Hi Paul, I did install chain-refine using Curlew but I have a peculiar problem in that that I see the following error when I try to install it - DEBUG:: in coot_get_url_and_activate_curl_hook https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/extensions/curlew/info.json coot-download/info.json No icon in item curlew-expand-map-radius.scm No icon in item curlew-stroke-characters.scm No icon in item curlew-find-atom-overlap-baddies.scm No icon in item curlew-refinement-tools.scm No icon in item curlew-keyboard-mutate.scm No icon in item curlew-gui-cablam.scm No icon in item curlew_add_a_3d_note.py No icon in item curlew-speedrun-timer.py debug:: curlew_install_extension() uninstall_button 0x4589410 DEBUG:: in coot_get_url_and_activate_curl_hook https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/extensions/curlew-chain-refine.scm coot-download/curlew-chain-refine.scm checksum compare 15756 15756 debug:: attempting to rename coot-download/curlew-chain-refine.scm as /home/pshah/.coot-preferences/curlew-chain-refine.scm WARNING:: rename status -1 failed to install curlew-chain-refine.scm WARNING:: rename error: Invalid cross-device link WARNING:: fall-back: run the script from download-dir: coot-download/curlew-chain-refine.scm debug:: run_script() on coot-download/curlew-chain-refine.scm debug:: run_guile_script() A on coot-download/curlew-chain-refine.scm debug:: run_guile_script() B on coot-download/curlew-chain-refine.scm This is likely due to something like this https://unix.stackexchange.com/questions/79132/invalid-cross-device-link-while-hardlinking-in-the-same-file-system/79161
Nevertheless, I am able to invoke it via Calculate > Run Script > coot-downloads/curlew-chain-refine.scm But running chain refine dies with the aforementioned error. Interestingly I am able to reproduce this problem on my M1 Mac (BigSur) with an older version of ccpem (late Dec'21)(Cootv0.9.6). I am currently in the process of updating my installation of Coot on my Mac but am pessimistic that that will solve the problem. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK On Tue, Feb 15, 2022 at 6:05 PM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > > On 15/02/2022 14:48, Pranav Shah wrote: > > Hi Paul, > > > > I am trying to use the chain refine functionality in Coot 0.9.7 which > > I have installed via ccpem in a CentOS8 environment and I am seeing > > the following message > > /// > > In /home/pshah/software/ccpem/ccpem-20220125/share/guile/gtk-2.0/gtk.scm: > > 147: 0* [apply #<procedure #f ()> ()] > > In unknown file: > > ?: 1 [#<procedure #f ()>] > > In coot-download/curlew-chain-refine.scm: > > ... > > 48: 2 (chain-refine aa-imol aa-chain-id) > > coot-download/curlew-chain-refine.scm:48:29: In expression > > (chain-refine aa-imol aa-chain-id): > > coot-download/curlew-chain-refine.scm:48:29: Unbound variable: chain-refine > > /// > > Could you [help] understand what the principle cause of death is and > > how I could revive the program? > > > This is my mistake - I had intended to bundle chain-refine in 0.9.7 but > it seems that I failed to do so. > > Please install the refinement tools using Curlew. > > Paul > > ######################################################################## > > 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/ ######################################################################## 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/
