On 15 août 2012, at 02:23, Wataru Kagawa wrote:
> Hi Jinyi,
>
> Do you have two versions of python installed?
> Maybe executing "fink remove python" will solve the problem (?)
Hi,
After updating to Mountain Lion, coot crashed when launched from the phenix
GUI. But launching coot from the term
Hi Jinyi,
Do you have two versions of python installed?
Maybe executing "fink remove python" will solve the problem (?)
Wataru
I have had success with the standalone Coot, found here:
http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot
It doesn't use the Fink package, which seems to be part of your problem. Try
completely uninstalling your version and reinstalling this one. I've had no
problems at
I'm unable to reproduce the error.
Can you try it in a temporary new account that doesn't have anything modified,
and see if it works?
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of Ca
Do you use CCP4-6.2? I met the similar problem before.
Try use the latest version of coot 0.7.
On Wed, Feb 15, 2012 at 8:42 AM, Christopher Browning <
christopher.brown...@epfl.ch> wrote:
> Hi Laurie,
>
>
> Not much, I did not get any useful feedback so I emailed Paul Emsley
> directly.
>
> C
Hi Laurie,
Not much, I did not get any useful feedback so I emailed Paul Emsley
directly.
Chris
On Tue, 2012-02-14 at 22:43 -0500, Laurie Betts wrote:
> Problem with COOT and MSE (SeMET ) residues
--
Dr. Christopher Browning
Post-Doctor to Prof. Petr Leiman
EPFL
BSP-416
1015 Lausanne
Swit
Hi,
I'm just writing to ask whether anybody has experienced the same problem
as me concerning mutation of Methionines (MET) to Seleno-Methionines
(MSE).
When I change the MET residues to MSE residues and do real space refine,
the chain goes completely bizerk and the MSE residue (and most of the
r
Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul
Emsley
Sent: Monday, February 13, 2012 1:49 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] problem with coot install
On 14/02/12 08:17, Alexander U. Singer wrote:
> Hi -- I was installing the latest version
On 14/02/12 08:17, Alexander U. Singer wrote:
Hi -- I was installing the latest version of CCP4 6.2.0 on my machine
which uses Linux Fedora Core 5. When downloading the CCP4 package, I
used the 'generic linux (x86) option'. The package contains an
package for Coot v 0.6.2 which I tar'ed and unc
Hi -- I was installing the latest version of CCP4 6.2.0 on my machine
which uses Linux Fedora Core 5. When downloading the CCP4 package, I
used the 'generic linux (x86) option'. The package contains an
package for Coot v 0.6.2 which I tar'ed and uncompressed, but when I
try to run it, I g
Dear all,
I have been using Coot during a long time without any problem, but
today, when I try to open the program, something has failed. The
message was:
/Applications/coot.app/Contents/Resources/script: line 205: 1965
Segmentation fault $COOT_PREFIX/bin/coot-real $command
coot-e
Dear Munan,
this is a question that should better go to the Coot mailing list.
Anyway - it is difficult to say what the problem is, without more
informations. It could be an X11 problem or a Coot installation problem.
Generally, on Mac OS X, you don't have to start X11 manually or at login
-
Dear BB
I have a problem with coot opening, i tried to open but its not opended.
Then I found some other problem, X11 terminal is not opened on login (even its
in the list on login items), if I open X11 and then tried to open coot still
not
working, I am using Macbook and the OS X is 10.6.1. (c
rlooked because
this is quite unexpected...
Regards,
Peter
> Date: Mon, 31 Aug 2009 01:17:39 +0200
> From: mark.vanra...@usc.es
> To: pc...@hotmail.com
> CC: paul.ems...@bioch.ox.ac.uk
> Subject: Re: [ccp4bb] Problem with Coot reading monomer library file.
>
> Peter, Pau
-2738eric.ortl...@emory.edu
> Date: Sat, 29 Aug 2009 07:02:12 +0100
> From: paul.ems...@bioch.ox.ac.uk
> To: pc...@hotmail.com
> Subject: Re: [ccp4bb] Problem with Coot reading monomer library file.
>
> Peter Chan wrote:
> > Dear Crystallographers,
> >
> >
Dear Crystallographers,
I've been spending >10 hours trying (googling, manually editting cif files
based on templates in Coot's library, asking around, rtfm and reading this bbs)
to figure out why Coot the geometric restraints wouldn't load.
The molecule I have is difluoroacetate (and some ana
Vellieux Frederic wrote:
No, I don't have a residue 8... Since Add Terminal Residue is the only
option to extend the chain (and we see density for the missing residues)
we are at loss there
So, you *do* have a residue 9 and 10 and want to add a residue 8. Did
I understand correctly? If you
No, I don't have a residue 8... Since Add Terminal Residue is the only
option to extend the chain (and we see density for the missing residues)
we are at loss there
Mark Roe wrote:
As far as I know, this would only happen if you already have a residue
number 8. Sometimes coot will put inserted
Dear All,
I haven't subscribed to the coot bb and hence thought I could get an
answer from this bb.
We cannot use the option "Add Terminal Residue" for the very first
N-terminal residue of the protein (residue number 9) and this is very
annoying. Does anyone know the solution to this problem
I installed mapman and it's also failed with similar error when trying to
convert with mapman. See below:
MAPMAN > re slot1 sa_omit_map.map
Format ? (CCP4) XPLOR
Try format "CNS" or "X-PLOR" and as I asked earlier what does "head
sa_omit_map.map" or the head output from your map file you tr
Hi All,
I am using COOT 0.5-pre and getting the following error when opening a cns map.
I can open that map in O.
CCP4 map filename: /Users/rajadey/yong/cns/coot/sa_omit_map.map
INFO:: map file type was determined to be CNS type
allocating space in read_ccp4_map
attempting to read CNS map: /Users
Uma Katre schrieb:
Dear all,
I recently installed CCP4 suite on a DELL workstation running Red Hat
Enterprise Linux 5. CCP4 seems to be working fine, however, Coot and
ccp4mg fail to open. This is what I get when I try to run Coot:
current_exe_dir is /usr/local/ccp4/ccp4-6.0.2/Coot-0.3.3/bin
Dear all,
I recently installed CCP4 suite on a DELL workstation running Red Hat
Enterprise Linux 5. CCP4 seems to be working fine, however, Coot and ccp4mg
fail to open. This is what I get when I try to run Coot:
current_exe_dir is /usr/local/ccp4/ccp4-6.0.2/Coot-0.3.3/bin
COOT_PREFIX is /usr/lo
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