> On 7 Oct 2024, at 10:43, SERGIO BARATA GARCIA
> wrote:
>
> I mean that I can´t see the molecule at all. No signal in the display window
> On 4 Oct 2024, at 09:24, SERGIO BARATA GARCIA
> wrote:
>
> Regarding the volume is quite big so I do not know if that could affect:
>
> (x,y,z,n)= 660
> On 17 Mar 2023, at 01:45, Oliver Clarke wrote:
>
> But - the window never used to get iconified after deleting things? Is this
> due to a change in Coot, or a change in Mac OS?
I believe it's a MacOS Ventura/XQuartz issue. Same thing was reported for other
software here: https://github.com/e
> On 1 May 2022, at 01:57, Paul Emsley wrote:
>
> This was discussed in issue 33 - we don't know what the problem is. But
> interestingly CCP4-pre-built binaries don't show the same problem, so it is
> fixable... it's something to do with Adwaita.
It's a change in icon name I think - version 4
Hi,
> On 1 Feb 2021, at 21:56, Huw Jenkins wrote:
>
> Either way I guess it will go away in the next XQuartz beta release.
Update: I just installed XQuartz 2.8.0_beta3 and Coot works fine.
Huw
To unsubscribe
> On 1 Feb 2021, at 21:44, Huw Jenkins
> <288da93ae744-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> As far as I can tell this is a bug in XQuartz 2.8.0_beta1 that has now been
> fixed:
or maybe more accurately a bug in Mesa fixed after 2.8.0_beta1 was released?
https://g
> On 1 Feb 2021, at 21:37, Paul Emsley wrote:
>
> I take it to mean the XQuartz 2.8.0 doesn't distribute the library against
> which Coot (0.9.x) is linked by CCP4 and CCPEM.
As far as I can tell this is a bug in XQuartz 2.8.0_beta1 that has now been
fixed:
https://github.com/XQuartz/XQuartz/
> On 21 May 2019, at 16:44, Darin Lory wrote:
>
> Huw,
>
> I found I'm having the same problem as I have with Chimera displaying on
> XQuartz on the Mac. Looks like OpenGL applications don't display correctly
> or if at all.
>
> I tested with Linux workstation displaying coot AND Pymol wor
Hi,
What's the output of glxinfo? It looks more like an OpenGL problem than a Coot
specific issue.
Best wishes,
Huw
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> On 11 Dec 2018, at 15:32, Andrea Thorn wrote:
>
> Can someone point out if the files for these entries are broken somehow, or
> if there is a bug in Coot?
5lza for me:
There was an error reading 5lza.cif.
ERROR 42 READ: Duplicate sequence number and insertion code.
CIF ITEM: loop _ato
On 19 Nov 2014, at 12:22, Tobias Beck wrote:
> I am using Coot 0.8.1-pre rev 5445 on Mac (OS 10.9.5) and would like to
> validate waters. However, after selecting the criteria and hitting 'Ok', the
> terminal only gives me
>
> (command-in-path-or-absolute? *probe-command*)
That is all I get
On 18 Jun 2014, at 19:09, Thomas, Leonard M. wrote:
> Number of OBSERVED reflections: 130799
> INFO:: finding ASU unique map points with sampling rate 10
> INFO grid sampling...Nuvw = ( 972,1728,2592)
> libc++abi.dylib: terminating with uncaught exception of type
> std::length_error: vector
Doe
On 12 Jun 2014, at 13:08, Bernhard Lohkamp wrote:
> Hi,
>
> this was due to some changes in the code when opening maps. For now I "fix"
> this to not make diff maps scrollable by default as before (some more
> sophistication may be used in the future). This is available from r5095.
Brilliant,
On 11 Jun 2014, at 11:30, Huw Jenkins wrote:
> Hi,
>
> The most recent pre-release of Coot I’ve compiled (revision 5094) has changed
> which map is set to scroll on Auto Open MTZ.
I must stop replying to my own bug reports, but this appears to have been
changed somewhere betwe
Hi,
The most recent pre-release of Coot I’ve compiled (revision 5094) has changed
which map is set to scroll on Auto Open MTZ. It’s now map 1 (which is the Fo-Fc
map) whereas before it was map 0 (2Fo-Fc). Is there a way to switch back to the
old behaviour?
Thanks,
Huw
On 1 May 2012, at 13:41, Paul Emsley wrote:
> Fixed in 4148 (I'm pretty sure).
Yep works for me - thanks for fixing this!
Huw
On 30 Apr 2012, at 19:47, William Scott wrote:
> Any hints how to get it not to work? Is there anything
> in the pdb I could use as an example?
Load the tutorial model and data, open add OXT dialogue box, change chain A to
B in drop-down box = instant segfault for me.
I've just built the late
On 18 Aug 2011, at 17:24, Paul Emsley wrote:
> So I endorse this solution. (I doubt that I will introduce this functionality
> into Coot any time soon.)
Another alternative (no phenix installation required) is the molprobity
webserver. The website for their stand-alone remediator software
(htt
so that it
matches the dictionary and real-space refinement works.
Given that Coot used by default to change nucleic acid to the old (Ur etc)
format and standard-residues.pdb is in the old format some of the code to do
this must already be there?
Thanks,
Huw
--
Dr Huw Jenkins
Astbury
the problem is...
Huw
--
Dr Huw Jenkins
Astbury Centre for Structural Molecular Biology
University of Leeds
ut when I use "get residue info" on a nucleotide I
get:
Failed to find atom name quads for residue type U
in the console but the residue info box pops up fine.
Huw
--
Dr Huw Jenkins
Astbury Centre for Structural Molecular Biology
University of Leeds
ine: 0 std_base_is_pyrimidine: -1 std_base_is_purine: -1
mol_res_name: U std_base_name: A
(do-add-terminal-residue 0)
The error is the same for additions at 5' or 3' ends (although at the 3' it
says "this is a term_type C").
Huw
--
Dr Huw Jenkins
Astbury Centre for Structural Molecular Biology
University of Leeds
n/coot (which is just a wrapper) to set
$COOT_REFMAC_LIB_DIR to /sw64/share/xtal/ccp4-6.2.0/lib but once that's done
real space refinement works again.
I hope that restores RNA refining functionality to your Coot too Francis!
Huw
--
Dr Huw Jenkins
Astbury Centre for Structural Molecu
ot; N" at
(32.2166,26.6043,25.0936)
(2) C6 /1/A/1/G, occ: 1 with B-factor: 20 element: " C" at
(32.7971,23.9412,24.1001)
(2) O6 /1/A/1/G, occ: 1 with B-factor: 20 element: " O" at
(32.9177,22.7756,23.6884)
(2) N2 /1/A/1/G, occ: 1 with B-factor: 20 element: " N" at
(30.0137,25.9864,25.1789)
Is this only an issue with the fink distributed Coot?
Huw
--
Dr Huw Jenkins
University of Leeds
Leeds, LS2 9JT
Hi
I have noticed this too - I think it's because when you start coot with the
command line argument '--pdb filename.pdb' the pdb is read *before* coot.py,
coot-preferences.scm or ~/.coot so the bond preferences are only applied to the
next pdb opened from within coot.
Mac Coot beta testers get their
fix...
Huw
--
Dr Huw Jenkins
Astbury Centre for Structural Molecular Biology
University of Leeds
Leeds, LS2 9JT
source but it was as simple as "fink -y
install coot" and leave it compiling overnight.
Huw
--
Dr Huw Jenkins
Astbury Centre for Structural Molecular Biology
University of Leeds
eers for the info. I was confused as to why all the Scheme scripts
were present in /Applications/coot.app/Contents/coot/share/coot/
scheme/ but not being read on start-up.
Thanks again,
Huw
--
Dr Huw Jenkins
Astbury Centre
University of Leeds
comparisons of the old and new coots.
Any ideas/suggestions would be great!
Thanks,
Huw
--
Dr Huw Jenkins
Astbury Centre
University of Leeds
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