_gui.py", 
line 931, in on_ok_button_clicked


callback_function(imol_model)

File "", line 1, in 

NameError: name 'coot' is not defined



OK, save state dialog is fixed now also. Same deal to install of course.

Alternatively, use Ctrl-S to save the session.

Thanks,

Paul.




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Re: [COOT] Mac Coot 1.0.06-pre mutate sequence not working

2022-06-25 Thread Sun, Chen 
Hi Paul,

Now the copy molecule is not working. The save coordinate also failed to launch 
after I have mutated a long sequence. It doesn’t allow me to save the session. 
Please see the error message below.



on_glarea_key_press_notify() key not found in map: 65505

debug:: safe_python_command() PyRun_SimpleString() import coot_gui; 
coot_gui.molecule_chooser_gui("Molecule to Copy...", lambda imol: 
coot.copy_molecule(imol))

Selected: imol=

Traceback (most recent call last):

  File 
"/opt/homebrew/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/coot/coot_gui.py",
 line 931, in on_ok_button_clicked

callback_function(imol_model)

  File "", line 1, in 

NameError: name 'coot' is not defined

Traceback (most recent call last):

  File 
"/opt/homebrew/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/coot/coot_gui.py",
 line 931, in on_ok_button_clicked

callback_function(imol_model)

  File "", line 1, in 

NameError: name 'coot' is not defined

(coot-bin:99643): Gtk-CRITICAL **: 11:52:47.895: 
gtk_file_chooser_set_do_overwrite_confirmation: assertion 'GTK_IS_FILE_CHOOSER 
(chooser)' failed



(coot-bin:99643): Gtk-CRITICAL **: 11:52:47.895: 
gtk_file_chooser_set_current_name: assertion 'GTK_IS_FILE_CHOOSER (chooser)' 
failed

sys:1: Warning: g_object_set_data: assertion 'G_IS_OBJECT (object)' failed



(coot-bin:99643): Gtk-CRITICAL **: 11:52:47.895: gtk_file_chooser_add_filter: 
assertion 'GTK_IS_FILE_CHOOSER (chooser)' failed



(coot-bin:99643): Gtk-CRITICAL **: 11:52:47.895: gtk_file_chooser_add_filter: 
assertion 'GTK_IS_FILE_CHOOSER (chooser)' failed



(coot-bin:99643): Gtk-CRITICAL **: 11:52:47.895: gtk_file_chooser_set_filter: 
assertion 'GTK_IS_FILE_CHOOSER (chooser)' failed



(coot-bin:99643): Gtk-CRITICAL **: 11:52:47.895: gtk_window_resize: assertion 
'GTK_IS_WINDOW (window)' failed



(coot-bin:99643): Gtk-CRITICAL **: 11:52:47.895: gtk_widget_show: assertion 
'GTK_IS_WIDGET (widget)' failed





Thanks,

Chen


From: Sun, Chen 
Date: Saturday, June 25, 2022 at 10:18 AM
To: Paul Emsley , COOT@JISCMAIL.AC.UK 

Subject: Re: Mac Coot 1.0.06-pre mutate sequence not working
Hi Paul,

It works now. Thank you so much!

Best,
Chen

From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Paul Emsley 
Date: Saturday, June 25, 2022 at 2:08 AM
To: COOT@JISCMAIL.AC.UK 
Subject: Re: Mac Coot 1.0.06-pre mutate sequence not working
* External Email - Caution *


On 25/06/2022 06:20, Paul Emsley wrote:
On 25/06/2022 04:12, Sun, Chen wrote:



I am able to run coot successfully from terminal. However, when I was trying to 
mutate sequences, it reported the following error message:


debug:: safe_python_command() PyRun_SimpleString() coot.mutate_residue_range(0, 
"C", 1, 2, "FF")

Traceback (most recent call last):

  File "", line 1, in 

NameError: name 'coot' is not defined
Is this my environment issue or something else? Any help would be appreciated.


I can reproduce this - I'll track it down.




OK done. Uninstall your coot and reinstall it as you did last time (using 
--verbose --HEAD)



Paul.





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Re: [COOT] Mac Coot 1.0.06-pre mutate sequence not working

2022-06-25 Thread Sun, Chen 
Hi Paul,

It works now. Thank you so much!

Best,
Chen

From: Mailing list for users of COOT Crystallographic Software 
 on behalf of Paul Emsley 
Date: Saturday, June 25, 2022 at 2:08 AM
To: COOT@JISCMAIL.AC.UK 
Subject: Re: Mac Coot 1.0.06-pre mutate sequence not working
* External Email - Caution *


On 25/06/2022 06:20, Paul Emsley wrote:
On 25/06/2022 04:12, Sun, Chen wrote:


I am able to run coot successfully from terminal. However, when I was trying to 
mutate sequences, it reported the following error message:


debug:: safe_python_command() PyRun_SimpleString() coot.mutate_residue_range(0, 
"C", 1, 2, "FF")

Traceback (most recent call last):

  File "", line 1, in 

NameError: name 'coot' is not defined
Is this my environment issue or something else? Any help would be appreciated.


I can reproduce this - I'll track it down.




OK done. Uninstall your coot and reinstall it as you did last time (using 
--verbose --HEAD)



Paul.





To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCOOT%26A%3D1=05%7C01%7Csun.c%40wustl.edu%7C2ae7148a08a248e42da108da5679762b%7C4ccca3b571cd4e6d974b4d9beb96c6d6%7C0%7C0%7C637917377074407371%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=BFytEspaRAFcpngpH4%2Bs69sqQWjUlmOEujab0eqqmQ4%3D=0>


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.



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Re: [COOT] Mac Coot 1.0.06-pre mutate sequence not working

2022-06-25 Thread Paul Emsley 


On 25/06/2022 06:20, Paul Emsley wrote:

On 25/06/2022 04:12, Sun, Chen wrote:

I am able to run coot successfully from terminal. However, when I was 
trying to mutate sequences, it reported the following error message:


debug:: safe_python_command() PyRun_SimpleString() 
coot.mutate_residue_range(0, "C", 1, 2, "FF")


Traceback (most recent call last):

File "", line 1, in 

NameError: name 'coot' is not defined

Is this my environment issue or something else? Any help would be 
appreciated.



I can reproduce this - I'll track it down.




OK done. Uninstall your coot and reinstall it as you did last time 
(using --verbose --HEAD)



Paul.




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Re: [COOT] Mac Coot 1.0.06-pre mutate sequence not working

2022-06-24 Thread Paul Emsley 

On 25/06/2022 04:12, Sun, Chen wrote:


Hello,


Hello.


I am using Coot 1.0.06-pre on MacOS Monterey installed with homebrew.


Good news in the pipeline, FWIW.

I am able to run coot successfully from terminal. However, when I was 
trying to mutate sequences, it reported the following error message:


debug:: safe_python_command() PyRun_SimpleString() 
coot.mutate_residue_range(0, "C", 1, 2, "FF")


Traceback (most recent call last):

File "", line 1, in 

NameError: name 'coot' is not defined

Is this my environment issue or something else? Any help would be 
appreciated.



I can reproduce this - I'll track it down.

Thanks,

Paul.




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