Hello all,
We had a recent discussion on this recently when I encountered similar issues.
The workaround suggested by Todd Green worked perfectly for me:
Here is the summary below:
Todd Green suggested installing CCP4 (see message below) with COOT.
It worked for me. There are still some issues
Mirek,
Yes, this is a known issue (I read about it previously either here or on
the Coot webpage, I can't recall which).
The only "workaround" is to check the "keep delete active" box before you
begin deleting. It took me a bit to realize this, so I'll share: The window
is still open and can be a
Hi,
I just upgrade my Mac to Ventura v13.2 from v12.6.3 and run into issue with
Coot. When I use the delete command it causes the main Coot window disappearing
while other Coot windows stay open. Has anyone had this issue? Is there a way
around it? No such problem on v12.6.3.
Best,
Mirek
#
Yes, Christian - that has happened to me. I found it by using the
Validation Density fit., and noticing that a residue number which was not
meant to exist had a Density fit bar. As you say there was a stray atom
with that ID - totally incorrect - in the coordinate file..
Eleanor
On Wed, 10 Apr
Well I think I recall one instance where it worked for me the way you
describe. I think there was either a stray residue atom somewhere or a
numbering not quite right. Could it be that this happens for you after
autobuilding?
Cheers
On Wed, Apr 10, 2019 at 7:11 PM Hillen, Hauke
wrote:
> Dear al
Dear all,
Thank you for your many suggestions!
Indeed, I was not able to fix the issue to my satisfaction. As Paul suspected,
set_add_terminal_residue_do_post_refine was already set to 0. The triple-refine
also did not improve anything. I also checked for the TER records, which I also
suspected
Or I am quite happy with the words REFINE
E
On Mon, 8 Apr 2019 at 21:02, Paul Emsley wrote:
> On 08/04/2019 20:36, Eleanor Dodson wrote:
> > Words - use WORDS - what does "the T key" mean in plain English!!!
> >
> >
>
> Dear Eleanor,
>
>
> T is for "Triple Refine"
>
> Extension -> Settings -
On 08/04/2019 20:36, Eleanor Dodson wrote:
> Words - use WORDS - what does "the T key" mean in plain English!!!
>
>
Dear Eleanor,
T is for "Triple Refine"
Extension -> Settings -> Key bindings: will give you a brief description
If you want words, you can of course do Calculate -> Scripting
One of the key bindings in Coot. Need to center on a residue surrounded
by a residue on the left and the right. Press "Shift+T" and Coot will
refine the three consecutive residues. There might be the refinement
quality window popping up, though I'm not sure. There is another
keybinding "h" or "s
Words - use WORDS - what does "the T key" mean in plain English!!!
Eleanor
On Mon, 8 Apr 2019 at 18:59, Paul Emsley wrote:
> On 08/04/2019 18:40, Hillen, Hauke wrote:
> >
> >
> > Lately I have been having a strange issue with Coot (0.8.9.2-pre on
> > MacOS X). Sometimes when I add residues
On 08/04/2019 18:40, Hillen, Hauke wrote:
>
>
> Lately I have been having a strange issue with Coot (0.8.9.2-pre on
> MacOS X). Sometimes when I add residues using “Add residue…”, they are
> not linked to the previous residue. When I try to real space refine /
> normalize they behave as if they wer
Hi All,
Lately I have been having a strange issue with Coot (0.8.9.2-pre on MacOS X).
Sometimes when I add residues using “Add residue…”, they are not linked to the
previous residue. When I try to real space refine / normalize they behave as if
they were part of the chain, but the atoms that sh
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