Dear Paul, thanks.
I just tried on my linux machine in the lab running kubunutu 20.4 and
coot 0.9.6
File --> Import CIF dictionary
then
File --> Open coordinates FTT_MYR-coot-start.pdb
But also here doing Regularize zone the link is not recognized.
(I have also phenix installed on the windows and linux machine. Could it
be that there is some interference from there?)
Regarding your answer to
And there is no FTT-MYR link in the mon_lib_list.cif
indeed.
even after importing in coot (attached).
mon_lib_list.cif and all monomer restraints are read-only for Coot.
Ok, so when doing Import CIF dictionary then File- the link is not
written into the mon_lib_list.cif ?
Where does coot write the link and is it transformed in some way?
I copied the whole text of the Link_FTT_MYR_link.cif into
mon_lib_list.cif . But this is not solving the issue.
Here is the terminal output when starting coot. The last two lines are
written out when doing File --> Import CIF dictionary
How can I help?
Many thanks again, for all your effort.
Br, Georg.
C:\WinCoot>title WinCoot
C:\WinCoot>set COOT_PREFIX=C:\WinCoot\
C:\WinCoot>set COOT_GUILE_PREFIX=C:/WinCoot/
C:\WinCoot>set COOT_HOME=C:\WinCoot\
C:\WinCoot>set COOT_BACKUP_DIR=C:\WinCoot\\coot-backup
C:\WinCoot>set COOT_SHARE=C:\WinCoot\\share
C:\WinCoot>if not exist "" (
echo no $CLIBD_MON found trying to setup CCP4
Call :setup_ccp4
)
no $CLIBD_MON found trying to setup CCP4
C:\WinCoot>For /F "Skip=1 Tokens=2*" %A In ('Reg Query
"HKLM\SOFTWARE\WOW6432Node\CCP4-7" /V "InstallDir" 2>Nul') Do Set
"CCP4Dir=%~B"
C:\WinCoot>Set "CCP4Dir=C:\CCP4-7"
C:\WinCoot>REM find latest dir
C:\WinCoot>FOR /F " tokens=*" %i IN ('dir "C:\CCP4-7\7.*" /b /ad-h /t:c
/od') DO SET vers=%i
C:\WinCoot>SET vers=7.1
C:\WinCoot>REM setup ccp4
C:\WinCoot>call "C:\CCP4-7\7.1\ccp4.setup.bat"
CCP4: C:\CCP4-7\7.1
CCP4_SCR: C:\ccp4temp
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON:
C:\CCP4-7\7.1\lib\data\monomers\
There are 249 data in C:/CCP4-7/7.1/lib/data/monomers//list/mon_lib_list.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//a/ALA.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//a/ASP.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//a/ASN.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//c/CYS.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//g/GLN.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//g/GLY.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//g/GLU.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//p/PHE.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//h/HIS.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//i/ILE.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//l/LYS.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//l/LEU.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//m/MET.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//m/MSE.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//p/PRO.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//a/ARG.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//s/SER.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//t/THR.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//v/VAL.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//t/TRP.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//t/TYR.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//p/PO4.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//s/SO4.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//g/GOL.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//c/CIT.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//e/EDO.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//a/A.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//c/C.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//g/G.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//u/U.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//d/DA.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//d/DC.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//d/DG.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//d/DT.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//h/HOH.cif
There are 2 data in C:/CCP4-7/7.1/lib/data/monomers//n/NA.cif
Spacegroup: P 1
(coot-bin.exe:1916): Pango-WARNING **: 11:30:24.083: couldn't load font
"Noto Sans Bold Not-Rotated 10.0615234375", falling back to "Sans Bold
Not-Rotated 10.0615234375", expect ugly output.
(coot-bin.exe:1916): Pango-WARNING **: 11:30:24.093: couldn't load font
"Noto Sans Bold Not-Rotated 7.751953125", falling back to "Sans Bold
Not-Rotated 7.751953125", expect ugly output.
(coot-bin.exe:1916): Pango-WARNING **: 11:30:24.100: couldn't load font
"Noto Sans Bold Not-Rotated 12", falling back to "Sans Bold Not-Rotated
12", expect ugly output.
(coot-bin.exe:1916): Pango-WARNING **: 11:30:24.107: couldn't load font
"Noto Sans Bold Not-Rotated 4", falling back to "Sans Bold Not-Rotated
4", expect ugly output.
(coot-bin.exe:1916): Pango-WARNING **: 11:30:24.111: couldn't load font
"Noto Sans Bold Not-Rotated 6", falling back to "Sans Bold Not-Rotated
6", expect ugly output.
(coot-bin.exe:1916): Pango-WARNING **: 11:30:24.134: couldn't load font
"Noto Sans Not-Rotated 15.1279296875", falling back to "Sans Not-Rotated
15.1279296875", expect ugly output.
(coot-bin.exe:1916): Pango-WARNING **: 11:30:24.136: couldn't load font
"Noto Sans Not-Rotated 11.7470703125", falling back to "Sans Not-Rotated
11.7470703125", expect ugly output.
(coot-bin.exe:1916): Pango-WARNING **: 11:30:24.163: couldn't load font
"Noto Sans Not-Rotated 10.6669921875", falling back to "Sans Not-Rotated
10.6669921875", expect ugly output.
(coot-bin.exe:1916): Pango-WARNING **: 11:30:24.172: couldn't load font
"Noto Sans Not-Rotated 18.1640625", falling back to "Sans Not-Rotated
18.1640625", expect ugly output.
(coot-bin.exe:1916): Pango-WARNING **: 11:30:24.180: couldn't load font
"Noto Sans Not-Rotated 27.775390625", falling back to "Sans Not-Rotated
27.775390625", expect ugly output.
filter_fileselection_filenames_state ()
get_active_map_drag_flag ()
use_graphics_interface_state ()
INFO:: coot.py imported
INFO:: coot_python initialized
Running python script
C:/WinCoot//lib/python2.7/site-packages/coot/coot_load_modules.py
Good Morning Mlynek, Welcome to Coot version 0.9.7
set_display_intro_string ("Good Morning Mlynek, Welcome to Coot version
0.9.7")
Coot Python Scripting GUI code found and loaded.
Coot Python Scripting GUI code found and loaded.
use_graphics_interface_state ()
Running python script C:/WinCoot//.coot-preferences/coot.py
Running python script C:/WinCoot//.coot-preferences/coot_preferences.py
set_filter_fileselection_filenames (0)
unset_sticky_sort_by_date ()
set_colour_map_rotation_on_read_pdb (21.00)
set_colour_map_rotation_on_read_pdb_c_only_flag (1)
set_density_size (20.00)
set_swap_difference_map_colours (0)
set_colour_map_rotation_for_map (14.00)
set_active_map_drag_flag (1)
set_idle_function_rotate_angle (1.00)
Running python script C:/WinCoot//.coot-preferences/coot_toolbuttons.py
Running python script C:/WinCoot//.coot-preferences/curlew_chain_refine.py
Running python script
C:/WinCoot//.coot-preferences/curlew_click_click_refine_residues.py
Running python script
C:/WinCoot//.coot-preferences/curlew_long_residues_refine.py
Running python script C:/WinCoot//.coot-preferences/quicksymm.py
set_show_symmetry_master (1)
set_show_unit_cells_all (1)
set_symmetry_colour_by_symop (0, 1)
set_symmetry_molecule_rotate_colour_map (0, 1)
set_symmetry_size (50.00)
symmetry_as_calphas (0, 1)
filter_fileselection_filenames_state ()
get_active_map_drag_flag ()
filter_fileselection_filenames_state ()
first_coords_imol ()
There are 5 data in G:/My Drive/boku/alla/paul/Link_FTT_MYR_link.cif
Read 3 atoms/links in restraints from G:/My
Drive/boku/alla/paul/Link_FTT_MYR_link.cif
Am 03.02.2022 um 00:06 schrieb Paul Emsley:
On 02/02/2022 22:44, Georg Mlynek wrote:
Dear Paul, many thanks for answering.
I am using Windows 10 and was running WinCoot-0.9.6.1.1 when I wrote
the mail and just upgraded to 0.9.7.
OK, sounds good.
Wincoot is located here C:\WinCoot
CCP4 and the mon_lib_list.cif here
OK.
And there is no FTT-MYR link in the mon_lib_list.cif
indeed.
even after importing in coot (attached).
mon_lib_list.cif and all monomer restraints are read-only for Coot.
I guess we have spotted the problem.
have we though? :-)
I also saw in your FTT_MYR-coot-start.pdb there is no LINKR record. I
thought this is needed?
It isn't, Coot reads LINKR as if it were a LINK. It doesn't write LINKRs.
There was no LINK either. Coot does "link" generation on the fly when
generating restraints as often LINKs were wrong or missing (at least a
few years ago that was the case).
Paul.
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