Dear Kay,
I am running WSL with xds also for my normal work. Your descriptions is
very good. The trick to get shelx running was new to me - thank you for
that!
However, on my AMD / Win 10 machine coot is not running with your
instructions. It only shows a grey area:
(I normally run XDS in /mnt/* and switch to the windows versions of ccp4
and phenix ....)
By the way, I just had an 4 weeks online course about crystallography
via zoom. I would say all students PC (regardless of Mac or Windows)
gave similar amount of troubles - with different programs though. To
some regard I regret that I didn't use a Virtualbox with Ubuntu...
Good Luck with the course!
Jan
Am 29.01.2021 um 19:01 schrieb Kay Diederichs:
Dear all,
today I finally tried WSL2 on Windows10, with the intent of being able to use
CCP4 including coot, and XDS / XDSGUI e.g. in workshops when many students have
Windows machines.
I was successful when using Xming (but not VcXsrv) as X-server. My writeup is
athttps://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Installation#WSL2
.
I'd appreciate it if people would check this out, and improve the
documentation. I'd also love hearing about the performance of coot, compared
with Linux and wincoot on Windows, from you.
HTH,
Kay
On Mon, 23 Nov 2020 15:01:58 +0100, Johannes Cramer<[email protected]>
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: image.png]
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AG Prof. Baumann
Institut für Biochemie / Uni-Köln
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