Hello, I am using Coot 0.9.5, installed from CCP4 package. It was working well until today I decided to install ccp4 again because I have some trouble of trying to install ARP package. So I guess that Coot also get reinstall after I reinstall the package. Coot runs normally, having some warning like in the attachment file ¨coot_warning.txt¨ but I am able to open the pdb, the map and most of the function are working normally. There is only one problem is that when I tried to refine the model with Ramachandran, it always give me the red ramachandran, even if I tried to refine in a place that according to coot validation, the ramachandran there was good, it also gave me only the red ramachandran.
Could anybody can help with this situation? it is not possible for me to refine a model with out ramachandran option. Thank you. Phong Nguyen ######################################################################## 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/
Gtk-Message: Failed to load module "gail" Gtk-Message: Failed to load module "atk-bridge" Gtk-Message: Failed to load module "canberra-gtk-module" (coot-bin:24933): GLib-GObject-WARNING **: g_object_set_valist: object class 'GtkSettings' has no property named 'gtk-application-prefer-dark-theme' INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /opt/xtal/ccp4-7.1/lib/data/monomers/ There are 166 data in /opt/xtal/ccp4-7.1/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/ALA.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/ASP.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/ASN.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/c/CYS.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/GLN.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/GLY.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/GLU.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/p/PHE.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/h/HIS.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/i/ILE.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/l/LYS.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/l/LEU.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/m/MET.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/m/MSE.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/p/PRO.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/ARG.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/s/SER.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/t/THR.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/v/VAL.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/t/TRP.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/t/TYR.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/p/PO4.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/s/SO4.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/GOL.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/c/CIT.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/e/EDO.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/A.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/c/C.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/G.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/u/U.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DA.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DC.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DG.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DT.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/h/HOH.cif There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/n/NA.cif Spacegroup: P 1 <font color="#310DF6"><b>(filter-fileselection-filenames-state)</b></font> <font color="#310DF6"><b>(get-active-map-drag-flag)</b></font> <font color="#310DF6"><b>(use-graphics-interface-state)</b></font> INFO:: coot.py imported ** (coot-bin:24933): WARNING **: Trying to register gtype 'GMountMountFlags' as enum when in fact it is of type 'GFlags' ** (coot-bin:24933): WARNING **: Trying to register gtype 'GDriveStartFlags' as enum when in fact it is of type 'GFlags' ** (coot-bin:24933): WARNING **: Trying to register gtype 'GSocketMsgFlags' as enum when in fact it is of type 'GFlags' INFO:: coot_python initialized Running python script /opt/xtal/ccp4-7.1/lib/python2.7/site-packages/coot/coot_load_modules.py Good Afternoon Phong,,,, Welcome to Coot version 0.9.5 <font color="#310DF6"><b>(set-display-intro-string "Good Afternoon Phong,,,, Welcome to Coot version 0.9.5")</b></font> Coot Python Scripting GUI code found and loaded. Coot Python Scripting GUI code found and loaded. <font color="#310DF6"><b>(use-graphics-interface-state)</b></font> <font color="#310DF6"><b>(filter-fileselection-filenames-state)</b></font> <font color="#310DF6"><b>(get-active-map-drag-flag)</b></font> <font color="#310DF6"><b>(use-graphics-interface-state)</b></font> Coot Scheme Scripting GUI code found and loaded. Good afternoon phong,,,. Welcome to Coot 0.9.5. <font color="#310DF6"><b>(set-display-intro-string "Good afternoon phong,,,. Welcome to Coot 0.9.5")</b></font> <font color="#310DF6"><b>(set-display-lists-for-maps 1)</b></font> <font color="#310DF6"><b>(filter-fileselection-filenames-state)</b></font> <font color="#310DF6"><b>(get-active-map-drag-flag)</b></font> <font color="#310DF6"><b>(use-graphics-interface-state)</b></font> <font color="#310DF6"><b>(command-in-path-or-absolute? *probe-command*)</b></font> State file 0-coot-history.py written. State file 0-coot-history.scm written. ######################################################################## 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/
