Hi Johannes, You can point Windows Phenix to Wincoot and it all works. Best, -da
On Tue, Dec 1, 2020 at 7:20 AM Johannes Cramer <[email protected]> wrote: > 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. You can read more about KI’s processing of personal >> data here<https://ki.se/en/staff/data-protection-policy>. >> >> ######################################################################## >> >> 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/ >> > > ------------------------------ > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > ######################################################################## 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/
