Re: [COOT] stero/Mono
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 nvidia invoke is. Perhaps you are refering to an environment variable? Chimerax works, In what way? What changes? however, this will stop the working for coot to display structure at the following view modes: `mono`, `side by side stereo`, and `side by side (wall eyed)`. What do you mean by "stop the working"? That Coot doesn't start up? Or freezes? It It? meaning Coot or the graphics card? still works if I click 'hardware stereo' or 'Zalman Stereo' and I can see it in `nvidia-smi`. "see it"? The graphics card? Without GPU, each mode works fine. Without the graphics card, Coot will fall back to software rendering on the backend. Not many people these days think that that is "fine." I wonder if we shouldn't run coot with GPU or if there are some potential issues. Does anyone have any idea about this? Thanks! For most people, Coot uses the GPU whether they like it or not. The advice I can give you is trite: use whatever gives you the best FPS. I'm not sure that I've been of much help. Paul. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Coot: Fitting a,b Methylene ATP (APC) into cryoEM Density
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 APC (in Monomer library) which is a non-hydrolyzable analog of ATP. I place the ligand and manually fit it into the correct density, however, when I use any of the Ligand functions (IE, jigglefit ligand, find ligands, etc.) nothing changes. I am a bit confused. If you have already fit the ligand correctly into the density, then jiggle fit or find ligands won't find a better solution. I am quite unsure how to validate this fitting such that torsions and restraints are correct. Are there any tutorials out there on how to do this? I cannot seem to find any. Ligand -> Display Ligand Distortions will colour the bonds, angle and chiral centres with a colour ramp green to red (read means more than 3 esds from the target value). Ligand -> Tabulate Ligand Distortions will list the bond, angle, chiral and plane restraints distortions. I haven't written a tutorial for this - that is a good idea. Paul. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] (Re)beginner question about coot binary version on Linux Ubuntu
Thanks Paul for both messages. Thanks a ton for a summary of the various projects underway. I’m working on the build-it script on the Linux side while I figure out a ccp4 full license for my “self learning” small use. The build it script runs aground with some numpy libraries missing , even though I had python-numpy-dev..but i’ll keep at it. In the case of openssl missing errors..it was certainly installed and pointed to by the LD_LIBRARY_PATH..but it probably was a version mismatch because I had different version Hari On Wed, May 24, 2023 at 3:26 PM Paul Emsley wrote: > > On 24/05/2023 14:24, hari jayaram wrote: > > > CAUTION: This email originated from outside of the LMB. > Do not click links or open attachments unless you recognize the sender and > know the content is safe. > *.-owner-c...@jiscmail.ac.uk-.* > > Hi All > I am making some progress--but still cant get any of the binaries working > > I have the openssl libraries installed but still get the following error > with coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python > > Thanks for your help > Hari > > > > > "hari@LT-Hari-Linux:/usr/lib/x86_64-linux-gnu$ > ~/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/bin/coot > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: > libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: > /lib/libssl.so.1.1: version `OPENSSL_1_1_1' not found (required by > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: > /lib/libssl.so.1.1: version `OPENSSL_1_1_0' not found (required by > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) > > > It is not clear to me if libcrypto is not installed (in which case you > should install it) or is a more modern version than my binary expects (in > which case, there is no hope for the binary that I have built (you might > like to try the build-it script)). > > Paul. > > > To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] (Re)beginner question about coot binary version on Linux Ubuntu
On 24/05/2023 14:24, hari jayaram wrote: CAUTION: This email originated from outside of the LMB. Do not click links or open attachments unless you recognize the sender and know the content is safe. *.-owner-c...@jiscmail.ac.uk-.* Hi All I am making some progress--but still cant get any of the binaries working I have the openssl libraries installed but still get the following error with coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python Thanks for your help Hari "hari@LT-Hari-Linux:/usr/lib/x86_64-linux-gnu$ ~/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/bin/coot /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_1' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) It is not clear to me if libcrypto is not installed (in which case you should install it) or is a more modern version than my binary expects (in which case, there is no hope for the binary that I have built (you might like to try the build-it script)). Paul. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] (Re)beginner question about coot binary version on Linux Ubuntu
On 24/05/2023 02:13, hari jayaram wrote: CAUTION: This email originated from outside of the LMB. Do not click links or open attachments unless you recognize the sender and know the content is safe. *.-owner-c...@jiscmail.ac.uk-.* Hi All I want to get back to using coot to build some models after a gap of 8 years. I have access to a Linux laptop and can put any OS version on it. I was wondering what the easiest way forward is —get the most recent Ubuntu and pull the latest binary ( 0.9.8.6 with binary for 20.04) or put the iso that coot was built for (20.04) on the laptop and start using it. The easiest way forward is to use the build from CCP4. They fiddle with it in minor annoying ways. It's robust. It comes with a lot of other stuff. You have to sign a license. Best way is to use the build-it script. Then you can track day-to-day development. The downside for this is that it often doesn't work out of the box. Having said that, all development tracking is a bit weird at the moment since there are 3 versions: - the 0.9.x series with old GTK and old python and old graphics - 1.0 the current release that depends on Gtk3 that doesn't work well on macOS - and maybe not Windows either - GTK4 Coot (which is another major rewrite). This is where I am spending my time (that and Moorhen). I want to get to a stage where GTK4 Coot is the only game in town. But there is a lot of work to do. And additional further work to make sure that it works well on macOS and Windows. What I can say about future Coots is that they will use your hardware - the more cores and better graphics card you have the more enjoyable/productive will be your Coot-using experience. Asking because I just tried using the newest mint distro ( Mint 21.1 Vera) and one of the binaries (coot-Linux-x86_64-scientific-linux-7.6-gtk2-python) and it runs aground without OpenSSL and ldap.so versions are being mismatched. OpenSSL and Python are particularly time-consuming to correctly configure. I don't know how many days and weeks I've spend fiddling with it. Lots. Wretched thing. When I switched to coot-0.9.8-binary-Linux-x86_64-ubuntu-20.04.4-python-gtk2 then it complained of a version mismatch for libssl.so.1.1 I should make a Linux Mint virtual machine... Regards, Paul To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[COOT] Coot 0.9.8.8
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 now drawn as CL. - BUG-FIX: the zoom state is now correctly set in the saved state file - BUG-FIX: additional symmetry check for peaks from flood filling (Paul Bond) - BUG-FIX: Link-generation improvements. Source: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.8.tar.gz Binaries: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/ Paul. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] [EXTERNAL] Re: (Re)beginner question about coot binary version on Linux Ubuntu
Hi Hari, To make it easy on Macs, we usually download and install CCP4, which comes with pre-compiled binaries for coot as well. In terms of size of the package it is an overkill but it is usually straight forward to install and it also provides a lot of other useful programs. You could try under Linux. Cheers, christian From: Mailing list for users of COOT Crystallographic Software on behalf of hari jayaram Date: Wednesday, May 24, 2023 at 09:24 To: COOT@JISCMAIL.AC.UK Subject: [EXTERNAL] Re: (Re)beginner question about coot binary version on Linux Ubuntu Hi All I am making some progress--but still cant get any of the binaries working I have the openssl libraries installed but still get the following error with coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python Thanks for your help Hari "hari@LT-Hari-Linux:/usr/lib/x86_64-linux-gnu$ ~/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/bin/coot /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_1' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) . -- Coot crashed - trying to diagnose - ldd -r on guile gives: linux-vdso.so.1 (0x7ffdbdfae000) libguile.so.17 => /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libguile.so.17 (0x7f6d85ccc000) libc.so.6 (0x7f6d85aa4000) libgmp.so.10 => /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libgmp.so.10 (0x7f6d85a2b000) libcrypt.so.1 (0x7f6d859ef000) libm.so.6 (0x7f6d85908000) libltdl.so.3 => /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libltdl.so.3 (0x7f6d858fd000) libpthread.so.0 (0x7f6d858f8000) /lib64/ld-linux-x86-64.so.2 (0x7f6d85dd2000) libdl.so.2 (0x7f6d858f3000) Guile 1.8.8 Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation Guile may be distributed under the terms of the GNU General Public Licence; certain other uses are permitted as well. For details, see the file `COPYING', which is included in the Guile distribution. There is no warranty, to the extent permitted by law. catching the crash log: coot-exe: "/home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin" /usr/bin/ls -rwxr-xr-x 1 hari hari 423402112 Mar 10 2022 /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin coot-version: /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_1' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) platform: /usr/bin/uname Linux LT-Hari-Linux 5.15.0-56-generic #62-Ubuntu SMP Tue Nov 22 19:54:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux core: #f No core file found. No debugging " On Tue, May 23, 2023 at 9:13 PM hari jayaram mailto:hari...@gmail.com>> wrote: Hi All I want to get back to using coot to build some models after a gap of 8 years. I have access to a Linux laptop and can put any OS version on it. I was wondering what the easiest way forward is —get the most recent Ubuntu and pull the latest binary ( 0.9.8.6 with binary for 20.04) or put the iso that coot was built for (20.04) on the laptop and start using it. Asking because I just tried using the newest mint distro ( Mint 21.1 Vera) and one of the binaries (coot-Linux-x86_64-scientific-linux-7.6-gtk2-python) and it runs aground without OpenSSL and ldap.so versions are being mismatched. When I switched to coot-0.9.8-binary-Linux-x86_64-ubuntu-20.04.4-python-gtk2 then it complained of a version mismatch for libssl.so.1.1 Thanks for your help in advance Hari To unsubscribe from the COOT list, click the following link: Bad URL Removed - see why - https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?SUBED1=COOT=1 CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the
