Thanks for the quick response Paul, appreciated
I edited the file and re-installed ccp4, so now Prosmart is available
The restraints menu still generates no restraints, and Prosmart has some
trouble as well.
I tried with different pdb just in case, but same issues. Restraints should
appear as in v-0.9 no?
###
----------- extra restraints ---------
0
55627
(MacCoot:91313): Gtk-WARNING **: 19:04:48.053: Broken accounting of active
state for widget 0x7fb8b16a8660(GtkLabel)
(MacCoot:91313): Gtk-WARNING **: 19:04:48.053: Broken accounting of active
state for widget 0x7fb8b16a84f0(GtkBox)
(MacCoot:91313): Gtk-WARNING **: 19:04:48.053: Broken accounting of active
state for widget 0x7fb8b16a8200(GtkToggleButton)
(MacCoot:91313): Gtk-WARNING **: 19:04:48.053: Broken accounting of active
state for widget 0x7fb8b16a7ff0(GtkMenuButton)
(MacCoot:91313): Gtk-WARNING **: 19:04:48.053: Broken accounting of active
state for widget 0x7fb8e3a8a6d0(GtkBox)
(MacCoot:91313): Gtk-WARNING **: 19:04:48.053: Broken accounting of active
state for widget 0x7fb8e3a8a550(GtkBox)
(MacCoot:91313): Gtk-WARNING **: 19:04:48.053: Broken accounting of active
state for widget 0x7fb8e3a868e0(GtkBox)
(MacCoot:91313): Gtk-WARNING **: 19:04:48.053: Broken accounting of active
state for widget 0x7fb8e389afb0(GtkApplicationWindow)
debug:: make_store_for_model_molecule_combobox appending 7 7 pdb3lkr.ent
debug:: make_store_for_model_molecule_combobox appending 7 7 pdb3lkr.ent
INFO:: Creating directory coot-ccp4
debug open write coot-ccp4/prosmart.log
Reading ProSMART restraints from ProSMART_Output/pdb3lkr.ent-prosmart.txt
not 24 words
INFO:: Failed to match restraint to templates:
# ProSMART Restraints File
not 24 words
INFO:: Failed to match restraint to templates:
#
not 24 words
INFO:: Failed to match restraint to templates:
# Comprises Chain-Chain Restraints Files:
not 24 words
INFO:: Failed to match restraint to templates:
# pdb3lkr.ent-prosmart_A_pdb3lkr.ent-prosmart-ref_A
not 24 words
INFO:: Failed to match restraint to templates:
# pdb3lkr.ent-prosmart_B_pdb3lkr.ent-prosmart-ref_B
not 24 words
INFO:: Failed to match restraint to templates:
# pdb3lkr.ent-prosmart_C_pdb3lkr.ent-prosmart-ref_C
not 24 words
INFO:: Failed to match restraint to templates:
#
not 24 words
INFO:: Failed to match restraint to templates:
#
not 24 words
INFO:: Failed to match restraint to templates:
# --------------------------------------------------
not 24 words
INFO:: Failed to match restraint to templates:
#
not 24 words
INFO:: Failed to match restraint to templates:
#
not 24 words
INFO:: Failed to match restraint to templates:
# ProSMART Restraints File
not 24 words
INFO:: Failed to match restraint to templates:
external generated ProSMART source
pdb3lkr.ent-prosmart_A_pdb3lkr.ent-prosmart-ref_A
not 24 words
INFO:: Failed to match restraint to templates:
# ProSMART Restraints File
not 24 words
INFO:: Failed to match restraint to templates:
external generated ProSMART source
pdb3lkr.ent-prosmart_B_pdb3lkr.ent-prosmart-ref_B
not 24 words
INFO:: Failed to match restraint to templates:
# ProSMART Restraints File
not 24 words
INFO:: Failed to match restraint to templates:
external generated ProSMART source
pdb3lkr.ent-prosmart_C_pdb3lkr.ent-prosmart-ref_C
INFO:: add_refmac_extra_restraints(): have 49248 bond restraints
INFO:: add_refmac_extra_restraints(): have 0 angle restraints
From: Paul Emsley <pems...@mrc-lmb.cam.ac.uk>
Date: Friday, 26 July 2024 at 18:29
To: Fernández-Leiro.Rafael <rfle...@cnio.es>, COOT@JISCMAIL.AC.UK
<COOT@JISCMAIL.AC.UK>
Subject: Re: Prosmart / Restraints on Mac
CAUTION: This email originated from outside of the organization. Do not click
links or open attachments unless you recognize the sender and know the content
is safe
On 26/07/2024 16:44, Fernández-Leiro.Rafael wrote:
--
Dear all,
I am having trouble running prosmart on the mac version (1.1.10 and previous
version).
Running any option from the “restraints” menu gives an error:
###
in generate_self_restraint_func() 6 A 3.7
----------- extra restraints ---------
0
9915
DEBUG:: --- new_startup_on_glarea_resize() 1929 1087
Traceback (most recent call last):
File
"/usr/local/Cellar/python@3.12/3.12.4/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/coot/gui_prosmart.py"<mailto:/usr/local/Cellar/python@3.12/3.12.4/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/coot/gui_prosmart.py>,
line 140, in <lambda>
lambda _simple_action, _arg: generate_all_molecule_self_restraints(6.0))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/usr/local/Cellar/python@3.12/3.12.4/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/coot/gui_prosmart.py"<mailto:/usr/local/Cellar/python@3.12/3.12.4/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/coot/gui_prosmart.py>,
line 81, in generate_all_molecule_self_restraints
generate_self_restraints(aa_imol, val)
^^^^^^^^^^^^^^^^^^^^^^^^
NameError: name 'generate_self_restraints' is not defined
####
Oh that's annoying.
Change line 89 of gui_prosmart.py to read
coot.generate_self_restraints(aa_imol, val)
(i.e. add a "coot." to the front of the line)
Using Prosmart shows a pop-up window that says “No prosmart”
It needs to be in your path. Coot does not bundle ProSMART.
Should Prosmart be installed separately?
Yes - typically as part of CCP4. At least for the moment.
(I used the brew install approach, which btw works fantastic)
Yes, it does:
("brew install brewsci/bio/coot" for the record).
Well done Yoshitaka Moriwaki.
Paul.
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