Dear Paul,
Thank you for these condolences :) I realize that the problems are very likely due to my setup, which is why I didn’t reach out. So please do not take any steps to resolve this, unless others are reporting these issues as well. I probably should not have taken it this far, but at one point I just wanted to stubbornly “make it happen”. Interestingly, I did not have these problems when installing the 0.9-beta. Now, a lot of these problems seem to be rooted in coot/WSL/Ubuntu not checking the correct lib folders; at one point, coot doesn’t even seem to find libraries that were in its own installation lib folder. I have tried to resolve this issue, but did not succeed in tricking the system to look in other library folders as well. Since quite some Linux experts seem to be on this mailing list, allow me to highjack this and ask: does anybody know how to do this? Thank you in advance, Erwin Van: Mailing list for users of COOT Crystallographic Software <[email protected]> Namens Paul Emsley Verzonden: woensdag 2 december 2020 17:08 Aan: [email protected] Onderwerp: Re: Coot installation in Ubuntu On 02/12/2020 15:54, Erwin Pannecoucke wrote: Hi all, I also had quite some libraries that were flagged as missing, and approached it as following: * In my setup, the coot folder was extracted in /mnt/c/WinCoot_0.9/ * In that folder, I checked if all library dependencies could be found by executing ldd libexec/coot-bin * You can execute ldd libexec/coot-bin | grep "not found" to get a list of the ones that are not found coot --check-libs * * For each of those libraries, 1. First tried to see if that library could be found in the lib/ folder of coot 2. If not, I tried to figure out if it was already installed using the locate command a. for example, if it couldn’t find libRDKitForceFieldHelpers.so.1, I executed the following command: locate libRDKitForceFieldHelpers.so There should absolutely not be any missing RDKit libraries. b. In that list, I tried to find the last version of libRDKitForceFieldHelpers.so , which could often be found in the CCP4 folder or in /lib/x86_64-linux-gnu/ or /usr/lib/x86_64-linux-gnu 3. If it couldn’t be found, I google which package I should install using apt-get to get that library. OK but it should only be libpng and libgnomecanvas-2 as Juan Pablo said. 4. * On my system, coot is apparently only looking in the /usr/lib/ folder, That's not coot's doing, that is the operating system. * when it can’t find a library. So you have to make a symlink in /lib/ to the library found in the previous step, for example: * sudo ln -s /mnt/c/WinCoot_0.9/latest/lib/libguile.so.17 /usr/lib/libguile.so.17 * sudo ln -s /usr/local/bin/CCP4/ccp4-7.1/lib/libmmdb2.so /usr/lib/libmmdb2.so * … That's hideous. I had no idea that it was so much of a pain. I don't know why you need to do this. It was not my plan that you should. Quite the opposite in fact. * * Finally, in the end I got a problem that a library gave a “relocation error” for another library. It took some time, but I figured out that this meant that SomeLib-a, which is the coot folder, is dependent on SomeLib-b, which is in the /usr/lib folder. To resolve this issue, just remove the SomeLib -a, so that coot starts looking for it in /usr/lib/ to find SomeLib-a , or make a symlink of /usr/lib/ SomeLib to /your/coot/folder/lib/SomeLib. Good grief. Paul. _____ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1> &A=1 ######################################################################## 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 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/
