66 lines
1.1 KiB
Markdown
Executable File
66 lines
1.1 KiB
Markdown
Executable File
# analysis_pdb
|
||
|
||
|
||
|
||
## install environment
|
||
|
||
```shell
|
||
micromamba create -n modeller modeller biopython pymol-open-source biopandas requests ipython ipykernel pydantic -y -c conda-forge -c salilab
|
||
# modeller注册码：MODELIRANJE (<conda_env>//lib/modeller-10.4/modlib/modeller/config.py)
|
||
```
|
||
|
||
modeller注册码：`MODELIRANJE``
|
||
|
||
## test
|
||
|
||
```shell
|
||
cp pdb_test/5isz.pdb pdb_gjm/
|
||
gmx_mpi pdb2gmx -f 5isz.pdb -o 5isz.gro -ff amber99sb-ildn -water tip3p -ignh -p topol.top
|
||
```
|
||
|
||
# 记录
|
||
|
||
`7rtr` 对比序列太长，需要去除尾端
|
||
|
||
无缺失：1bd2,
|
||
|
||
`1d9k`
|
||
|
||
tcr: AB
|
||
mhc CD
|
||
peptide P
|
||
|
||
`1kj2` p周围只有三条链
|
||
|
||
`3C5Z` `3C60` `3O6F` `3PL6` `3RDT` `4MAY` `4P4K` 没有peptide
|
||
|
||
`3GJF` K、L链 空间位置不正确。
|
||
|
||
`4z7u` 重叠，缺失链，tcr，hmc只有一半
|
||
|
||
`6avf` H 链太长
|
||
|
||
`6px6` B 链太长
|
||
|
||
`6py2` B 链太长
|
||
|
||
`6u3n` B 链111修复失败
|
||
|
||
`7rk7` `7rtr` 拖尾
|
||
|
||
`6uk4` `6uln` `6vm8` `7l1d` `7rrg` 仅有HMC呈递peptide，没有TCR识别互相作用
|
||
|
||
`7jwj` A链拖尾太长
|
||
|
||
|
||
|
||
tcr: DE
|
||
mhc I
|
||
|
||
peptide Q
|
||
|
||
`3mv7` `3mv8` `3mv9` D链修复有问题，没有修复成功。
|
||
|
||
``
|
||
|