【Rosetta】RoseTTAFold安装

1、下载

git clone https://github.com/RosettaCommons/RoseTTAFold

cd RoseTTAFold

2、配置环境
cuda11

conda env create -f RoseTTAFold-linux.yml

cuda10

conda env create -f RoseTTAFold-linux-cu101.yml

3、下载权重文件并解压

wget https://files.ipd.uw.edu/pub/RoseTTAFold/weights.tar.gz
tar xfz weights.tar.gz

4、安装依赖

./install_dependencies.sh

5、下载数据库
uniref30 [46G]解压后194.3G

wget http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz
mkdir -p UniRef30_2020_06
tar xfz UniRef30_2020_06_hhsuite.tar.gz -C ./UniRef30_2020_06

BFD [272G]解压后1.9T

wget https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz
mkdir -p bfd
tar xfz bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz -C ./bfd

structure templates[122.9G]解压后716.1G

wget https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz
tar xfz pdb100_2021Mar03.tar.gz

6、安装pyrosetta
[1]创建conda环境

conda env create -f folding-linux.yml

[2]激活环境

conda activate folding

[3]安装pyrosetta

conda install --channel https://levinthal:paradox@conda.graylab.jhu.edu pyrosetta=2021.29+release.d8f5566

[4]测试

python
>>>import pyrosetta

7、使用测试

cd example
../run_e2e_ver.sh input.fa .
../run_pyrosetta_ver.sh input.fa .

8、psipred core dumped 问题解决
从github重新下载

git clone https://github.com/psipred/psipred.git

进入文件夹下到src目录

cd psipred-master
cd src

修改sspred_avpred.c文件的241行

    char            buf[256], *p;

将256改为512

    char            buf[512], *p;

保存后编译

make

之后该文件夹下会出现chkparse、psipass2、psipred、seq2mtx四个文件
将其覆盖到conda环境下

/anaconda3/envs/RoseTTAFold/bin

问题解决