Re: [COOT] applying link restraints in coot
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 f
Re: [COOT] applying link restraints in coot
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. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] applying link restraints in coot
Sorry for the delay. Better late than never, perhaps? On 12/01/2022 23:04, Georg Mlynek wrote: With the help of ccp4 people I created link records to build a large ligand from smaller monomers. One link is FTT-MYR. Cif file attached. I also put this record in the pdb file LINKR O3 FTT E 2 C1 MYR E 3 FTT-MYR and did Import CIF dictionary in coot with the FTT-MYR.cif However doing sphere_refine the restraints seem to be not applied, because the residues are repelled. I attach my test molecule. I read in your dictionary and did a regularization - it seemed to work fine. (I didn't use sphere refine because I didn't have density). I am using Coot 0.9.7. Why don't you say what you are using? What am I doing wrong? Why do I have to import the cif file via File --> Import CIF dictionary in coot and can't just past the cif files in C:\CCP4-7\7.1\Lib\data\monomers\list ? Does this link exist in mon_lib_list.cif? Coot reads mon_lib_list.cif as it starts up. Paul. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ FTT_MYR-coot-start.pdb Description: application/aportisdoc
[COOT] applying link restraints in coot
Dear Scientific community, Paul and Bernhard, With the help of ccp4 people I created link records to build a large ligand from smaller monomers. One link is FTT-MYR. Cif file attached. I also put this record in the pdb file LINKR O3 FTT E 2 C1 MYR E 3 FTT-MYR and did Import CIF dictionary in coot with the FTT-MYR.cif However doing sphere_refine the restraints seem to be not applied, because the residues are repelled. What am I doing wrong? Why do I have to import the cif file via File --> Import CIF dictionary in coot and can't just past the cif files in C:\CCP4-7\7.1\Lib\data\monomers\list ? Many thanks and best regards, Georg. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ #ACEDRG_VERSION 222 #ACEDRG_DB_VERSION 11 #RDKit_VERSION 2017.03.2 #REFMAC_VERSION5.8.0267 # data_mod_list loop_ _chem_mod.id _chem_mod.name _chem_mod.comp_id _chem_mod.group_id FTTm1 "3-HYDROXY-TETRADECANOIC ACID" FTT . MYRm1 "MYRISTIC ACID" MYR . data_link_list loop_ _chem_link.id _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 _chem_link.name FTT-MYRFTT FTTm1 non-polymer MYR MYRm1 non-polymer FTT-MYR data_mod_FTTm1 loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_charge FTTm1 delete HO3 . H H 0 FTTm1 change O3. O O20 loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd FTTm1 delete O3HO3 single . . FTTm1 change C3O3single 1.462 0.0100 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd FTTm1 delete C3O3HO3 . . loop_ _chem_mod_tor.mod_id _chem_mod_tor.function _chem_mod_tor.atom_id_1 _chem_mod_tor.atom_id_2 _chem_mod_tor.atom_id_3 _chem_mod_tor.atom_id_4 _chem_mod_tor.new_value_angle _chem_mod_tor.new_value_angle_esd FTTm1 delete C2C3O3HO3 . . data_mod_MYRm1 loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_charge MYRm1 delete O2. O OC-1 loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd MYRm1 delete C1O2single . . MYRm1 change C1O1double 1.203 0.0150 MYRm1 change C1C2single 1.503 0.0174 loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd MYRm1 delete O1C1O2. . MYRm1 delete O2C1C2. . MYRm1 change O1C1C2124.7142.71 loop_ _chem_mod_plane.mod_id _chem_mod_plane.function _chem_mod_plane.plane_id _chem_mod_plane.atom_id _chem_mod_plane.dist_esd MYRm1 delete plan-1 C1 0.020 MYRm1 delete plan-1 C2 0.020 MYRm1 delete plan-1 O1 0.020 MYRm1 delete plan-1 O2 0.020 data_link_FTT-MYR loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link
