Looks like i misread your last missive... indeed installing refinement tools fixes the problem (on both the mac and the Linux boxes)... Thanks Paul for thehelp! 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 6:29 PM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > > On 15/02/2022 18:19, Pranav Shah wrote: > > Hi Paul, > > > > I did install chain-refine using Curlew > > I said "refinement tools" - as in "Refinement Tools" > > > > 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 > > This is a problem on your computer or for your system administrator. > > > > 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. > > > Indeed - that's why you need Refinement Tools. > > > > > > Interestingly I am able to reproduce this problem on my M1 Mac > > (BigSur) with an older version of ccpem (late Dec'21) > > surely you mean 63? > > > > I > > am currently in the process of updating my installation of Coot on my > > Mac but am pessimistic that that will solve the problem. > > All the necessary code is already built into the main binary, you just > need the right bit of scripting to activate it. > > > Paul. > > > > 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/ > > ######################################################################## > > 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/
