Hi there, I’m using Coot 0.9.8.95 for OS X from CCP4. I notice that in real
space refinement coot does not show Ramachandran spheres for peptide bonds that
include an insertion code for one or more residues. See for example
3SOB//H/82-82A//.
Best wishes
Kevin
--
Kevin Jude, PhD
Structural Biol
On 2/20/25 09:36, Mary Ortmayer wrote:
--
Hi all,
Hi Mary,
I’ve made the move to Coot-1 as its impressive.
I agree/thanks/yay.
However, I get this error when I move the coot-1 window from my laptop
display to a monitor.
(MacCoot:78468): Gtk-*WARNING***: 13:28:32.724: Allocating size
t: Wednesday, August 28, 2024 6:32 PM
To: David J. Schuller ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot 1.* in CCP4 9
Hello David,
One need not change anything. Just run it from where it is (for now probably
best not to override the path while other programs expect coot to be coot
y, August 28, 2024 4:54 PM
*To:* David J. Schuller ; CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Coot 1.* in CCP4 9
On 8/28/24 21:53, David J. Schuller wrote:
I installed CCP4 9 on Alma 9 Linux. I requested installation of both
Coot-0.9.8.95 and Coot-1.1.08.
How do I execute the latter?
ley
Sent: Wednesday, August 28, 2024 4:54 PM
To: David J. Schuller ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot 1.* in CCP4 9
On 8/28/24 21:53, David J. Schuller wrote:
I installed CCP4 9 on Alma 9 Linux. I requested installation of both
Coot-0.9.8.95 and Coot-1.1.08.
How do I execute th
On 8/28/24 21:53, David J. Schuller wrote:
I installed CCP4 9 on Alma 9 Linux. I requested installation of both
Coot-0.9.8.95 and Coot-1.1.08.
How do I execute the latter?
It's in the coot_py3 directory after installation.
I believe that Charles has recently made a binary update to 1.1.10.
I installed CCP4 9 on Alma 9 Linux. I requested installation of both
Coot-0.9.8.95 and Coot-1.1.08.
How do I execute the latter?
===
All Things Serve the Beam
==
On 15/08/2024 17:14, Petr Pachl wrote:
[And now this part]
Also two off topic questions regarding coot-1 and coot. I tried to
transfer some of my keybindings and settings to coot-1 "language".
The language is Python (well, one of them is).
Unfortunately, there is not a good web resource for
On 12/07/2024 13:12, Karol Woloszyn wrote:
Hello,
I’m a COOT 1.1.09 user on Fedora 40 as well as MacOS, working on DNA model
refinement.
I’ve noticed since updating to 1.1.09, the cell and symmetry master switch no
longer brings up any symmetry molecules. I remember in older versions (I was
On 12/07/2024 13:12, Karol Woloszyn wrote:
Hello,
Hello Karol,
I’m a COOT 1.1.09 user
exciting.
on Fedora 40 as well as MacOS,
a rare breed.
working on DNA model refinement.
OK...
I’ve noticed since updating to 1.1.09, the cell and symmetry master switch no
longer brings up any s
Hello,
I’m a COOT 1.1.09 user on Fedora 40 as well as MacOS, working on DNA model
refinement.
I’ve noticed since updating to 1.1.09, the cell and symmetry master switch no
longer brings up any symmetry molecules. I remember in older versions (I was
last most active on COOT 0.9.8) there was al
Lucrezia,
Thanks for your help!
1) This works very well -- thanks for pointing me in the right direction.
2) Thanks
3) When I do this, no anchor appears. There's a "no intermediate atoms"
error, with a 0x0 matrix of fixed atoms. Maybe it's a DNA refinement error?
Cheers
On Mon, Jun 3, 2024 at
Dear Simon,
1. The new clipping keybindings are ‘1’ and ‘2’ for clipping front and ‘3’ and
‘4’ for clipping back (like in Moorhen as well). You can find them in ‘About’-
’Shortcuts' (page 2 to be precise).
2. We need to fix this (about a week)
3. You center on an atom, then click on ‘Fixed atom’
Paul and CCP4 Community,
Emailing the larger listserv because some of these might be useful to all.
Thanks for the updates to the latest build.
1) In Coot 1.1.08, the graphics are fantastic! I've been struggling to clip
the view for figure building. In old Coot, there was a "d" and "f" keyset
tha
On 13/05/2024 11:23, Laurent Maveyraud wrote:
Hello,
I like the function "update NCS ghosts with local match" found in the
calculate/NCT tools menu. It's really helpful when NCS is not really
strict. However, I find it clumsy that you have to go in a submenu to
get it, so I would like to defin
Hello,
I like the function "update NCS ghosts with local match" found in the
calculate/NCT tools menu. It's really helpful when NCS is not really
strict. However, I find it clumsy that you have to go in a submenu to
get it, so I would like to define a keyboard shortcut... this would be
much fa
On 26/04/2024 02:44, Paul Emsley wrote:
On 25/04/2024 16:07, Simon Vecchioni wrote:
Paul,
Many thanks for fixing the [simple mutate] button for DNA in
v1.1.08--works like a charm!
I would ask about two other DNA features--
1) The [add terminal residue] button seems unresponsive for DNA,
On 25/04/2024 16:07, Simon Vecchioni wrote:
--
Paul,
Many thanks for fixing the [simple mutate] button for DNA in
v1.1.08--works like a charm!
I would ask about two other DNA features--
1) The [add terminal residue] button seems unresponsive for DNA,
I see what you mean. From the termina
Paul,
Many thanks for fixing the [simple mutate] button for DNA in v1.1.08--works
like a charm!
I would ask about two other DNA features--
1) The [add terminal residue] button seems unresponsive for DNA, and is
often quite useful;
2) There was a button chain in v0.8.9 to add base pair restraints
Paul,
That's fantastic and swift. Many thanks for your help, and for making COOT
the go-to for DNA slice and dice.
Cheers
Simon Vecchioni
NYU Chemistry
On Thu, Apr 4, 2024, 5:43 AM Paul Emsley wrote:
>
> On 04/04/2024 02:27, Simon Vecchioni wrote:
> >
> >
> > Dear CCP4 Wizards,
> Hello Simon.
On 04/04/2024 02:27, Simon Vecchioni wrote:
Dear CCP4 Wizards,
Hello Simon.
I've upgraded to COOT v1.1.07 from 0.9.6, and am working on DNA model
refinement.
exciting.
The current setup does not seem to let me sequence mutate (simple
mutate or mutate residue range), as it's hard coded t
Dear CCP4 Wizards,
I've upgraded to COOT v1.1.07 from 0.9.6, and am working on DNA model
refinement.
The current setup does not seem to let me sequence mutate (simple mutate or
mutate residue range), as it's hard coded to an amino acid drop down menu.
Edit-->Replace residue with three letter code
On 18/03/2024 10:26, Petr Pachl wrote:
--
Does anybody know if there is a function (or procedure) how to get info
about closest symmetry atom? For picking coot is performing something
like "Model atom pick (if failed) -> Symmetry atom pick", then it
returns to console and atom info at the botto
Hi all.
Does anybody know if there is a function (or procedure) how to get info
about closest symmetry atom? For picking coot is performing something
like "Model atom pick (if failed) -> Symmetry atom pick", then it
returns to console and atom info at the bottom of the screen the found
atom. But ca
ssful!
>
> I am deeply grateful for your guidance.
>
> Best regards,
> Xin
> --
> *From:* zx2...@connect.hku.hk
> *Sent:* 16 February 2024 17:26
> *To:* Paul Emsley
> *Subject:* Re: [ccp4bb] Coot SSM Superpose Problem
>
> Dear Paul,
>
&
aul Emsley
Subject: Re: [ccp4bb] Coot SSM Superpose Problem
Dear Paul,
I apologize for the confusion in my previous description. To clarify, there are
actually 4 copies within a single ASU.
Following your suggestion, I tried the "Symm Shift Reference Chain Here" , and
it worked suc
On 16/02/2024 01:45, zx2...@connect.hku.hk wrote:
Dear all,
Hello Xin,
I encountered an issue while attempting to calculate the RMSD between
two PDB files (each containing 4 ASUs)
do they really though?
using the SSM Superpose tool in Coot. Unfortunately, the tool was
unable to superpos
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot query
On 06/07/2023 08:51, Tom Peat wrote:
Hello All,
I just had a very strange experience- I rebooted my linux machine (Ubuntu jammy
7.81.0) and tried to start up Coot and received the following error message:
It is my understanding that jammy jellyfish
On 06/07/2023 08:51, Tom Peat wrote:
Hello All,
I just had a very strange experience- I rebooted my linux machine
(Ubuntu jammy 7.81.0) and tried to start up Coot and received the
following error message:
It is my understanding that jammy jellyfish, by default, uses Wayland as
the display
Hello All,
I just had a very strange experience- I rebooted my linux machine (Ubuntu jammy
7.81.0) and tried to start up Coot and received the following error message:
The program 'coot-bin' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadValue (
Hi Evgenii,
quick workaround is to add "--auto" before the mtz path
like this:
$coot --pdb --auto
Best,
Mahmoud
On 19/06/2023 15:07, Evgenii Osipov wrote:
Dear CCP4BB,
I used to run coot from terminal using $coot map mtz>
However this way is no longer working after I updated CCP4 to 8
Dear CCP4BB,
I used to run coot from terminal using $coot
However this way is no longer working after I updated CCP4 to 8.0 with
Coot 0.9.8.7
In similar way, dimple script run-coot.py doens't work as intended — it
will just open Coot but won't load structures and maps.
Coordinates/maps still
When using the COOT (0.9.8.5 EL) on a Mac, the behavior appears to have changed
for manually rotating a fragment (Rotate/Translate Zone/Chain Molecule tool)
When activated, the pop-up window allows me to use the sliders to rotate or
translate. That works as advertised.
However, I used to be abl
Last week I was using 13.2 and could reproduce the snap iconification on
delete item.
This morning I updated to 13.3 and the iconification problem is no more
- so the update fixed it. Apple didn't mention XQuartz or Coot in the
release notes (fwiw).
Paul.
##
I hadn’t noticed until just now, but this also happens on Linux machines at
SLAC -
> Distributor ID: Debian
> Description: Debian GNU/Linux 10 (buster)
> Release: 10
> Codename: buster
:-(
Harry
> On 29 Mar 2023, at 15:02, Joseph Cockburn wrote:
>
> Dear BB,
> Quite a few o
Hi Jinhua,
Following on from Mike's great tip, if you do forget to tick the "Keep
Delete Active" dialog box and your coot window crashes, you can recover
your old session. After coot crashes, open a new coot window and go to
"File" then "Save Coordinates", a new dialogue box pops up asking to
"Se
To: Wu, Jinhua
Cc: ccp4bb@jiscmail.ac.uk
Subject: Re: [ccp4bb] Coot crashes when delete side chain
EXTERNAL sender! Do you TRUST this email? If you are unsure, send the email to
InfoSec for review by using the Report Phish button.
Jinhua,
As Michael stated
Chemistry and Drug Discovery
University of Dundee
Dow Street
Dundee DD1 5EH
From: CCP4 bulletin board on behalf of Nicholas Clark
Date: Wednesday, 8 March 2023 at 00:21
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot crashes when delete side chain
CAUTION: This email originated from
Jinhua,
As Michael stated, ticking "keep delete active" will prevent the window
from closing. Additionally, if you accidentally forget to do this, Coot
does not actually crash. The window gets "hidden" or "minimized". If you
right click on the XQuartz icon, you will see the window at the top of th
Hi Jinhua,A temporary fix to the problem I have seen is to tick the 'Keep
Delete Active' dialog box. Strange, but I'm sure Paul will come up with a fix
soon.HTHMike
On Wednesday, 8 March 2023, 09:11:08 am AEDT, Wu, Jinhua
wrote:
Hi all,
I recently upgraded my iMac to a 6-Core
Hi all,
I recently upgraded my iMac to a 6-Core Intel i5 running Ventura 13.2.1. I
installed Coot 0.9.8.7 together with CCP4. Now every time when I select delete
sidechain (or sidechain zone) and click on the residue, Coot crashes. Does
anyone have the same problem or know the solution to this
pretty well summarises my knowledge, hopefully others will fill in the
gaps.
Charles
From: CCP4 bulletin board on behalf of Patrick Loll
Date: Thursday, 16 February 2023 at 13:27
To: ccp4bb
Subject: [ccp4bb] Coot (& phenix) on Ventura
Hi everyone,
I’ve been putting off upgrading to Mac O
Hi everyone,
I’ve been putting off upgrading to Mac OS 13 Ventura, but my computer is
getting more and more pushy in its demands for a new OS.
Hence I ask, What’s the current status of coot running on Ventura? I’m aware of
the issues that have been discussed in this forum, but that thread seems
Hi Cheng,
this a problem related to gtk+3 installation. There is a workaround to
solve the issue. You need to install a previous version of gtk+3. All
the instructions are here:
https://github.com/pemsley/coot/issues/33#issuecomment-1374409909
Bw,
Lucrezia
On 2023-01-25 15:53, Cheng Zhang wr
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
#
Hi Elsa,
I'm still on high sierra but just updated quartz to the latest version.
Coot also suddenly stopped when I clicked the duck icon on the dock, but I
still can run it using command in the terminal (after going to the coot
folder).
Best regards,
wangsa
On Sat, 31 Dec 2022 at 00:15, Elsa Garci
,
Jiazhi
Dr. Jiazhi Tang
School of Pharmacy
University College London
29-39 Brunswick Square
London WC1N 1AX
From: Paul Emsley<mailto:pems...@mrc-lmb.cam.ac.uk>
Sent: 30 December 2022 17:28
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Coot on MacOS Ve
Hello Elsa,
On 30/12/2022 17:13, Elsa Garcin wrote:
Is it possible to run coot on MacOS Ventura and xquartz version 2.8.4?
I believe so, but people have reported minimizing window when they try
to do so.
I tried installing coot with homebrew (instructions from Scottlab webpage),
This is a qu
Hello all,
Is it possible to run coot on MacOS Ventura and xquartz version 2.8.4?
I tried installing coot with homebrew (instructions from Scottlab webpage), but
was not successful.
Has anyone figured out how to install it so it runs properly? If so, could you
please share how you did it?
Thank y
Dear MacOS Ventura users,
If you have issues with deleting residues/molecules/etc in COOT. Please try to
open the delete dialogue, check the box "Keep dialogue active", delete what is
needed and the close dialogue manually.
There may be other issues with the new macOS, the general recipe is to
Coot is not (yet) an official part of brewsci, so the goocanvas update
bonked coot.
This morning I uninstalled my coot and rebuilt it with YoshitakaMo's
coot.rb. The second time it worked (i.e. build and installed just fine).
You can see from the patch
https://github.com/brewsci/homebrew-bio
homebrew heavy-handedly wiped out coocanvas v. 2 when upgrading.
I made a temp fix with a sym link as follows:
ln -s /usr/local/Cellar/goocanvas/3.0.0/lib/libgoocanvas-3.0.9.dylib
/usr/local/lib/libgoocanvas-2.0.9.dylib
your path prefix will be different, but you get the idea.
> On Sep 30, 2
Hi All,
I am having an issue with installing coot. Here is the outcome when I type
coot in command line. I am using M1 mac pro. Thank you.
Best regards
Tim
CSI363227 ~ % coot
dyld[11265]: Library not loaded:
'/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
Referenced from: '/opt/hom
On 06/08/2022 09:08, Cryo EM wrote:
Hi everyone,
I am trying to mutate modified RNA nucleotide to standard nucleotide
by coot using "Simple Mutate" button. But it is not working despite
selecting the correct residue from the standard base list that pop up
on clicking "simple mutate button". D
Hi everyone,
I am trying to mutate modified RNA nucleotide to standard nucleotide by
coot using "Simple Mutate" button. But it is not working despite selecting
the correct residue from the standard base list that pop up on clicking
"simple mutate button". Does anyone and an idea what could be the
Hi no - Mac. I’ll have a look next time it occurs.
Adrian
Sent from my iPhone
> On 9 Jul 2022, at 14:41, Paul Emsley wrote:
>
> On 09/07/2022 12:36, Goldman, Adrian wrote:
>> On a related theme, Paul, I often find that the undo button doesn’t work,
>> but I can’t figure out why it sometime
On 09/07/2022 12:36, Goldman, Adrian wrote:
On a related theme, Paul, I often find that the undo button doesn’t
work, but I can’t figure out why it sometimes does and sometimes
doesn’t. Is this something to do with how I open .pdb files - that
somehow Coot can’t find the backup files, even tho
On a related theme, Paul, I often find that the undo button doesn’t work, but I
can’t figure out why it sometimes does and sometimes doesn’t. Is this
something to do with how I open .pdb files - that somehow Coot can’t find the
backup files, even though they exist? What should I do to rectify
Thank you, Paul!
From: CCP4 bulletin board On Behalf Of Paul Emsley
Sent: Friday, July 8, 2022 11:50 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot sporadically crashes
Is there an option to save the session automatically every 10-15 minutes or so?
And now to actually answer
Is there an option to save the session automatically every 10-15
minutes or so?
And now to actually answer your question:
yes: Edit -> Settings ->Enable Quick-Save Check-pointing... (the default
is 30 seconds)
On 08/07/2022 16:30, Oganesyan, Vaheh wrote:
Hi All,
Sorry for posting on CCP4BB.
This is an appropriate venue for such a message.
Coot installed together with latest CCP4 on Win10 crashes time to time
with no messages/warnings. Is there an option to save the session
automatically every
Hi All,
Sorry for posting on CCP4BB.
Coot installed together with latest CCP4 on Win10 crashes time to time with no
messages/warnings. Is there an option to save the session automatically every
10-15 minutes or so?
Thank you.
Vaheh
On 27/05/2022 19:22, Jan Abendroth wrote:
Hi all,
not sure if this appropriate for this BB, since right at the interface
between CCP4, Coot and Phenix.
I wonder if someone else also experiences these issues after upgrading
to CCP4 8.0 (or 8.001) and with that to Coot 0.9.8.1. This happens
b
Hi all,
not sure if this appropriate for this BB, since right at the interface
between CCP4, Coot and Phenix.
I wonder if someone else also experiences these issues after upgrading to
CCP4 8.0 (or 8.001) and with that to Coot 0.9.8.1. This happens both on OSX
and windows.
- coot *mydata*.pdb *
On 06/04/2022 07:05, Laurent wrote:
Good morning (French time…)
Two unrelated questions…
Using Coot, I would like to define some key binding… How can I find
the command that is actually issued from an option in the
« calculate » menu ? I would like to define a key binding for the
function « N
/pandda_inspect_tools
Let me know in case you have any problems.
Best,
Tobias
From: CCP4 bulletin board on behalf of Laurent
Reply to: Laurent
Date: Wednesday, 6 April 2022 at 08:05
To: "CCP4BB@JISCMAIL.AC.UK"
Subject: [ccp4bb] Coot and Pandda questions
Good morning (French t
Good morning (French time…)
Two unrelated questions…
Using Coot, I would like to define some key binding… How can I find the command
that is actually issued from an option in the « calculate » menu ? I would like
to define a key binding for the function « NCS Tools -> Update NCS ghost using
loc
Isn’t that what we all say every year on the day after March finishes?
Harry
> On 1 Apr 2022, at 23:46, Paul Emsley wrote:
>
> That, for the record, is more or less what Ralf said 18 years ago.
> On 01/04/2022 23:38, Pavel Afonine wrote:
>> It's April 1st today, isn't it? -;)
>>
>>
>> On Fri,
16 99766-0021
"A sorte acompanha uma mente bem treinada"
De: Jurgen Bosch<mailto:jxb...@case.edu>
Enviado:sexta-feira, 1 de abril de 2022 19:59
Para: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Assunto: Re
Yay!!
I can now blend it with blender.
Jürgen
__
Jürgen Bosch, PhD, MBA
Center for Global Health & Diseases
Case Western Reserve University
https://www.linkedin.com/in/jubosch/
CEO & Co-Founder at InterRayBio, LLC
Johns Hopkins University
Bloomberg
That, for the record, is more or less what Ralf said 18 years ago.
On 01/04/2022 23:38, Pavel Afonine wrote:
It's April 1st today, isn't it? -;)
On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley
wrote:
Coot 1
18 years after the release of Coot 0 it's time that I actually
released
It's April 1st today, isn't it? -;)
On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley
wrote:
> Coot 1
>
> 18 years after the release of Coot 0 it's time that I actually released
> Coot 1.
>
> Coot 1 is a major change beyond Coot 0. It has required a lot of writing
> and rewriting [1]
> and has been th
Coot 1
18 years after the release of Coot 0 it's time that I actually released
Coot 1.
Coot 1 is a major change beyond Coot 0. It has required a lot of writing
and rewriting [1]
and has been the preponderance of my work since 2017. I have had to
learn how to program
graphics from scratch usi
Dr. Pearl,
I have used the pre-built installer here:
http://scottlab.ucsc.edu/xtal/wiki/index.php/Stand-Alone_Coot
This worked on my Mac running Monterey OS with an intel i7.
Best regards,
Nick Clark
On Fri, Feb 11, 2022 at 4:53 PM Laurence Pearl
wrote:
> Does anyone know where I can downlo
On 11/02/2022 21:53, Laurence Pearl wrote:
Does anyone know where I can download a pre-built Coot that will work
on OS X Monterey (12.2) on an iMac with an Intel i7 ?
The packages I can find all fail at the File finder which comes up
blank. X11 latest is installed.
Not an answer to your que
Does anyone know where I can download a pre-built Coot that will work on OS X
Monterey (12.2) on an iMac with an Intel i7 ?
The packages I can find all fail at the File finder which comes up blank. X11
latest is installed.
Laurence
-
This is probably a FLEV specific issue.
Have you tried external software such as LigPlot+ or Schrodinger’s Maestro to
see if they can better handle the modified residue ?
> Le 27 janv. 2022 à 01:03, Sergio A. Sampieri a écrit :
>
> Greetings all,
>
> Sorry for the naive question, but I'm havin
Greetings all,
Sorry for the naive question, but I'm having problems trying to FLEV a
modified residue in COOT.
I have modeled a modified CYS into an structure following these steps:
1. Generate a SMILES string for L-cysteine bonded the modification.
C1=CC=C(C=C1)C(=O)SCC(C(O)=O)N.
htt
: Montag, 22. November 2021 22:09
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [ccp4bb] COOT RSR
What's the difference between a dummy water and a real one?
Paul
On 22/11/2021 14:34, Schreuder, Herman /DE wrote:
Dear Paul,
I agree with Oliver and Norbert, in the early phases of refin
Dear Paul,
with "dummy water" I refer to a water molecule, which I place at the center of
a (usually positive) difference electron density peak to be able to measure the
distances to the environment and decide, what the density actually might be. I
do that quite often. It could also be any othe
ftrag von
*Norbert Straeter
*Gesendet:* Sonntag, 21. November 2021 12:24
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* Re: [ccp4bb] COOT RSR
Dear Paul,
I agree to Oliver. In situations where you want to fit a "dummy water"
to a difference density peak (to determine distances to the
environm
. However, it would be much more
convenient if the repulsions with water molecules would not be taken into
account.
Thank you,
Herman
Von: CCP4 bulletin board Im Auftrag von Norbert Straeter
Gesendet: Sonntag, 21. November 2021 12:24
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] COOT RSR
Dear
Dear Paul,
I agree to Oliver. In situations where you want to fit a "dummy water" to a
difference density peak (to determine distances to the environment) or try the
fit of solvent molecules to yet unexplained density, it would be nice to first
obtain an optimal fit and next think about the env
ere extensive rebuilding is required.
Best regards
Oliver
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Paul Emsley
[pems...@mrc-lmb.cam.ac.uk]
Sent: 20 November 2021 11:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] COOT RSR
On 20/11/2021 09
_
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Paul Emsley
[pems...@mrc-lmb.cam.ac.uk]
Sent: 20 November 2021 11:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] COOT RSR
On 20/11/2021 09:42, Matthew Snee wrote:
I had a bit of trouble getting used to the new COOT real space
On 20/11/2021 09:42, Matthew Snee wrote:
I had a bit of trouble getting used to the new COOT real space
refine... it took me an embarrassingly long time to work out that
there is nothing wrong with the fitting/restraints..
You are not alone in finding Coot's RSR unintuitive (at least initia
Hi all
I had a bit of trouble getting used to the new COOT real space refine... it
took me an embarrassingly long time to work out that there is nothing wrong
with the fitting/restraints.. it just doesn't seem to allow clashes with parts
of the model that aren't in the selected RSR zone even wh
Hi,
I am trying to open coot remote using ssh -X or -Y but this is what I am
getting
[vbanerjee@c110279 ~]$ coot
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON:
/opt/xtal/ccp4-7.1/lib/data/monomers/
There are 244 data in /opt/xtal/ccp4-7.1/lib/data/monomers/list/mon_lib_list.cif
Th
I apologize if this question has been raised before. But I am still
struggling with running Coot 0.95 on my mac laptop (Catalina) with an
external display.
Coot is functioning normal without the external display. But with external
display, the window for displaying models doesn't open properly. Is
Dear all,
I installed the ccp4-7.1 and it loads fine but coot crashes with the
following error message. I would really appreciate any help.
[1m(filter-fileselection-filenames-state) [0m
[1m(get-active-map-drag-flag) [0m
[1m(use-graphics-interfa
Hi all,
If anyone is interested in the question, coot (and any graphical
application I tried) is now fully functional in Windows 11 and the newest
WSLg.
No configuration is needed, everything works out of the box, with full
hardware acceleration.
Clément
On Wed, 25 Mar 2020 at 15:58, Clement Deg
Hi,
I updated my ccp4 and it came with Coot 0.9.6.EL where the sequence view does
not show the numbers of amino acids in the sequence and some letters overlap -
anyone having the same problem? Do I need to install some other version?
Thanks,
Andrea
#
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>
>
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kay
> Diederichs [kay.diederi...@uni-konstanz.de]
> Sent: 16 September 2021 12:19
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] COOT running on Macbook Pro M1 chip
On 16/09/2021 08:40, WENHE ZHONG wrote:
Dear CCP4 community,
The COOT is not running smoothly on my M1 chip Macbook. For example,
when both model and the electron density map are displayed, the moving
from one residue to the next (pressing SPACE bar) is lagging/slow
(>2s). This only happened
t; Tel.: +49 2461 61-2028
> Fax: +49 2461 61-9540
> ==
>
>
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kay Diederichs
> [kay.diederi...@uni-konstanz.de]
> Sent: 16 September 2021 12:19
> To: CCP4BB@J
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] COOT running on Macbook Pro M1 chip
Dear Wim,
on my M1 Macbook Air, coot 0.9.6 (latest from CCP4) works smoothly/fast. What
is your XQuartz version? I have 2.8.1 .
HTH,
Kay
On Thu, 16 Sep 2021 15:40:53 +0800, WENHE ZHONG
wrote:
>Dear C
Hi Claude,
Pymol 2.4.0 (installed via homebrew) works fine for me in Apple M1 MacBook Pro,
2020.
Ciao,
S
> On 16 Sep 2021, at 12:12, Claude Sauter wrote:
>
> Dear all,
>
> to continue on the same theme, a colleague biochemist asked me a couple of
> days ago if there is any incompatibility bet
Dear Wim,
on my M1 Macbook Air, coot 0.9.6 (latest from CCP4) works smoothly/fast. What
is your XQuartz version? I have 2.8.1 .
HTH,
Kay
On Thu, 16 Sep 2021 15:40:53 +0800, WENHE ZHONG
wrote:
>Dear CCP4 community,
>
>The COOT is not running smoothly on my M1 chip Macbook. For example, when
>
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