Oh... Wow... Thanks, I'll try that! On Tue, Dec 1, 2020, 18:37 Daniel Asarnow <[email protected]> wrote:
> 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/
