Dear Bernhard, Thank you for your email. I am using wincoot most of the time, however, sometimes it is nice to have integration into linux programs (i.e. phenix) for refinement. But you are right, it is slow...
Cheers, Johannes Am Di., 1. Dez. 2020 um 14:12 Uhr schrieb Bernhard Lohkamp < [email protected]>: > Not really answering your question but if you are on windows maybe you > want to try native WinCoot instead? There is an installer for 0.9.2 now: > > https://github.com/bernhardcl/coot/releases/tag/Release-0.9.2 > > https://bernhardcl.github.io/coot/wincoot-releases.html > > So far I only tried on WSL and it worked (using VcXsrv using native > opengl) but it was slow... > > B > > On 23/11/2020 15:01, Johannes Cramer wrote: > > Dear all, > > > > I recently tried to get my work environment running on Ubuntu20.04 run > > through Windows10 with WSL2. So far it was a great experience, but I > > cannot get coot to work properly. > > I installed ccp4 and coot with it. > > When I start coot, the gui starts, there are some warnings (see below) > > and I can see all the elements however the coordinate space is not > > completely on the screen (s. screenshots). > > Can anyone help? > > When I type ldd /opt/xtal/ccp4-7.1/libexec/coot-bin I get no missing > > libraries. > > > > Cheers, > > Johannes > > > > > > terminal output > > > > (coot-bin:18683): 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: > > /mnt/d/monomers > > There are 166 data in /mnt/d/monomers/list/mon_lib_list.cif > > There are 2 data in /mnt/d/monomers/a/ALA.cif > > There are 2 data in /mnt/d/monomers/a/ASP.cif > > There are 2 data in /mnt/d/monomers/a/ASN.cif > > There are 2 data in /mnt/d/monomers/c/CYS.cif > > There are 2 data in /mnt/d/monomers/g/GLN.cif > > There are 2 data in /mnt/d/monomers/g/GLY.cif > > There are 2 data in /mnt/d/monomers/g/GLU.cif > > There are 2 data in /mnt/d/monomers/p/PHE.cif > > There are 2 data in /mnt/d/monomers/h/HIS.cif > > There are 2 data in /mnt/d/monomers/i/ILE.cif > > There are 2 data in /mnt/d/monomers/l/LYS.cif > > There are 2 data in /mnt/d/monomers/l/LEU.cif > > There are 2 data in /mnt/d/monomers/m/MET.cif > > There are 2 data in /mnt/d/monomers/m/MSE.cif > > There are 2 data in /mnt/d/monomers/p/PRO.cif > > There are 2 data in /mnt/d/monomers/a/ARG.cif > > There are 2 data in /mnt/d/monomers/s/SER.cif > > There are 2 data in /mnt/d/monomers/t/THR.cif > > There are 2 data in /mnt/d/monomers/v/VAL.cif > > There are 2 data in /mnt/d/monomers/t/TRP.cif > > There are 2 data in /mnt/d/monomers/t/TYR.cif > > There are 2 data in /mnt/d/monomers/p/PO4.cif > > There are 2 data in /mnt/d/monomers/s/SO4.cif > > There are 2 data in /mnt/d/monomers/g/GOL.cif > > There are 2 data in /mnt/d/monomers/c/CIT.cif > > There are 2 data in /mnt/d/monomers/e/EDO.cif > > There are 2 data in /mnt/d/monomers/a/A.cif > > There are 2 data in /mnt/d/monomers/c/C.cif > > There are 2 data in /mnt/d/monomers/g/G.cif > > There are 2 data in /mnt/d/monomers/u/U.cif > > There are 2 data in /mnt/d/monomers/d/DA.cif > > There are 2 data in /mnt/d/monomers/d/DC.cif > > There are 2 data in /mnt/d/monomers/d/DG.cif > > There are 2 data in /mnt/d/monomers/d/DT.cif > > There are 2 data in /mnt/d/monomers/h/HOH.cif > > There are 2 data in /mnt/d/monomers/n/NA.cif > > INFO:: Reading coordinate file: > > /opt/xtal/ccp4-7.1/share/coot/standard-residues.pdb > > INFO:: file /opt/xtal/ccp4-7.1/share/coot/standard-residues.pdb has > > been read. > > Spacegroup: P 1 > > (filter-fileselection-filenames-state) > > (get-active-map-drag-flag) > > (use-graphics-interface-state) > > INFO:: coot.py imported > > ** (coot-bin:18683): WARNING **: Trying to register gtype > > 'GMountMountFlags' as enum when in fact it is of type 'GFlags' > > ** (coot-bin:18683): WARNING **: Trying to register gtype > > 'GDriveStartFlags' as enum when in fact it is of type 'GFlags' > > ** (coot-bin:18683): 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 ,,,, Welcome to Coot version 0.9.2 > > (set-display-intro-string "Good Afternoon ,,,, Welcome to Coot > > version 0.9.2") > > Coot Python Scripting GUI code found and loaded. > > Coot Python Scripting GUI code found and loaded. > > (use-graphics-interface-state) > > (filter-fileselection-filenames-state) > > (get-active-map-drag-flag) > > (use-graphics-interface-state) > > Coot Scheme Scripting GUI code found and loaded. > > Good afternoon ,,,. Welcome to Coot 0.9.2. > > (set-display-intro-string "Good afternoon ,,,. Welcome to Coot > 0.9.2") > > (set-display-lists-for-maps 1) > > ----------------------------- with enhanced-ligand! > ------------------- > > load /home/cramejo/.coot-preferences/coot-preferences.scm > > (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 16.00) > > (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) > > (filter-fileselection-filenames-state) > > (get-active-map-drag-flag) > > (use-graphics-interface-state) > > WARNING: couldn't write to state file 0-coot-history.py > > WARNING: couldn't write to state file 0-coot-history.scm > > > > > > image.png > > > > ------------------------------------------------------------------------ > > > > To unsubscribe from the COOT list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > > < > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cb4c1905213994845127908d88fb9c780%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637417375800455223%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=oxB09RBxf6AK0F8Xq0trRWBXWZlIkglkX09CpMAyIlU%3D&reserved=0 > > > > > > > > -- > *************************************************** > > Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent > > Div. Molecular Structural Biology/Biomedicum D9 > Dept. of Medical Biochemistry and Biophysics (MBB) | > Karolinska Institutet > SE-171 77 Stockholm > Sweden > +46 8 52487055 > [email protected] | ki.se > > > När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI > kommer att behandla dina personuppgifter. Här finns information om hur KI > behandlar personuppgifter< > https://ki.se/medarbetare/integritetsskyddspolicy>. > > > Sending email to Karolinska Institutet (KI) will result in KI processing > your personal data. 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