Re: [COOT] Chain refine woes
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 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 > > 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 # ()] > >>> In unknown file: > >>> ?: 1 [#] > >>> 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=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=1 > > > >
Re: [COOT] Chain refine woes
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 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 # ()] In unknown file: ?: 1 [#] 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=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=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=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] Chain refine woes
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 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 # ()] > > In unknown file: > > ?: 1 [#] > > 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=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=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] Chain refine woes
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 # ()] In unknown file: ?: 1 [#] 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=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/
