Chimera をテンプレートにして作成
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開始行:
本家様 [[http://www.cgl.ucsf.edu/chimera/index.html>+http...
MRCファイルを閲覧するために取得
他にも多彩な機能が用意されている
[[http://www.cgl.ucsf.edu/chimera/tutorials.html>+http://...
[[http://www.cgl.ucsf.edu/chimera/videodoc/videodoc.html>...
[[ChimeraX]]
実行環境
#code(nonumber){{
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.7 (Blue Onyx)
[root@rockylinux9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX Open Kernel Module for x86_64 ...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@rockylinux9 ~]#
}}
下準備
#code(nonumber){{
[root@rockylinux9 ~]# dnf install libXScrnSaver -y
}}
インストール
#code(nonumber){{
[root@rockylinux9 ~]# ls -lh /Public/em/chimera-1.19-linu...
-rw-rw-rw-. 1 1001 users 149M Dec 10 03:00 /Public/em/chi...
[root@rockylinux9 ~]# chmod +x /Public/em/chimera-1.19-li...
[root@rockylinux9 ~]# /Public/em/chimera-1.19-linux_x86_6...
[root@rockylinux9 ~]# /Public/em/chimera-1.19-linux_x86_6...
UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs@lis...
Original path: '/root'
inflating: chimera_install_qPwP5T/installer
inflating: chimera_install_qPwP5T/chimera.bin
Enter install location: /apps/chimera-1.19 <--...
Extracting files. This may take a few minutes.
Executing command: './chimera.bin -q -d /apps/chimera-1.19'
UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://ww...
Install desktop menu (icon has to be done by user)? yes ...
Install symbolic link to chimera executable for command l...
0 -- no link
1 -- /root/.local/bin
2 -- /root/bin
3 -- /usr/local/sbin
4 -- /usr/local/bin
5 -- /usr/sbin
6 -- /usr/bin
[hit Enter for default (0)]: <-- そのままリターン
:
:
-------------------------------------------------
To (re)install desktop menu and icon later, run:
/apps/chimera-1.19/bin/xdg-setup install
If run as root, then it only installs the menu
(for all users). Otherwise, it installs the icon
(and menu, if need be) for the current user.
-------------------------------------------------
result code from installer: 0
Install succeeded.
Cleaning up extract dir, 'chimera_install_qPwP5T'
Installation is done; press return. <-- りたんーキーを...
[root@rockylinux9 ~]#
}}
これで完了
「/apps/chimera-1.19」にchimeraがインストールされました。
***Environment-modules [#cdb01e7d]
「/apps/modulefiles/chimera」
#code(nonumber){{
#%Module1.0
set-alias chimera /apps/chimera-1.19/bin/chimera
}}
***plugin [#s4c329ec]
-PlaceObject [[https://www.biochem.mpg.de/7939908/Place-O...
UCSF Chimera plugin to display the spatial distribution o...
#code(nonumber){{
[root@rockylinux9 ~]# cd /apps/src/
[root@rockylinux9 src]# wget https://www.biochem.mpg.de/7...
[root@rockylinux9 src]# unzip PlaceObject-2_1_0.zip
[root@rockylinux9 src]# cp -r ./PlaceObject /apps/chimera...
[root@rockylinux9 src]# chmod 755 /apps/chimera-1.16/shar...
[root@rockylinux9 src]# find /apps/chimera-1.16/share/Pla...
[root@rockylinux9 src]# find /apps/chimera-1.16/share/Pla...
}}
解凍したフォルダのパーミッションに修正が必要でした
このあと chimera を立ち上げて、Tools -> Utilities とする...
&ref(2025y09m21d_180623407.png,nolink,70%);
-PickParticle [[https://www.biochem.mpg.de/7940000/Pick-P...
#code(nonumber){{
UCSF Chimera plugin to pick 3D particles in tomograms.
#code(nonumber){{
[root@rockylinux9 src]# wget https://www.biochem.mpg.de/7...
[root@rockylinux9 src]# unzip PickParticle-2_0_0.zip
[root@rockylinux9 src]# cp -r ./PickParticle /apps/chimer...
[root@rockylinux9 src]# chmod 755 /apps/chimera-1.16/shar...
[root@rockylinux9 src]# chmod 644 /apps/chimera-1.16/shar...
}}
chimera を再度立ち上げて、Tools -> Utilities とすると「P...
&ref(2025y09m21d_181402802.png,nolink,70%);
終了行:
本家様 [[http://www.cgl.ucsf.edu/chimera/index.html>+http...
MRCファイルを閲覧するために取得
他にも多彩な機能が用意されている
[[http://www.cgl.ucsf.edu/chimera/tutorials.html>+http://...
[[http://www.cgl.ucsf.edu/chimera/videodoc/videodoc.html>...
[[ChimeraX]]
実行環境
#code(nonumber){{
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.7 (Blue Onyx)
[root@rockylinux9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX Open Kernel Module for x86_64 ...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@rockylinux9 ~]#
}}
下準備
#code(nonumber){{
[root@rockylinux9 ~]# dnf install libXScrnSaver -y
}}
インストール
#code(nonumber){{
[root@rockylinux9 ~]# ls -lh /Public/em/chimera-1.19-linu...
-rw-rw-rw-. 1 1001 users 149M Dec 10 03:00 /Public/em/chi...
[root@rockylinux9 ~]# chmod +x /Public/em/chimera-1.19-li...
[root@rockylinux9 ~]# /Public/em/chimera-1.19-linux_x86_6...
[root@rockylinux9 ~]# /Public/em/chimera-1.19-linux_x86_6...
UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs@lis...
Original path: '/root'
inflating: chimera_install_qPwP5T/installer
inflating: chimera_install_qPwP5T/chimera.bin
Enter install location: /apps/chimera-1.19 <--...
Extracting files. This may take a few minutes.
Executing command: './chimera.bin -q -d /apps/chimera-1.19'
UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://ww...
Install desktop menu (icon has to be done by user)? yes ...
Install symbolic link to chimera executable for command l...
0 -- no link
1 -- /root/.local/bin
2 -- /root/bin
3 -- /usr/local/sbin
4 -- /usr/local/bin
5 -- /usr/sbin
6 -- /usr/bin
[hit Enter for default (0)]: <-- そのままリターン
:
:
-------------------------------------------------
To (re)install desktop menu and icon later, run:
/apps/chimera-1.19/bin/xdg-setup install
If run as root, then it only installs the menu
(for all users). Otherwise, it installs the icon
(and menu, if need be) for the current user.
-------------------------------------------------
result code from installer: 0
Install succeeded.
Cleaning up extract dir, 'chimera_install_qPwP5T'
Installation is done; press return. <-- りたんーキーを...
[root@rockylinux9 ~]#
}}
これで完了
「/apps/chimera-1.19」にchimeraがインストールされました。
***Environment-modules [#cdb01e7d]
「/apps/modulefiles/chimera」
#code(nonumber){{
#%Module1.0
set-alias chimera /apps/chimera-1.19/bin/chimera
}}
***plugin [#s4c329ec]
-PlaceObject [[https://www.biochem.mpg.de/7939908/Place-O...
UCSF Chimera plugin to display the spatial distribution o...
#code(nonumber){{
[root@rockylinux9 ~]# cd /apps/src/
[root@rockylinux9 src]# wget https://www.biochem.mpg.de/7...
[root@rockylinux9 src]# unzip PlaceObject-2_1_0.zip
[root@rockylinux9 src]# cp -r ./PlaceObject /apps/chimera...
[root@rockylinux9 src]# chmod 755 /apps/chimera-1.16/shar...
[root@rockylinux9 src]# find /apps/chimera-1.16/share/Pla...
[root@rockylinux9 src]# find /apps/chimera-1.16/share/Pla...
}}
解凍したフォルダのパーミッションに修正が必要でした
このあと chimera を立ち上げて、Tools -> Utilities とする...
&ref(2025y09m21d_180623407.png,nolink,70%);
-PickParticle [[https://www.biochem.mpg.de/7940000/Pick-P...
#code(nonumber){{
UCSF Chimera plugin to pick 3D particles in tomograms.
#code(nonumber){{
[root@rockylinux9 src]# wget https://www.biochem.mpg.de/7...
[root@rockylinux9 src]# unzip PickParticle-2_0_0.zip
[root@rockylinux9 src]# cp -r ./PickParticle /apps/chimer...
[root@rockylinux9 src]# chmod 755 /apps/chimera-1.16/shar...
[root@rockylinux9 src]# chmod 644 /apps/chimera-1.16/shar...
}}
chimera を再度立ち上げて、Tools -> Utilities とすると「P...
&ref(2025y09m21d_181402802.png,nolink,70%);
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