Re: [COOT] Linking two sidechains with a double bond and refining
Hi David Briggs,
Thank you for the suggestion of AceDrg. I gave it a try, using the Coot way
and the Jligand way for AceDrg. For some reason the Coot method didn't make a
cif, only jligand did. But the cif didn't have any effect on refinement. What
did work for Phenix was to define the planarity in a phil file:
planarity {
action = *add
atom_selection = \
chain A and resname LIG and resid 3 and name C1 or \
chain A and resname LIG and resid 3 and name C2 or \
chain A and resname IGL and resid 6 and name C3 or \
chain A and resname IGL and resid 6 and name C4
sigma = 0.02
}
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Re: [COOT] Linking two sidechains with a double bond and refining
Hi Joel, That's a great idea! I've considerd it, and technically it would work as you suggest to refine correctly. However, that would look like more carbons come from one of the two precursor molecules than the other, which chemically would be wrong. I really want to avoid giving the impression that different chemistry happened to form this covalent bond. It's just unfortunate that the created bond isn't more easily defined for these programs. Thanks, David To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=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] Linking two sidechains with a double bond and refining
Message was attached instead of in the body for some reason. Here it is" Hi Learned Friends, I'm trying to refine a structure that has a very similar staple to the one in 8GJS. In that structure, there's a double bond between residue 5 and 12 in chain B. I've tried to define a link using jligand and I get a cif that looks like it would define the double bond. But when I load that into Coot and try to refine the link, the bond blows up, bonded atoms seperate. Has anyone had any luck with this? What should I use to define a double bond link such that Coot (and Phenix) doesn't blow it up, but also keeps the appropriate atoms in plane (either trans or cis, NOT something in between). Thanks, David To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=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/
[COOT] Linking two sidechains with a double bond and refining
Hi Learned Friends, I'm trying to refine a structure that has a very similar staple to the one in 8GJS. In that structure, there's a double bond between residue 5 and 12 in chain B. I've tried to define a link using jligand and I get a cif that looks like it would define the double bond. But when I load that into Coot and try to refine the link, the bond blows up, bonded atoms seperate. Has anyone had any luck with this? What should I use to define a double bond link such that Coot (and Phenix) doesn't blow it up, but also keeps the appropriate atoms in plane (either trans or cis, NOT something in between). Thanks, David To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=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/
[COOT] WinCoot preferences
Hi Friends,
I have sucessfully used preference files for WinCoot for that last 8 years
across 3 laptops, but with this new laptop it's not working. It looks like the
files are read, but I don't see the output in the terminal to indicate that it
has any effect. And the preferences are not updated. I've always put coot.py
and coot_preferences.py into C:\WinCoot\.coot-preferences. I've attached my
preferences files and the terminal output. Any ideas what changed? I'm using
Wincoot 0.9.8.1.
These are the commands I'm most interested in having run on each startup:
set_show_symmetry_master (1)
set_show_environment_distances (1)
set_environment_distances_label_atom (1)
set_refine_ramachandran_angles (1)
set_default_initial_contour_level_for_map (1)
set_nomenclature_errors_on_read ("ignore")
Thanks!
-David
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coot_preferences.py
Description: Binary data
coot.py
Description: Binary data
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>REM find latest dir
C:\WinCoot>FOR /F " tokens=*" %i IN ('dir "\7.*" /b /ad-h /t:c /od') DO SET
vers=%i
File Not Found
C:\WinCoot>REM setup ccp4
C:\WinCoot>call "\\ccp4.setup.bat"
The filename, directory name, or volume label syntax is incorrect.
C:\WinCoot>Exit /B 0
C:\WinCoot>if not exist "" (
echo no $CLIBD_MON found setting COOT_REFMAC_LIB_DIR
set COOT_REFMAC_LIB_DIR=C:\WinCoot\\share\coot\lib
)
no $CLIBD_MON found setting COOT_REFMAC_LIB_DIR
C:\WinCoot>set COOT_SCHEME_DIR=C:\WinCoot\\share/coot/scheme
C:\WinCoot>set
COOT_STANDARD_RESIDUES=C:\WinCoot\\share\coot\standard-residues.pdb
C:\WinCoot>set COOT_PIXMAPS_DIR=C:\WinCoot\\share\coot\pixmaps
C:\WinCoot>set COOT_RESOURCES_FILE=C:\WinCoot\\share\coot\cootrc
C:\WinCoot>set COOT_DATA_DIR=C:\WinCoot\\share\coot
C:\WinCoot>set COOT_REF_STRUCTS=C:\WinCoot\\share\coot\reference-structures
C:\WinCoot>set COOT_PYTHON_DIR=C:\WinCoot\\lib\python2.7\site-packages\coot
C:\WinCoot>REM set
COOT_REF_SEC_STRUCTS=C:\WinCoot\\share\coot\ss-reference-structures
C:\WinCoot>REM set PYTHONHOME=C:\WinCoot\\python27
C:\WinCoot>set
GUILE_LOAD_PATH=C:/WinCoot//share/guile/1.8;C:/WinCoot//share/guile;C:/WinCoot//share/guile/gtk-2.0;C:/WinCoot//share/guile/gui;C:/WinCoot//share/guile/www;C:/WinCoot//share/guile/site
C:\WinCoot>set SYMINFO=C:\WinCoot\\share\coot\syminfo.lib
C:\WinCoot>set
PATH=C:\WinCoot\\bin;C:\WinCoot\\lib;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\WINDOWS\System32\OpenSSH\;C:\Users\David\AppData\Local\Microsoft\WindowsApps;;C:\WinCoot\\bin\extras
C:\WinCoot>coot-bin.exe
There are 143 data in
C:/WinCoot//share/coot/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/a/ALA.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/a/ASP.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/a/ASN.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/c/CYS.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/g/GLN.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/g/GLY.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/g/GLU.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/p/PHE.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/h/HIS.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/i/ILE.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/l/LYS.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/l/LEU.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/m/MET.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/m/MSE.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/p/PRO.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/a/ARG.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/s/SER.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/t/THR.cif
There are 2 data in C:/WinCoot//share/coot/lib/data/monomers/v/VAL.cif
There are 2 data
