Re: [ccp4bb] Coot crashes when delete side chain

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

Re: [ccp4bb] Coot crashes when delete side chain

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

Re: [ccp4bb] Coot crashes when delete side chain

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

Re: [ccp4bb] Coot crashes when delete side chain

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

Re: [ccp4bb] Coot crashes when delete side chain

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

[ccp4bb] Coot crashes when delete side chain

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

Re: [ccp4bb] Coot crashes on CentOS 7.9

Dear Kay, Thanks for the reply. Some information regarding our system are as follows: >your processor came out in 2008, and it seems that Paul Emsley used compiler options that require newer capabilities than this processor has, likely in an attempt to speed up coot. Wikipedia says that AVX cameo

Re: [ccp4bb] Coot crashes on CentOS 7.9

Dear Karthik, your processor came out in 2008, and it seems that Paul Emsley used compiler options that require newer capabilities than this processor has, likely in an attempt to speed up coot. Wikipedia says that AVX came out in 2011 and AVX2 in 2013, so your processor supports neither exten

Re: [ccp4bb] Coot crashes on CentOS 7.9

Dear Kay, Thanks for the suggestions. The model name for the computer is "Intel(R) Xeon(R) CPU E5440  @ 2.83GHz". As suggested, I downloaded and installed the latest ccp4 (7.1) which bundles with coot 0.9.5. The coot works just fine with the latest ccp4 bundle. I used the graphic driver fro

Re: [ccp4bb] Coot crashes on CentOS 7.9

Dear Karthikeyan Subramanian, which processor does your computer have? Look at the output of e.g. "head -20 /proc/cpuinfo". What is "model name"? To my understanding, the main problem is > >*./coot: line 264:  5365 Illegal instruction (core dumped) $coot_bin This means that the compiler, w

[ccp4bb] Coot crashes on CentOS 7.9

Dear CCP4 members, I am trying to install the coot-Linux-x86_64-scientific-linux-7.6-gtk2-python on CentOS 7.9 with Nvidia Quadro FX 4800 graphics card. Coot crashes soon after launching the window.  The log file is shown below. Not sure what is missing. The only error I can see is *./coot

Re: [ccp4bb] COOT crashes when I merge molecules

On 10/06/2019 19:53, Franz St John wrote: > I'm having a similar issue with the same Coot version in both Ubuntu 18.04.2 > LTS and Win 10 (WinCoot). Merging an added water crashes Sorry about that. We have a fix in the works (I think (it's hard to know without seeing the core dump)). It's on git

Re: [ccp4bb] COOT crashes when I merge molecules

I also faced this problem. Manjula On Tue, 11 Jun 2019, 1:48 a.m. Tanner, John J., wrote: > Merging EDO into a structure also crashes in Coot 0.8.9.2 running on > linux. > > > John J. Tanner > Professor of Biochemistry and Chemistry > Department of Biochemistry > University of Missouri > 117 Sc

Re: [ccp4bb] COOT crashes when I merge molecules

Merging EDO into a structure also crashes in Coot 0.8.9.2 running on linux. John J. Tanner Professor of Biochemistry and Chemistry Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Email: tanne...@missouri.edu

Re: [ccp4bb] COOT crashes when I merge molecules

I'm having a similar issue with the same Coot version in both Ubuntu 18.04.2 LTS and Win 10 (WinCoot). Merging an added water crashes while an added K or PO4 does not. To unsubscribe from the CCP4BB list, click the followi

[ccp4bb] COOT crashes when I merge molecules

Dear CPP4 people, COOT (0.8.9.2 EL) crashes everytime I merge my model with the monomer EDO (1,2-Ethanediol, cryoprotectant). The same issue does not occur with other monomers. I tried to replace EDO.cif in a new monomer (EDQ.cif) and COOT works fine. Any suggestion? Thanks in advance, Luca M

Re: [ccp4bb] Coot crashes on starting baton mode.

Dave: This may or may not help. I have not seen this particular error before, but I I have discovered that sometimes coot can crash in newer versions of OSX. I actually keep two "flavors" of coot in my system: one from the CCP4 suite and the other from the Scott lab website. Somehow those two vers

[ccp4bb] Coot crashes on starting baton mode.

Hi all, I'm running Coot 0.8.7 (as distributed with the CCP4 package) on OSX 10.11.6. As soon as I click to enter CA-baton mode, coot crashes (terminal output pasted below). All I have done prior to this is load a pdb and an mtz, build skeletons and pick a start point. Has anyone seen this befo

Re: [ccp4bb] coot crashes

On Mar 2, 2009, at 7:47 AM, Justin Lecher wrote: William G. Scott schrieb: On Mar 2, 2009, at 4:25 AM, Vellieux Frederic wrote: Any idea? Is it there? http://www.mail-archive.com/ubuntu-b...@lists.ubuntu.com/msg663049.html It was on the ccp4bb not on thc COOT list. Sue me. -- Justin

Re: [ccp4bb] coot crashes

William G. Scott schrieb: > On Mar 2, 2009, at 4:25 AM, Vellieux Frederic wrote: > >> Any idea? > > Is it there? > > http://www.mail-archive.com/ubuntu-b...@lists.ubuntu.com/msg663049.html It was on the ccp4bb not on thc COOT list. -- Justin Lecher Institute for Neuroscience and Biophysics IS

Re: [ccp4bb] coot crashes

Hi Tim, Coot crashes only when I try to mutate the residue. There has been no system update on my machine (I prevented that just so that library problems would not occur!). I ran the same version of coot on another machine, and coot did not crash when mutating. I don't know why. Fred Tim Gr

Re: [ccp4bb] coot crashes

Hi Fred, does coot crash upon start-up, or when you try to mutate the sequence? I can imagine that Gtk issues such a warning about a missing library without failing to start. In that case, the line you are posting is not the cause of error. If it is the cause, than you must find the package

[ccp4bb] coot crashes

Hello all, Until now I was using coot on my Linux box without problems. Now I have a new structure (molecular replacement) that I try to mutate to the correct sequence. Coot crashes with the following error message: Gtk-WARNING **: Failed to load module "libgnomebreakpad.so": libgnomebreakp