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' (Co
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' (Coot 0.9.8).
With both Coot versions, the program
Dear Paul,
Same problem as previously shown.
Thanks.
Yours sincerely
HK
To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1
This message was issued
On Fri, 2021-07-16 at 05:07 +0100, Heng-Keat Tam wrote:
> To whom it may concern,
>
> Recently, I have a problem with coot after Ubuntu upgrade from 18.04 to 20.04.
>
> I could not launch the coot as it showed the message below. May I know what
> is going wrong with the software?
If you are try
To whom it may concern,
Recently, I have a problem with coot after Ubuntu upgrade from 18.04 to 20.04.
I could not launch the coot as it showed the message below. May I know what is
going wrong with the software?
Thanks for the help.
Best regards
HK
coot-bin:4860): GLib-GObject-WARNING **: 12
On Wed, 2021-04-21 at 16:48 +0100, DougB wrote:
> Hello.
>
> I'm attempting to run coot on CentOS 7 using
> "coot-Linux-x86_64-scientific-linux-7.6-gtk2-python" binaries
>
> I'm getting the splash screen, but then coot crashes. I appreciate any help!
>
It would be better if Coot could exit mo
Hello.
I'm attempting to run coot on CentOS 7 using
"coot-Linux-x86_64-scientific-linux-7.6-gtk2-python" binaries
I'm getting the splash screen, but then coot crashes. I appreciate any help!
Here is the output:
./coot
CLIBD_MON not set using COOT_REFMAC_LIB_DIR
(coot-bin:13947): GLib-GObject
Hello.
I'm trying to get Coot working on Centos 7. Currently trying to use the
Scientific Linux 7.6 gtk2-python binaries.
At start, I get the splash screen, but then it crashes before the program
window appears. Any help is appreciated!
Here is the output:
./coot
CLIBD_MON not set using CO
I installed 0.9.5 on RHEL7.9 and it does not work. Just crashes. Enclosed is
the txt file of the output.
kas
Kenneth A. Satyshur, M.S., Ph.D.
Senior Scientist,
College of Ag and Life Sciences: Department of Bacteriology;
School of Medicine and Public Health:
Departments of Biomolecular Chem
On 22/01/2018 07:40, Marko Hyvonen wrote:
Dear Cooters,
I seem not to be able to read in coordinates which has two different residues (=heterogeneity) in a
particular position. The residues have the same residue number, but differ in residue name. They are
market as alternatives A and B for
Not an accurate subject line I realise now.
Coot does _not_ crash, just refuses to read the coords.
Marko
On 22/01/2018 07:40, Marko Hyvonen
wrote:
Dear Cooters,
I seem not to be able to read in coordinat
Dear Cooters,
I seem not to be able to read in coordinates which
has two different residues (=heterogeneity)
in a particular position. The residues have
the same residue number, but differ
in residue name. They are market as
alter
Reducing the sampling rate did it. Not sure how it got set that high.
Len
From: Mailing list for users of COOT Crystallographic Software
[COOT@JISCMAIL.AC.UK] on behalf of Huw Jenkins [h.t.jenk...@me.com]
Sent: Thursday, June 19, 2014 12:41 PM
To: COOT@
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 Jun 19, 2014, at 10:13 AM, Thomas, Leonard M. wrote:
> Here is what the path currently is with out modification. Nothing about CCP4.
>
> DYLD_LIBRARY_PATH=/usr/local/xia2-0.3.1.0/xia2-0.3.1.0//binaries/mac_386:/usr/local/xia2-0.3.1.0/xia2-0.3.1.0//binaries/mac_386:/usr/local/DTREK99/lib
>
>
Here is what the path currently is with out modification. Nothing about CCP4.
DYLD_LIBRARY_PATH=/usr/local/xia2-0.3.1.0/xia2-0.3.1.0//binaries/mac_386:/usr/local/xia2-0.3.1.0/xia2-0.3.1.0//binaries/mac_386:/usr/local/DTREK99/lib
Len
From: Mailing list fo
On 19 June 2014 17:54, William G. Scott wrote:
> On Jun 19, 2014, at 9:33 AM, William G. Scott wrote:
>
>> If the user has set $DYLD_LIBRARY_PATH (perhaps via ccp4), it is possible
>> this gets over-ridden.
>
> I can reproducibly mess coot up with this:
>
>export DYLD_LIBRARY_PATH=/Applicat
On Jun 19, 2014, at 9:33 AM, William G. Scott wrote:
> If the user has set $DYLD_LIBRARY_PATH (perhaps via ccp4), it is possible
> this gets over-ridden.
I can reproducibly mess coot up with this:
export DYLD_LIBRARY_PATH=/Applications/ccp4-6.4.0/lib
and un-mess it up with this:
export
On Jun 19, 2014, at 9:09 AM, Paul Emsley wrote:
> On 19/06/14 11:29, Paul Emsley wrote:
>> On 18/06/14 19:09, Thomas, Leonard M. wrote:
>>> OK this has me puzzled. Coot was working fine until I had to update
>>> something in order to install the latest version of Phenix. I don't
>>> remember
On 19/06/14 11:29, Paul Emsley wrote:
On 18/06/14 19:09, Thomas, Leonard M. wrote:
OK this has me puzzled. Coot was working fine until I had to update
something in order to install the latest version of Phenix. I don't
remember exactly what the module was but Phenix needed it.
Now the lates
On 18/06/14 19:09, Thomas, Leonard M. wrote:
OK this has me puzzled. Coot was working fine until I had to update something
in order to install the latest version of Phenix. I don't remember exactly
what the module was but Phenix needed it.
Now the latest version of Coot crashes when loading
Yep that was what got updated. Now why does it screw up coot? Anyone? Anyone?
Bueller?
Len
From: Nat Echols [nathaniel.ech...@gmail.com]
Sent: Wednesday, June 18, 2014 1:14 PM
To: Thomas, Leonard M.
Cc: COOT@jiscmail.ac.uk
Subject: Re: coot crash when loading
On Wed, Jun 18, 2014 at 11:09 AM, Thomas, Leonard M.
wrote:
> OK this has me puzzled. Coot was working fine until I had to update
> something in order to install the latest version of Phenix. I don't
> remember exactly what the module was but Phenix needed it.
>
Probably the command-line devel
OK this has me puzzled. Coot was working fine until I had to update something
in order to install the latest version of Phenix. I don't remember exactly
what the module was but Phenix needed it.
Now the latest version of Coot crashes when loading an mtz file with the
following error
INFO::
Hmm - do I like updates?
Here is the message from a Fedora 10 based machine..
It was working yesterday evening..
Eleanor
[c...@roo hypFdemo]$ coot-latest
COOT_PREFIX is /y/programs/xtal/coot/coot-Linux-i386-fedora-8-gtk2-python
/y/programs/xtal/coot/coot-Linux-i386-fedora-8-gtk2-python/
Hi Paul,
The new coot version (0.5.2) seems to crash while using the "Fit Loop"
option under 'Calculate' menu.
The error message is
** WARNING **: Widget not found:
mutate_sequence_use_ramachandran_restraints_checkbutton
Gtk-CRITICAL **: file gtkwidget.c: line 1427 (gtk_widget_show):
assertio
I'm in the process of fixing it, but if you want, just edit the file
/sw/fink/dists/unstable/main/finkinfo/gnome/pygtk2-gtk-py.info
and change the line
Type: python (2.5)
to
Type: python (2.5 2.6)
or sit tight for about an hour and I'll have a newer update that works
around this problem.
Thank you Bill.
Updating python to 2.6 solves the problem.
Raj
--- On Thu, 2/5/09, William Scott wrote:
From: William Scott
Subject: Re: [COOT] Coot crash (0.6-pre-1-revision-1834-10)
To: COOT@JISCMAIL.AC.UK
Date: Thursday, February 5, 2009, 4:58 PM
Sorry.
Basically, coot built with
Sorry.
Basically, coot built with python2.6 instead of python2.5. I'll try
to fix it the right way, but this one will work if you install fink's
python26 and python packages , and then pygtk2-gtk-py26
The catch is there is no pygtk2-gtk-py26 in fink yet (they claim it
doesn't work, but
I get the same message after my fink update to that version of coot.
I'm also using OSX10.5.6 on a MacIntel.
Anyone find a fix yet?
Jon
On Feb 5, 2009, at 12:11 PM, S. Shanmuga Sundara Raj wrote:
Hi,
I updated the Coot pre-release 0.6-pre-1-revision-1834-10 using
fink. When I try to ru
Hi,
I updated the Coot pre-release 0.6-pre-1-revision-1834-10 using fink. When I
try to run Coot, I am getting the following error. I am using OSX 10.5.6
sssraj% coot
dyld: Library not loaded: /sw/lib/python2.6/config/libpython2.6.dylib
Referenced from: /sw/bin//coot
Reason: image not fo
Roger Rowlett wrote:
I am experiencing a strange Coot crash issue on some of my Linux
workstations. Coot 0.5.2 or 0.6-pre1 crashes with an identical failure
mode with the following Coot output (last few lines):
[...]
load "tips.scm"
load "americanisms.scm"
load "group-settings.scm"
(set-disp
I am experiencing a strange Coot crash issue on
some of my Linux workstations. Coot 0.5.2 or 0.6-pre1 crashes with an
identical failure mode with the following Coot output (last few lines):
[...]
load "tips.scm"
load "americanisms.scm"
load "group-settings.scm"
(set-display-lists-for-maps 0
On Dec 11, 2008, at 12:25 AM, Paul Emsley wrote:
One day, I hope to have the skills to build Coot on Mac myself (that
day seems a long way off...)
Nonsense. Come to California for a visit, and we'll have it going in
no time. (I'd come to balmy ol' England, but I'm under US State
Depar
I'll remake the others if using the most current version is all that
is needed.
On Dec 11, 2008, at 12:47 AM, Miguel Ortiz Lombardia wrote:
Dear Valerie, Paul and others,
FWIW, rather interestingly, we don't observe this crash on:
Intel-Mac OS X.5.5
Coot 0.5.1-pre-1 rev. 1626
Bill's fink b
Dear Valerie, Paul and others,
FWIW, rather interestingly, we don't observe this crash on:
Intel-Mac OS X.5.5
Coot 0.5.1-pre-1 rev. 1626
Bill's fink build
All SSM seems to work all right, including superposing one of the
monomers on top of another one (by moving a copy of the molecule)
Best
Valerie Biou wrote:
Hello
I have coot v. 0.5 with macosx 10.5.5 with an intel processor. Each time I
try to display the ncs ghost coot crashes. Is this a known problems?
Dear Valerie,
That sounds bad, and yes, I think there is a known problem of using SSM
(which is what 0.5 uses to generate
Hello
I have coot v. 0.5 with macosx 10.5.5 with an intel processor. Each time I
try to display the ncs ghost coot crashes. Is this a known problems?
best wishes,
Valerie Biou
Try moving .coot out of the way, or leaving out any command line
argument and see if it works.
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
On Jul 11, 2008, at 2:56 PM, Jianghai Zhu wrote:
Hi,
I just updated COOT to 0.5-pre-1-1223 using Bill's fink binary under
OS
Hi,
I just updated COOT to 0.5-pre-1-1223 using Bill's fink binary under
OS X 10.5.4. X11 is version 2.2.3. Coot crashes at startup and gives
the following error.
Good afternoon Jianghai Zhu. Welcome to Coot.
(set-display-intro-string "Good afternoon Jianghai. Welcome to Coot")
load "muta
40 matches
Mail list logo
