auto-DRRAFTER

auto-DRRAFTER is used to build RNA coordinates into cryo-EM maps. Unlike DRRAFTER, it does not require initial manual helix placement. Currently, auto-DRRAFTER works only for systems that only contain RNA.
 
deepL様翻訳
auto-DRRAFTERは、クライオ電子顕微鏡マップにRNA座標を構築するために使用される。DRRAFTERとは異なり、最初に手動でらせんを配置する必要はない。現在のところ、auto-DRRAFTERはRNAのみを含む系に対してのみ機能する。

[root@rockylinux ~]# cd /apps/
 
[root@rockylinux apps]# bzip2 -cd  /Public/em/rosetta_bin_linux_3.14_bundle.tar.bz2 | tar xf - 
 
[root@rockylinux apps]# ls -lF
 :
drwxr-xr-x.  3 2456 1002   18 Mar  1 15:23 rosetta.binary.linux.release-371/
 :
[root@rockylinux apps]#
[root@rockylinux apps]# ls -lF rosetta.binary.linux.release-371/main/
total 56
-rw-r--r--.  1 2456 1002 3439 Mar  1 15:23 CITING_ROSETTA.md
-rw-r--r--.  1 2456 1002 6342 Mar  1 15:23 CLA.md
-rw-r--r--.  1 2456 1002 6222 Mar  1 15:23 CONTRIBUTING.md
drwxr-xr-x. 17 2456 1002 4096 Mar  1 15:23 database/
drwxr-xr-x.  8 2456 1002 4096 Mar  1 15:31 demos/
drwxr-xr-x. 16 2456 1002 4096 Mar  1 15:31 documentation/
-rw-r--r--.  1 2456 1002 5832 Mar  1 15:23 LICENSE.md
drwxr-xr-x.  5 2456 1002 4096 Mar  1 15:31 PyRosetta.notebooks/
drwxr-xr-x.  8 2456 1002  119 Mar  1 15:31 pyrosetta_scripts/
-rw-r--r--.  1 2456 1002 3535 Mar  1 15:23 README.md
drwxr-xr-x.  4 2456 1002  153 Mar  1 15:31 rosetta_scripts_scripts/
drwxr-xr-x. 17 2456 1002 4096 Mar  1 15:46 source/
drwxr-xr-x.  9 2456 1002  158 Mar  1 15:23 tests/
drwxr-xr-x. 42 2456 1002 4096 Mar  1 15:31 tools/
[root@rockylinux apps]#
[root@rockylinux apps]# ls -lF rosetta.binary.linux.release-371/main/tools/rna_tools/     <-- rosettaに含まれているここを使うみたい
total 24
drwxr-xr-x. 2 2456 1002 4096 Mar  1 15:30 bin/
drwxr-xr-x. 2 2456 1002   58 Mar  1 15:30 cluster_script_template/
drwxr-xr-x. 2 2456 1002  153 Mar  1 15:30 cluster_setup/
-rw-r--r--. 1 2456 1002  374 Mar  1 15:30 INSTALL
drwxr-xr-x. 2 2456 1002 4096 Mar  1 15:30 job_setup/
drwxr-xr-x. 2 2456 1002 4096 Mar  1 15:30 pdb_util/
drwxr-xr-x. 2 2456 1002 4096 Mar  1 15:30 silent_util/
-rw-r--r--. 1 2456 1002 1207 Mar  1 15:30 sym_link.py
[root@rockylinux apps]#

git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
 
pyenv install miniforge3-23.11.0-0
source /apps/pyenv/versions/miniforge3-23.11.0-0/etc/profile.d/conda.sh

[root@rockylinux ~]# conda create -n auto-DRRAFTER eman-dev networkx mrcfile -c cryoem -c conda-forge
 
[root@rockylinux ~]# conda activate auto-DRRAFTER
 
(auto-DRRAFTER) [root@rockylinux ~]# conda list
 :
eman-dev                  2.99.55         gui_h1173e1f_100    cryoem
 :
mrcfile                   1.5.0              pyhd8ed1ab_0    conda-forge
 :
networkx                  3.3                pyhd8ed1ab_1    conda-forge
 :
numpy                     1.23.5          py311h7d28db0_0    conda-forge
 :
(auto-DRRAFTER) [root@rockylinux ~]# 
 
(auto-DRRAFTER) [root@rockylinux ~]# pip install numpy==1.21
 
(auto-DRRAFTER) [root@rockylinux ~]# e2version.py
EMAN 2.99.55 ( GITHUB: 2023-12-10 01:18 - commit: NOT-INSTALLED-FROM-GIT-REPO )
Your EMAN2 is running on: Linux-4.18.0-477.10.1.el8_8.x86_64-x86_64-with-glibc2.28 4.18.0-477.10.1.el8_8.x86_64
Your Python version is: 3.11.9
 
(auto-DRRAFTER) [root@rockylinux ~]# e2proc3d.py -h
Usage: e2proc3d.py [options] <inputfile> <outputfile>
        Generic 3-D image processing and file format conversion program.
        All EMAN2 recognized file formats accepted (see Wiki for list).
 :
(auto-DRRAFTER) [root@rockylinux ~]# e2segment3d.py  -h
  [numpyのワーニングが表示される]
usage: prog <input volume> [options]
        This program provides access to various algorithms for segmenting a 3-D volume into multiple pieces automatically.
        Note that you MUST have sufficient RAM to hold at least two copies of the volume in memory. Some segmentation algorithms
        may require more. The actual segmentation is performed using one of the segment.* processors. 'e2help.py processor segment'
        for more information (-v 1 will give even more).
 :
(auto-DRRAFTER) [root@rockylinux ~]# conda deactivate
[root@rockylinux ~]# 
 

#%Module1.0
 
set          root       /apps/pyenv/versions/miniforge3-23.11.0-0/envs/auto-DRRAFTER
set          ROSETTA    /apps/rosetta.binary.linux.release-371/main
 
setenv       EMAN2DIR        $root
setenv       ROSETTA         $ROSETTA
setenv       RNA_TOOLS       $ROSETTA/tools/rna_tools
setenv       PYTHONPATH      $ROSETTA/tools/rna_tools/bin
 
prepend-path PATH            $ROSETTA/tools/rna_tools/bin:$root/bin
prepend-path LD_LIBRARY_PATH $root/lib

[root@rockylinux ~]# module use /apps/modulefiles/
[root@rockylinux ~]# module load auto-DRRAFTER
 
[root@rockylinux ~]# which python
/apps/pyenv/versions/miniforge3-23.11.0-0/envs/auto-DRRAFTER/bin/python
 
[root@rockylinux ~]# python $RNA_TOOLS/sym_link.py

[saber@rockylinux ~]$ module use /apps/modulefiles/
 
[saber@rockylinux ~]$ module load auto-DRRAFTER
 
[saber@rockylinux ~]$ rna_helix.py -h
usage: rna_helix.py [-h] -seq SEQ SEQ [-resnum RESNUM [RESNUM ...]] [-o O] [-weights WEIGHTS] [-finish_weights FINISH_WEIGHTS] [-silent SILENT] [-dump]
                    [-put_intra_into_total] [-rosetta_folder ROSETTA_FOLDER] [-extension EXTENSION]
 
Run rna_helix to build a helix
 
options:
  -h, --help            show this help message and exit
  -seq SEQ SEQ          Sequence of the helix, in the format: ggaa uucc
  -resnum RESNUM [RESNUM ...]
                        Renumber the residues with input format: 13-16 30-33
  -o O                  Filename of output pdb
  -weights WEIGHTS      Weights file defining score function
  -finish_weights FINISH_WEIGHTS
                        Weights file defining a finisher score function
  -silent SILENT        silent file output
  -dump                 dump intermediate pdbs
  -put_intra_into_total
                        calculate intra-res terms and include in totals
  -rosetta_folder ROSETTA_FOLDER
                        path to /Rosetta/
  -extension EXTENSION  executable extension
[saber@rockylinux ~]$