On 02/05/2022 12:44, John R Helliwell wrote:
I was intrigued by Paul’s 5sigma Fo-Fc default cut off, rather than 3.
It's 5.6 now :-)
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On 15/04/2022 16:32, Qiuye Li wrote:
We recently centralized our high-end workstations and no longer have
easy access to their displays,
Someone drew the short straw there :-(
I found coot 0.9/wincoot 0.9 are a bit laggy on our less frequently
updated office computers,
You mean hardware
Hello Kenneth,
On 06/05/2022 23:48, Kenneth Satyshur wrote:
I use the sphere refine in coot all the time. It's great. And when I
turn on 'Environmental Distances'. I can see the H-bonding to the
residue. Great. I have recently been using Isolde in ChimeraX to fit 3
A CryoEM density. When I
On 02/05/2022 20:19, Dale Tronrud wrote:
When I watch people model building I see many scrolling the
contour level up and down without regard for the numeric value of the
level, apparently just choosing a value that makes the peaks appear
the way they prefer the peaks to appear.
I
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
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 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,
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
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
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
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 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 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 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 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
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 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
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 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 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 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 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 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 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,
@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
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
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 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
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 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.
On 14/06/2023 22:24, David Aparicio wrote:
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Dear community,
When loading some pdb files on coot they are
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
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 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
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
On 24/05/2023 02:13, hari jayaram wrote:
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Hi All
I want to get back to using coot to build some models
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
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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Do not 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 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-0.9.8.91.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 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.
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
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
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
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…
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 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
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 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
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
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
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 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 22/11/2023 14:02, Keitaro Yamashita wrote:
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Great, you are using the very latest CCP4 (with the latest
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 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
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 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
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
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
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"
Coot 1.1 on Fedora 40 is now a thing
https://pemsley.github.io/coot/blog/2024/04/27/fedora-40.html
To unsubscribe from the COOT list, click the following link:
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On 03/05/2024 14:56, Nav wrote:
--
Hi Coot users,
I'm a new Coot user and using Coot version 0.9.8.
I'm trying to do the following in a Python script.
I have loaded a PDB structure and then inserted a new monomer in a particular
location.
Then I want to find the closest atom from the PDB
On 07/03/2024 07:18, 신진우(생명과학과) wrote:
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Do not click links or open attachments unless you recognize the sender
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If you think this is a phishing email, please forward it to
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 21/05/2024 15:29, Murpholino Peligro wrote:
--
Dear Paul
I re-refined using phenix.refine (same job as before, but without
using the anomalous intensities). So I got the proper labels.
H 54730 100.00% 0.00 74.00 H: index h,k,l
K 54730 100.00% 0.00 52.00 H: index
On 19/05/2024 23:32, Murpholino Peligro wrote:
In old coot: File -> Open Map -> Click on "Is Difference Map"
In new coot, how can I make a map a "difference map"?
Ah, I see what you mean. The file dialogs have been rewritten and I have
forgotten to add a button for that. I will add one.
,SIGIMEAN, instead of I(+),SIGI(+),
I(-),SIGI(-).
Thanks Paul
El lun, 20 may 2024 a la(s) 4:56 p.m., Paul Emsley
(pems...@mrc-lmb.cam.ac.uk) escribió:
The "Updating Map" feature in Coot expects (plain old) Fobs,
SIGFobs, Rfree columns - you have lots of exciting columns in yo
The "Updating Map" feature in Coot expects (plain old) Fobs, SIGFobs,
Rfree columns - you have lots of exciting columns in your mtz file but
not those ones.
It would be cool if Coot could handle anomalous intensities, but at the
moment it doesn't. I'll add it to the list.
Regards,
Paul
On 20/05/2024 09:09, Paul Emsley wrote:
On 19/05/2024 23:32, Murpholino Peligro wrote:
In old coot: File -> Open Map -> Click on "Is Difference Map"
In new coot, how can I make a map a "difference map"?
Ah, I see what you mean. The file dialogs have been rewri
On 5/31/24 13:10, Paul Emsley wrote:
--
On 31/05/2024 08:54, Marko Hyvonen wrote:
--
Hello all,
Hello Marko.
Would anyone have a template/example to create a custom pop-up window
(a bit like “Go to atom….” one) for Coot? We’d like to have
something to help to browse through
On 31/05/2024 08:54, Marko Hyvonen wrote:
--
Hello all,
Hello Marko.
Would anyone have a template/example to create a custom pop-up window
(a bit like “Go to atom….” one) for Coot? We’d like to have something
to help to browse through a large number of sizeable structures
(oligomeric
On 6/11/24 16:39, Gu Shaocheng wrote:
Hi coot community,
Hello Shaocheng,
I can't click to open most of the items under 'Validate' menu, such as
'Ramachandran Plot' on version 0.9.5 and 0.9.8.
I can't think of why that should be. Some of those functions are written
using guile-gtk (which
On 6/11/24 14:52, Elżbieta Dorota Wątor wrote:
--
Dear Coot fellow,
I recently several encounter the same problem during structure
refinement in Coot (Wincoot to be more specific, different versions).
During adding waters/going along the protein chain, sometimes the
opened pdb file get
On 13/06/2024 20:15, David Dranow wrote:
We finally installed Coot 1! We were waiting for it to be packaged by CCP4.
However, it doesn't seem to work so well, so I think that's my fault.
Maybe.
We used the linux package manager to install it. But that didn't change what
"coot" pointed
On 14/06/2024 13:21, Nav wrote:
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Only one update worthy of note:
o BUG-FIX: allow bonding of het residue in polymer bonds
(it is important enough for a release)
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.95.tar.gz
I am no longer building binaries for the 0.9.x branch.
Regards,
Paul.
Release 1.1.09
o FEATURE: Coot is now a (mostly) XDG Base Directory-compliant
application
[guano-be-gone]
o FEATURE: tomo_section_view() function added to the API
o FEATURE: to_generic_object_add_points() added to the API (so that
many point
can now be
On 17/06/2024 17:39, Auffinger Pascal wrote:
--
Hi,
I would like to disable automatic NCS calculations in coot.
Is there a script command for that ?
I don't think that there is a way. What harm do they do?
Paul.
On 01/07/2024 11:59, Noha Elhosseiny wrote:
--
I am new to coot and structural analysis in general. I am trying to do
model building for a symmetric protein consisting of 15 identical
chains, using the density map from cryoEM analysis. I made an initial
model by first fitting one chain
On 7/1/24 12:24, Noha Elhosseiny wrote:
Thanks Paul,
I replied below in a different color
On Mon, Jul 1, 2024 at 2:17 PM Paul Emsley
wrote:
On 01/07/2024 11:59, Noha Elhosseiny wrote:
>
>
> --
>
>
>
> I am new to coot and structural a
for real space refinement. I guess the problem is that the
map coordinates are not exactly correct.
Noha
On Mon, Jul 1, 2024 at 7:20 PM Paul Emsley
wrote:
On 7/1/24 12:24, Noha Elhosseiny wrote:
Thanks Paul,
I replied below in a different color
On Mon, Jul 1, 2024 at 2:17 PM Paul
On 15/07/2024 07:26, Nav wrote:
Thanks for the help in using coordinates to insert a typed atom with
'place_typed_atom_at_pointer' routine.
But I get the following warning when I try to insert a water 'WARNING:: new
atom addition blocked by nearby atom' and the insertion fails.
Is there a
Dear all,
Coot 1.1.10 has been released
o FEATURE: Noughties-physics - add a refinement/atom manipulation mode
so that Coot behaves like it used to up to (and including) version
0.8.x: |coot.set_refine_use_noughties_physics()|
o FEATURE: Layla now displays QED
On 26/07/2024 16:44, Fernández-Leiro.Rafael wrote:
--
Dear all,
I am having trouble running prosmart on the mac version (1.1.10 and
previous version).
Running any option from the “restraints” menu gives an error:
/###/
/in generate_self_restraint_func() 6 A 3.7/
/--- extra
On 26/07/2024 18:10, Fernández-Leiro.Rafael wrote:
--
Thanks for the quick response Paul, appreciated
I edited the file and re-installed ccp4, so now Prosmart is available
OK, good.
The restraints menu still generates no restraints, and Prosmart has
some trouble as well.
I tried with
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