On 16/11/2022 19:19, Dr. Kevin M Jude wrote:
Hopping onto this thread:
Besides the sugar connectivity, I see that when I Draw > Sequence
View, the sequence opens in a pop-up window instead of the main window
and does not show gaps or numbering. This is coot 0.9.8.5 from ccpem
nightly 20221108 on M1 chip, Mac OS Monterey 12.6.
*From: *Mailing list for users of COOT Crystallographic Software
<[email protected]> on behalf of Xavier Brazzolotto
<[email protected]>
*Date: *Wednesday, November 16, 2022 at 10:04 AM
*To: *[email protected] <[email protected]>
*Subject: *Re: MacCoot 0.9.8.5 issues
H Paul,
* When I delete a molecule, my Coot/X11 window
« disappears ». It is not closed/killed but somehow
minimized. I can get it back from my dock, but a bit annoying.
Here’s what the console says.
*(set-delete-residue-mode)*
(2) " O5 "/1/chainid="A"/625/FUC, occ: 1.000 with B-factor:
66.076 element: " O" at (26.959,-34.446,11.593) : 0.132
INFO:: backup file name
coot-backup/_Users_xbrazzolotto_Desktop_Crystallography_20221116_MR37216_MR-CoX_Phenix_MR372016_20221116_refine_3-coot-1.pdb_Wed_Nov_16_18:30:17_2022_modification_11.pdb.gz
*(delete-residue 2 "A" 625 "")*
*(clear-pending-delete-item)*
Pending Picks Cleared
*(delete-residue-by-atom-index 2 4280 1)*
debug:: g.safe_scheme_command() with command
post-manipulation-hook
I have not heard of that before.
The terminal doesn’t seem to report any bug, this is probably related
to macOS. It's just annoying, it still works, it is not like it
crashes every time I delete a molecule.
* When I build sugar chains with the N-linked Glycan module,
they are not building correctly. It looks like it messes
up with the wrong atom for linking.
I am part-way through a fix for this. It is high priority and will
require a new release.
Good to know that it is already known and handled. Will wait for the
next release.
It may be to restore a previous coot version (without such bugs) by
downgrading the last update of CCP4i
There are 2 different sequence view widgets. What I susppect you are
seeing is the earlier sequence view widget that gets used when you have
insertion code - maybe you are looking at an antibody or some such.
Paul.
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