48 lines
803 B
Markdown
Executable File
48 lines
803 B
Markdown
Executable File
# analysis_pdb
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## install environment
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```shell
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micromamba create -n modeller modeller biopython pymol-open-source biopandas requests ipython ipykernel pydantic -y -c conda-forge -c salilab
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# modeller注册码：MODELIRANJE (<conda_env>//lib/modeller-10.4/modlib/modeller/config.py)
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```
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modeller注册码：`MODELIRANJE``
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## test
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```shell
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cp pdb_test/5isz.pdb pdb_gjm/
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gmx_mpi pdb2gmx -f 5isz.pdb -o 5isz.gro -ff amber99sb-ildn -water tip3p -ignh -p topol.top
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```
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# 记录
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`7rtr` 对比序列太长，需要去除尾端
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无缺失：1bd2,
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`1d9k`
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tcr: AB
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mhc CD
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peptide P
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`1kj2` p周围只有三条链
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`3C5Z` `3C60` `3O6F` `3PL6` `3RDT` `4MAY` `4P4K` 没有peptide
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`3GJF` K、L链 空间位置不正确。
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`4z7u` 重叠，缺失链，tcr，hmc只有一半
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tcr: DE
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mhc I
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peptide Q
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``
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