Coot 1.1 on Fedora 40 is now a thing
https://pemsley.github.io/coot/blog/2024/04/27/fedora-40.html
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We are talking about different things, I think.
Coot's glyco builder builds alpha 1-6 linked FUC correctly.
Coot's glyco validator used to (until this evening) identify the alpha
1-6 linked FUC as a beta anomer (it no longer does).
See for example the G8 FUC in 8q5u: Coot 0.9.8.94 now
It's been a few months since the last bug release of the 0.9.x. series.
Here's an update so the fixes are available for CCP4 builds.
o CHANGE: Add a more informative message on failure to generate rtop in
transform-map-using-lsq-matrix [Martin Maly]
o CHANGE: The pyranose link
Not many user-visible changes in this one.
o FEATURE: Scene Presets added to the Draw menu
o CHANGE: "Mutate" is now a button so that it can now be
used to mutate RNA and DNA.
o BUG-FIX: mutate_by_overlap() fixed [thanks Simon Vecchioni]
o BUG-FIX: The "Generic Display Objects"
On 17/04/2024 21:07, Markus Meier wrote:
Hi Paul,
thank you for implementing the Glyco module in Coot!
It is not in Coot 1 (yet). It needs to be rewritten.
I used its "Add N-linked Glycan" function to build an N-linked glycan
which contains L-fucose with an alpha1-6 glycosidic linkage on
On 07/03/2024 07:18, 신진우(생명과학과) wrote:
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something more fundamental/trivial in your setup.
Thank you for your help as always!
You're welcome
Paul.
Best,
‘Kate’ Sun Kyung Kim
*From: *Paul Emsley
*Date: *Wednesday, February 21, 2024 at 9:35 AM
*To: *Kim, Sun Kyung , COOT@JISCMAIL.AC.UK
*Subject: *Re: How does COOT determine p
On 21/02/2024 02:50, Kim, Sun Kyung wrote:
Thank you Paul for that information. I will look into Acedrg and Grade2!
Sounds good.
I have an unrelated question… I’ve never encountered this before, but
all of a sudden my COOT is complaining that it doesn’t have restraints
for refinement…
Thank you in advance for your time in answering my questions!
Best,
‘Kate’ Sun Kyung Kim
*From: *Paul Emsley
*Date: *Thursday, February 15, 2024 at 4:39 PM
*To: *Kim, Sun Kyung , COOT@JISCMAIL.AC.UK
*Subject: *Re: How does COOT determine protonation states
It is in the directory from which yo
It is in the directory from which you started coot (that is, if coot can
create and write to such a directory (if not it is in your home directory)).
Paul.
On 15/02/2024 23:51, Kim, Sun Kyung wrote:
Thank you Lucrezia for your informative reply!
You suggested I look into coot-molprobity
On 01/02/2024 14:03, Kim Walbrunn wrote:
Dear mailing list,
I am writing about some problems with Coot when trying to run the
Jiggle-fit command.
I have tried to jiggle fit (simple / FT) coordinates into a CryoEM
map, using the Cryo-EM module (Coot 1.1.07) or the curlew add-on
'Morph'
On 16/01/2024 23:55, Braviner, Leah wrote:
Hello all,
Hello Leah,
I encountered an issue whereby files are not visible in the ‘open
coordinates’ or ’open MTZ’ pop-ups – and therefore cannot be opened.
There is a file filter, bottom right. The opions are "all files" and
"coordinates
Source:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.1.04.tar.gz
Release 1.1.04
o FEATURE: Particle effects for done difference map peaks
o CHANGE: Refinement cannot now proceed if there are no bond
restraints for any
of the refining
Source:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.93.tar.gz
Release 0.9.8.93
o CHANGE: Electrostatic surface removed from the UI
o CHANGE: Clean-up for the residue selection in peptide omega
analysis (don't draw
cis-peptides for
On 06/01/2024 10:54, sriram raghavan wrote:
Dear coot user,
There's more than one of use, I hope.
I attempted to generate an image of a specific residue which has
negative density in the isomorphous difference map. I tried using
Python scripting and accomplished generating a basic image
On 08/01/2024 15:57, Murpholino Peligro wrote:
How do I change the default colors in coot?
for all three maps, the "normal" density, the difference map and the
anomalous map?
(set-colour-map-rotation-for-maps 28) ; or some such.
On 31/12/2023 16:01, Gang Du wrote:
Hi Coot,
Hi Gang Du.
I solve the structure from cryosparc. The resolution is 3.2A. But I
have a problem opening the map by coot. The chimera and ChimerX can
open the map successfully and correctly. You can see the following
image. But it cannot be
On 13/12/2023 16:37, Fabian Heide wrote:
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Dear all,
I recently installed WinCoot 0.9.8.92 on a 4k monitor
On 08/12/2023 13:19, Mark Saper wrote:
For Paul,
After enabling pointer distances, the distances don’t update (most of
the time) when moving to a different place in the molecule. The Coot
version is 0.9.8.92 running on macOS 13.6.1.
Thank you Mark.
For ther record, this is the sort of
Source:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.1.03.tar.gz
Many gui bugs fixes, still quite a number left (sadly).
o FEATURE: outline active residue on leftquote
o FEATURE: Shortcuts dialog
o FEATURE: Goodsell NCS colouring mode
o FEATURE:
On 29/11/2023 10:58, Subscribe COOT Marie M üller wrote:
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Dear all,
I am wondering if it is somehow
On 22/11/2023 14:02, Keitaro Yamashita wrote:
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Great, you are using the very latest CCP4 (with the latest
On 13/11/2023 21:16, Mohamed Ibrahim wrote:
Dear All,
During pdb submission, I lost the link information in the pdb file
during the conversion to mmcif file. It does not matter if I did this
in Phenix or wwpdb server.
How to fix this issue?
Coot can add a struct_con record for you if
On 03/11/2023 20:57, Ma, Boyuan wrote:
Dear Cooters,
I want to use a python script to select several disconnected fragments
to perform refinement in one time, for example,
"coot.some_refinement_by_residue_range(imol, /1/A/1-20 || /1/A/22-30)."
However, after searching previous messages in
On 02/11/2023 07:55, Marija Backovic wrote:
Hello,
I have just installed Coot 0.9.8.91, but when I try to access the PDB files,
which are in my Documents directory, I get a message 'Could not read the
content of Documents' / 'Operation not permitted'. The operating system is
MacOS Ventura
l features to have.
Ctrl-D is the hot-key for delete-residue btw.
Regards,
Paul.
On Wed, Nov 1, 2023 at 12:22 PM Paul Emsley
wrote:
On 01/11/2023 16:34, Xuewu Zhang wrote:
>
> Dear Paul,
> Can Coot handle heparin chains (not attached to protein) now? I was
18 months after the release of Coot 1 it's time for Coot 1.1
Coot 1.1 is a major change beyond Coot 1. It has required a lot of
writing and rewriting and has been the focus of my work since last year.
Technically (but briefly) we have rewritten the GUI again so that it is
now is based on GTK4
On 14/10/2023 23:34, Zhu JiaPeng wrote:
Dear all,
I am currently working with a protein containing multiple subunits.
For each subunit, I need Coot to perform rigid body fitting followed
by real-space refinement. Manually inputting the Python commands
rigid_body_refine_zone(reso_start,
On 13/10/2023 13:12, Neil Rzechorzek wrote:
Dear colleagues,
Hi Neil,
I have been iteratively rebuilding and refining a crystal structure
using coot (v. 0.9.8.91) and Phenix.
Refinement makes use of NCS restraints, and the structure additionally
has some covalent links between protein
On 12/10/2023 05:46, Goode Shelter wrote:
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Dear Sir/Madam,
I am a user of Wincoot0.9.8.7 in win10
On 21/09/2023 18:58, Paul Emsley wrote:
On 21/09/2023 18:05, Kelvin Lau wrote:
Dear all
I am having trouble with an unnatural ligand/amino acid.
I have a structure very similar to PDB 6Q6H, 7TQR. They all have an
MDO residue that replaces three residues in a series G-A-S-G-D to
become G-MDO
On 21/09/2023 22:25, Kelvin Lau wrote:
Hi Eleanor
Thanks for catching that..
I was under the impression that when I am fetching the monomer, MDO,
it was defined as a peptide, not a non polymer … at least that’s what
is listed here: https://www.rcsb.org/ligand/MDO
I guess I have to go about
On 21/09/2023 21:56, Eleanor Dodson wrote:
And in fact it doesnt..
Wasn't that implied by my reply?
:-)
Paul.
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On 21/09/2023 18:05, Kelvin Lau wrote:
Dear all
I am having trouble with an unnatural ligand/amino acid.
I have a structure very similar to PDB 6Q6H, 7TQR. They all have an MDO residue
that replaces three residues in a series G-A-S-G-D to become G-MDO-D. MDO is in
the Coot library.
I have
On 13/09/2023 08:39, Adrián González López wrote:
Hi Paul,
I have been using CCPEMs coot (version 0.9.8.5) for a while but
decided to change to ccp4 to get the newest updates (coot version
0.9.8.91). I have noticed that something in the graphics has changed.
In version 0.9.8.91 there is
This release should address the problematic linking discussed here over
the last few weeks.
At least, I hope so (as noted before, what is needed is a complete
rewrite of the link-finding code - an algorithm that believes the headers).
Regards,
Paul.
Source
On 04/09/2023 22:50, Georg Mlynek wrote:
Dear Paul and community, I am loading several generated maps in coot via a
script. Now I want that coot sets a specific map used for refinement
automatically.
very good.
What would be the code for that?
For Python in Coot 0.9.x that would be
l.
On Fri, 1 Sep 2023 at 17:37, Paul Emsley
wrote:
Dear Eleanor
[snip]
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Thi
Dear Eleanor
On 01/09/2023 13:19, Eleanor Dodson wrote:
*COOT problem first: or is it REFMAC ? *
REFMAC outputs coordinates in both pdb and cif format. They are
identical
*This model has ZN linked to CYSs etc..*
The PDB files provides the link records but the cif file does not.
On 01/09/2023 11:37, Guenter Fritz wrote:
Dear Paul,
I had a strange issue today when refining a structure with latest coot
(0.9.9.91) from CCP4.
Two cysteines with Calpha-Calpha distance of about 6 A do not form a
disulfide bond, but coot wants to enforce a disulfide, although no
I don't know much about CCP4-built binaries on macOS. I do know that one
is supposed to reinstall XQuartz after updating the OS.
Paul.
On 31/08/2023 21:52, Andrea Smith wrote:
P.S. Found this in the log file from Cloud:
dyld: Library not loaded: /usr/X11/lib/libpixman-1.0.dylib
On 25/08/2023 06:56, Daniel Larsson wrote:
Hi Paul,
I have some suggestions/requests for facilitating sidechain modelling.
* Option to have the rotamer tool default to the rotamer most
closely resembling the current rotamer (now it defaults to the
most common rotamer)
That seems
On 24/08/2023 15:53, Helge Paternoga wrote:
I just had the chance to try out the new Coot version 9.8.91 from CCP4
and I would like to report that RSR of ribosomes is still broken
Thank you.
I will get to this shortly. I had been hoping to solve the problem
without a general-purpose (and
On 09/08/2023 10:51, 次田篤史 wrote:
Dear all
I just installed the latest version coot (0.9.8.8) and checked if it
works by Bernhards key bindings.
As far as I remember, on the "Accept Refinement?" tab, the "accept"
button was selected automatically and if we did not need to fix the
On 08/08/2023 06:49, Edward A. Berry wrote:
> I would appreciate instruction for getting a downloaded coot binary to
> run.
Fair enough.
The idea is that you untar the binary tar file and put
/somewhere/coot-something/bin in your PATH. That's it. You shouldn't
need to edit any coot files.
Source:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.91.tar.gz
Scientific Linux 7.6 binary:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/coot-0.9.8.91-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz
Release
On 27/07/2023 02:58, Mark Saper wrote:
Hi Paul,
Does this new release address the problems with Real Space Refinement that I
reported several months ago?
I believe so.
Paul.
To unsubscribe from the COOT list, click
Source:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.9.tar.gz
Scientific Linux 7.6 binary:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/coot-0.9.8.9-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz
Release 0.9.8.9
o
On 18/07/2023 19:09, Radford, Katelyn M. (Kate) wrote:
Hi all,
I'm trying to fit a model into a low resolution (5.88 Å) EM density.
When I refine in Phenix and Coot, the default settings fit all atoms
into the density, including side chains. While this would be great if
I had a sub-3 Å
On 11/07/2023 09:53, Charles BARCHET wrote:
Dear all,
I am currently trying to compile Coot 1.0 on Ubuntu 22.04.
After downloading all the necessary binaries, I end up with a python
version error message :
*:1: DeprecationWarning: The distutils.sysconfig module is
deprecated, use
On 14/06/2023 22:24, David Aparicio wrote:
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Dear community,
When loading some pdb files on coot they are
Hi Dale,
Without testing, I guess that you can replace get_ebi.py with this one
https://github.com/pemsley/coot/blob/refinement/python/get_ebi.py
(use Raw of course)
Paul.
On 08/06/2023 08:35, Sameer Velankar wrote:
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On 12/05/2023 17:00, Gu Shaocheng wrote:
Hi,
Hi.
Here is a GPU issue related to chimerax and coot (0.9.8) on the Linux system.
OK...
To be able to call GPU in chimerax, I put the nvidia invoke in .bashrc file.
I don't know what it means to call the GPU in ChimeraX. I don't know
what the
I think this slipped by on the coronation break and I didn't get to see
it until recently.
So... for the record then...
On 10/05/2023 17:23, Karl Herbine wrote:
I am relatively new to model building in coot.
Belated welcome.
I am having trouble finding the correct fitting for the ligand
On 24/05/2023 14:24, hari jayaram wrote:
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Hi All
I am making some progress--but still cant get any of
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Hi All
I want to get back to using coot to build some models
We are pleased to release Coot 0.9.8.8
- FEATURE: Better atom colours in colour-by-chain-and-dictionary mode.
- CHANGE: Monomer search now uses the new dictionary
- CHANGE: Molecules read in as mmCIF (.cif) are now by default saved
as .cif
- CHANGE: Atoms with element "Cl" are
Bleugh. Sorry about that. If it happens again I will get in touch with
Jiscmail.
Paul.
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This
On 04/04/2023 08:07, Mark Saper wrote:
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Dear Paul,
I’ve discovered a serious problem when running Coot 0.9.7 from
On 15/03/2023 13:54, Ramón Hurtado Guerrero wrote:
> Dear Paul,
>
> Thank you. Yes, this happens in mac and you are right since the coot
> icon is in the dock. How can I avoid this?
>
>
The key-binding Ctrl-D deletes the residue at then centre of the screen
(including waters) - this by-passes the
On 12/03/2023 16:20, Ramón Hurtado Guerrero wrote:
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To whom it may concern,
On 17/02/2023 08:28, ZOEY wrote:
Hi,
I am currently working on refining a protein/RNA complex. I am using coot to
build my model and am wondering if anyone has any experience in dealing with
RNA's modifications on them? I am working with a N6-methyl-adenine and am
having problems with it in
On 14/02/2023 09:28, Zeelen, Johan Philip wrote:
Dear All,
I am using Coot 0.9.8.7 EL (ccp4) on a macOS 10.15.7 and have the
following problems.
I am refining structures with 2 SS-bridges close together. When I use
Sphere Refine+ the refinement gives me a cluster of the 4 Cys.
molecules.
Systemic failure. Oh dear.
Add an extra 1 after the 1 1.
The difference map peak list navigation key bindings are "." and ","
FWIW (but you probably already know that).
Regards,
Paul
On 18/01/2023 07:45, Seth Harris wrote:
Hi all,
this used to work (a while ago) from my-settings.scm for
@kas, check that your using Modern dialogs.
On 21/01/2023 12:25, Pedro Matias wrote:
Hi Ken,
When you save coordinates there should be a check box to save hydrogen
atom coordinates. Maybe yours is off by default?
BR,
Pedro
On 19/01/2023 22:55, Kenneth Satyshur wrote:
I added H
On 18/01/2023 08:51, Lau Kelvin wrote:
Dear Paul
I got around to updating via ccp4.
In 0.9.8.7 EL I can add the glycans like before, but I do not see a
link. The glyco module also no longer recognises that there is a
glycan present at the Asn, so when I add another NAG, they just overlap.
On 27/12/2022 18:59, Kelvin Lau wrote:
Dear Paul
I looked back the forum and similar to Taka's issue in 0.9.8.4 I am also
experience it with both Coot 0.9.8.6 EL (ccp4 build) and 0.9.8.5 (ccpEM) build.
MacOS 12.6.1
Hello Kelvin,
I believe that this issue is fixed in 0.9.8.7.
Paul.
Coot-0.9.8.7 has been released
source:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.7.tar.gz
Release 0.9.8.7
o FEATURE: res_tracer() added to the API
o FEATURE: read_mtz() added to the API [ChatGPT guessed at this
function name, and there is
On 23/12/2022 16:48, Joshua Arribere wrote:
Hello,
I am trying to understand how to restore a chain after a deletion in
coot. I have deleted some residues (using delete-residue-range). The
residues are visually gone, and replaced with a dotted line (a loop)
between the flanking residues. I
On 15/12/2022 13:01, Paul Emsley wrote:
On 14/12/2022 18:59, Ing. Yan Alejandro García Hernández wrote:
1. Update to MacOS Ventura
2. Install CCP4 last versión
3. Open a file and try to delete a residue/monomer, the window
disappears.
I’ve posted an issue in GitHub with a video
On 14/12/2022 18:59, Ing. Yan Alejandro García Hernández wrote:
1. Update to MacOS Ventura
2. Install CCP4 last versión
3. Open a file and try to delete a residue/monomer, the window
disappears.
I’ve posted an issue in GitHub with a video obout it: Unexpected
window minimize · Issue
On 14/12/2022 16:39, Yan Alejandro wrote:
I have the same problem. Is there a solution for this?
This is not a good bug report.
Give me a recipe to reproduce the problem.
Regards,
Paul.
To unsubscribe from the COOT
On 12/12/2022 16:29, Paul Kraft wrote:
just needed to close the old sequence view and open a new one to see the
updates.
Thanks for your extremely prompt help. [...] Using simple mutate it seems I
must close and reopen the sequence viewer for it to update the sequence even
though it is
On 12/12/2022 15:49, Paul Kraft wrote:
sorry,
I am using Coot 0.9.8.5 EL (ccp4) on Ubuntu LInux 22.04 LTMD amd64,
Ah, OK. Up to date. Good start.
using the Replace Residue command under Edit or under Calculate-Modelling
the command Cd does not function.
Interesting. I think that you want
On 12/12/2022 15:09, Paul Kraft wrote:
Hello,
I am trying to mutate DNA, and can with Gd, Td, and Ad, but the Cd command is
inopporative.
Hello.
I'm not a mind-reader. You need to start off with which version of Coot
you're using and on which system (that matters less usually).
You need
Coot-0.9.8.6 has been released
source:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.6.tar.gz
binaries:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/
Release 0.9.8.6
o CHANGE: More auto-read column pairs added [Clemens
On 02/12/2022 20:24, David J. Schuller wrote:
The files in the coot-backup directory incorporate the date into their
name. This caused a problem for one of our users, as the colon is a
forbidden character in the file transfer application used, which is
Globus.[...] I suggest it would be
On 02/12/2022 15:30, John Smith wrote:
Dear all!
I am using Coot 0.9.8.5 EL (ccp4) and I want to add K/potassium ions
during model building.
Adding Na and Cl is straightforward, but if I click on Pointer Atom
Type other, enter K and hit OK, then a grey atom is added, but it does
not refine.
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
On 16/11/2022 17:39, Xavier Brazzolotto wrote:
>
> Hello,
>
> I’ve noticed 2 issues in the recent update of coot (v0.9.8.5 from
> CCP4i) on an Intel mac updated to Ventura (13.0.1). I did not test on
> Linux.
>
> * When I delete a molecule, my Coot/X11 window « disappears ». It is
> not
On 15/11/2022 14:26, Mohamed Nasef wrote:
Im working with a 23S rRNA that is 2900 nucleotides long. In sequence view, I
can only see up to nucleotide number 2245 although the rest of the sequence is
there. I couldn't find a solution to this issue anywhere in the archive.
Hello Mohamed,
On 09/11/2022 19:25, Rogerio Sotelo wrote:
I have not been able to locate binaries to install Coot, as they
appear not to be included in Phenix. Some colleagues installed the
CCP4 platform to get it to work on Mac.
I will appreciate the info about where to obtain Mac OSX Coot binaries,
On 17/10/2022 06:30, Taka wrote:
Dear Coot developers,
I use Coot 0.9.8.4 on macOS 12.0.1 Monterey.
The present program does not generate LINK of glycans, such as GlnNAc-Asn, which was
added using Modules>Carbohydrate>N-linked Glycan Addition tool, and C1-O6 of
two glucose monomers.
Excuse me
On 25/10/2022 03:28, zheng zhou wrote:
Dear Coot experts
My middle mouse scroll did not work on Coot 0.9.8.3 EL. I am using
centos 7. It works on other programs. I did search online, and tried
to add
set_scroll_by_wheel_mouse(1) to my
~/.coot-preferences/coot_preferences.py and restart coot,
We are pleased to release Coot 0.9.8.5
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.5.tar.gz
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/
Paul.
Release 0.9.8.5
o FEATURE: AlphaFold pLDDT colour scheme.
o CHANGE: Don't
in anger (as it were). For this sort of thing, I would
use Edit Chi Angles, and I suspect that if you edit your restraints
dictionary as suggested then that will "just work."
Regards,
Paul.
p.s. It is a bug though and I've made a note.
Zhen
*From: *Paul Emsley
*Date: *Tuesday,
On 31/08/2022 01:17, Gong, Zhen wrote:
Hi Paul,
Thank you very much for your timely reply. There are still some
puzzles for me.
I would like to change some torsion angles of a ligand in coot but it
did not work as what I expected. I was able to play with the torsion
angles formed by C06
On 30/08/2022 22:26, Gong, Zhen wrote:
Dear Coot developers and users,
I would like to change some torsion angles of a ligand in coot but it
did not work as what I expected. I was able to play with the torsion
angles formed by C06 C07 N08 O10 but not C06 C07 N08 O09 (shown in the
figure
On 07/08/2022 21:56, Bernhard Rupp wrote:
Dear Coot Developers,
I have a minor suggestion: I view many open Marina Bay coots at the
same time, and it would be helpful
if the selection status line at the bottom would, instead of the
somewhat uninformative (mol. no: x), display
the name
On 09/08/2022 02:40, Cryo EM wrote:
Hi everyone,
In one my PDBs, I see that there is a linkage break in
ribonucleotides. Specifically one of the phospodiester bond seems to
be broken and thus O3' needs to be bonded to P atom of next
nucleotide. What is the easiest way to do this in coot ? Or
On 08/08/2022 16:04, Kenneth Satyshur wrote:
You can tell phenix where to find coot. Point coot to the ccp4
version, which has the libs. The stand alone version may not have the
link to the lib that is maintained by ccp4.
I thought that it was the other way around! :-)
Use the
Sorry, this somehow dropped off my radar (maybe because I accidentally
left it as read).
On 15/07/2022 12:34, Gundala Viswanath wrote:
Hi,
Notice that it has high outliers content. I want to manually drag those
red dots into some part of the region. Eventually, I expect it to be
reflected
On 21/07/2022 10:49, Filomeno Sanchez Rodriguez wrote:
I finally managed to write a script to do this, I will leave it here for future
reference in case someone has the same question:
# Auto-correct nomenclature errors
set_nomenclature_errors_on_read("auto-correct")
# Read in
On 06/07/2022 22:57, Rajiv Singh wrote:
Dear Paul and the coot community
I am trying to compile coot-1 on Ubuntu 20.04 using Coot 1 (GTK-+-3-based) From
Scratch script build-it-3-3
This started by creating auto-build directory and downloading several
dependencies and then It stopped with this
, 2022 at 5:37 PM Paul Emsley
wrote:
This is primarily my mistake. I now think that coot's configure
should check for the version of clipper that has top8000.
If it doesn't find that clipper, then Coot's configure should fail.
You should never get to the make stage.
I
(because,
clearly, it isn't).
A few days.
Paul.
On 27/06/2022 03:12, Paul Emsley wrote:
That clipper is old clipper. You need the clipper from the build script.
Paul.
On 27/06/2022 03:10, hari jayaram wrote:
Dear Paul and the coot community
It's been 6 years since I posted on any coot
^~~~
residue_by_phi_psi.cc:871:41: error: ‘Pro2’ is not a member of
‘clipper::Ramachandran’
871 | rama_pro.init(clipper::Ramachandran::Pro2);
| ^~~~
make[1]: *** [Makefile:1324: residue_by_phi_psi.lo] Error 1
ma
On 25/06/2022 17:57, Sun, Chen wrote:
Hi Paul,
Now the copy molecule is not working. The save coordinate also failed
to launch after I have mutated a long sequence.
OK, copy_molecule is fixed.
It doesn’t allow me to save the session. Please see the error message
below.
On 25/06/2022 06:20, Paul Emsley wrote:
On 25/06/2022 04:12, Sun, Chen wrote:
I am able to run coot successfully from terminal. However, when I was
trying to mutate sequences, it reported the following error message:
debug:: safe_python_command() PyRun_SimpleString
On 25/06/2022 04:12, Sun, Chen wrote:
Hello,
Hello.
I am using Coot 1.0.06-pre on MacOS Monterey installed with homebrew.
Good news in the pipeline, FWIW.
I am able to run coot successfully from terminal. However, when I was
trying to mutate sequences, it reported the following error
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