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
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